https://www.open-bio.org/Recent content in Home on Open Bioinformatics FoundationHugoen-USboard@open-bio.org (Open Bioinformatics Foundation)board@open-bio.org (Open Bioinformatics Foundation)Tue, 31 Mar 2026 18:50:23 +0000https://www.open-bio.org/events/bosc-2026/panels/Tue, 31 Mar 2026 18:50:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2026/panels/<p>For the first time ever, BOSC will include <strong>two</strong> panels on important and timely topics.</p> <h1 id="policies-and-strategies-for-resilient-open-science">Policies and Strategies for Resilient Open Science</h1> <p>As we gather in Washington, D.C. for BOSC 2026, we stand at the literal and figurative crossroads of the policies that dictate the pulse of our field. For years, the open science community has operated under a steady wind of progress, but the past year has shifted the weather. We have moved from an era of &ldquo;open by default&rdquo; to an environment where the infrastructure of open science—funding, federal data repositories, and international collaborations—is increasingly under scrutiny. This panel moves beyond theoretical support for open science to focus on the strategies of resilience and active advocacy required to navigate a landscape that is being rapidly redefined.</p> <p>The current climate in the United States has seen federal agencies, which are the traditional engines of open research, reorienting under new mandates that prioritize &ldquo;national interest&rdquo; and &ldquo;operational efficiency.&rdquo; While these shifts have created uncertainty, they have also demonstrated <strong>the power of the community</strong>; despite early threats of deep cuts, concerted advocacy has kept certain key research budgets remarkably stable. Resilience, therefore, is not just about surviving these shifts; it is about building a proactive presence in the rooms where these decisions are made. We will explore how these domestic tensions mirror global trends, from the rise of protectionist data policies to the decentralized alternatives emerging in the wake of federal volatility.</p> <p>Our discussion will range from high-level policy to the practical &ldquo;how-to&rdquo; of remaining principled and productive, addressing topics that include: the Advantage of Advocacy, Navigating Funding Fragility, Protecting the Digital Commons, and Institutional Fortification.</p> <h1 id="panelists">Panelists</h1> <h3 id="to-be-named">To be named</h3> <h3 id="moderator-mónica-muñoz-torres">MODERATOR: Mónica Muñoz Torres</h3> <p>Dr. Muñoz Torres is an Associate Professor at the University of Colorado Anschutz. Her work focuses on the critical challenge of developing the socio-technical foundations needed to realize the promise of artificial intelligence in biomedical sciences. Her expertise includes genomics, biocuration, knowledge representation, and data harmonization. She leads the NIH-funded Bridge to Artificial Intelligence (Bridge2AI)’s teams focused on Standards, Practices, and Quality Assessment. She is also Co-Lead of the Clinical &amp; Phenotypic Data Capture Work Stream of the Global Alliance for Genomics and Health (GA4GH).</p> <h1 id="open-source-in-the-age-of-ai">Open Source in the Age of AI</h1> <p>Open-source software has been a key part of the bioinformatics landscape for decades, enabling large-scale collaboration and supporting reproducible science. The emergence of generative AI represents a fundamental shift in how code is authored, maintained, and shared. This panel will examine the &ldquo;elephant in the room&rdquo;: is generative AI a powerful advantage for open-source communities, or a threat to their long-term health, or both? We will explore how AI tools—which can generate thousands of lines of code in seconds—challenge our notions of contribution, reuse, and the value of human-authored frameworks.</p> <p>While AI makes it easier than ever to code solutions from scratch, it raises critical questions about the sustainability of existing projects and the scientific accuracy of machine-generated results. As the difficult part of software development shifts from writing code to verifying it for scientific integrity, our communities and the way they operate must evolve. From assessing pull requests submitted by AI agents to debating the merits of bans on AI-generated submissions, the open-source community is at a crossroads in defining how humans and AI agents can best work together.</p> <p>This panel will bring together a variety of perspectives to discuss topics including: Reuse, Attribution and Accountability, Licensing, Sustainability, and the Future of Open Data.</p> <h1 id="panelists-1">Panelists</h1> <h3 id="to-be-named-1">To be named</h3> <h3 id="moderator-jason-williams">MODERATOR: Jason Williams</h3> <p>Jason Williams is Assistant Director of Cold Spring Harbor&rsquo;s Dolan DNA Learning Center. He was elected an AAAS Fellow in 2026. In 2025, he won the Elizabeth W. Jones Award for Excellence in Education! Williams has been instrumental in helping to bring the latest technologies and teaching approaches for working with DNA into classrooms around the world through dedicated hands-on programs for students and teachers. He develops national and international biology education and professional development programs. In addition to his work at the DNALC, Williams is the founder of LifeSciTrainers.org, a global initiative promoting a community of practice among professionals who develop short-format training for life scientists. He is also the Lead Investigator of the <a href="https://areciboc3.org/">NSF Arecibo Center for STEM Education, Computing, and Community Engagement</a>.</p>https://www.open-bio.org/posts/Open-Source-in-the-Age-of-AI/Mon, 30 Mar 2026 02:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/posts/Open-Source-in-the-Age-of-AI/<p>At BOSC 2026, we want to talk about the elephant in the open-source room: <strong>Is generative AI an advantage or a hindrance to open source?</strong> <img src="https://www.open-bio.org/img/2026/2026-03-29-elephant-and-pears.png" alt ="AI-generated image of an elephant surrounded by colorful pears" style="width:50%"/></p> <p>We invite abstracts on this topic. Some might be selected to give talks at BOSC (which will be part of ISMB 2026). We may also invite some of the chosen speakers to participate in a panel. The <a href="https://www.open-bio.org/events/bosc-2026/submit/">submission deadline</a> is April 9.</p> <p>For example, here are some possible topics (but don&rsquo;t feel restricted to these):</p> <ul> <li>Reuse: how can we encourage and facilitate reuse of tools and frameworks when AI makes it easy to code things up from scratch?</li> <li>Evaluating open source projects: AI tools can generate thousands of lines of code in seconds. The most costly process is now verifying that code for scientific accuracy (<a href="https://arxiv.org/abs/2507.09089)">https://arxiv.org/abs/2507.09089)</a>. What are some good approaches to address this?</li> <li>Contribution guidelines: balancing scale and utility of AI-assisted development with community-building <ul> <li>How should an open source project assess pull requests from AI agents?</li> <li>Are zero-tolerance bans on submissions generated using AI reasonable? (e.g., <a href="https://medium.com/@livewyer/ai-disruption-to-open-source-software-oss-377f10be2d8a">https://medium.com/@livewyer/ai-disruption-to-open-source-software-oss-377f10be2d8a</a>)</li> <li>How can humans and AI agents best work together?</li> </ul> </li> <li>Attribution and credit: <ul> <li>How should we recognize contributions in an age of AI-assisted commits?</li> <li>Transparency: Should there be mandatory requirements to disclose AI use, including models and prompts used?</li> <li>Human ownership: should authors always remain legally and ethically accountable for the outputs of their code?</li> <li>Licensing: do open source licenses still mean anything when coding agents can translate or reimplement code?</li> </ul> </li> <li>Sustainability: who does the long-term hard work of maintaining open source projects when AI does the &ldquo;easy&rdquo; work?</li> <li>Credit for training data: part of what AI proposes is reusing existing human-coded work without crediting it. Can there be a way to fairly credit the contribution of an open source project to the (often non open-source) models?</li> <li>When AI is the user: should open source projects be designed for machine consumers?</li> <li>The deadly feedback loop: models are trained on what they produce. Does this really work?</li> <li>Open data in the AI era: balancing access with protection from misuse</li> </ul> <p>We look forward to seeing your thoughts on these topics! Please be sure to <a href="https://www.open-bio.org/events/bosc-2026/submit/">submit your abstract</a> by April 9 if you want to be considered for a talk.</p>https://www.open-bio.org/events/bosc-2026/bosc-2026-keynotes/Fri, 06 Mar 2026 04:29:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2026/bosc-2026-keynotes/<img src="https://www.open-bio.org/img/2026/2026-03-06-Eric-Green.jpeg" alt ="Eric Green" style="width:55%"/> <h2 id="eric-green-illumina">Eric Green (Illumina)</h2> <h3 id="from-the-human-genome-project-to-the-realization-of-genomic-medicine-a-scientific-medical-and-societal-journey">From the Human Genome Project to the Realization of Genomic Medicine: A Scientific, Medical, and Societal Journey</h3> <h4 id="abstract">Abstract</h4> <p>The coming decade offers great promise for human genomics and genomic medicine. Since the completion of the Human Genome Project over two decades ago, genomics has become progressively entrenched within the bedrock of the biomedical research enterprise. Capitalizing on the momentum of the project’s successful completion, the field of genomics has increasingly expanded and matured, such that genomics is now central and catalytic in basic and translational research, and studies now regularly demonstrate the vital role that genomic information can play in clinical care. Looking ahead, the anticipated advances in technologies, biological insights, and clinical applications (among others) will lead to more widespread dissemination of genomics throughout biomedical research, a growing adoption of genomics into medical and public health practices, and an increasing relevance of genomics in everyday life. At the same time, many challenges remain and require ongoing attention, such as understanding the biological complexities of the human genome, untangling the complex roles that genomic variants play in health and disease, and ensuring that genomics gets broadly and equitably integrated in medicine around the world.</p> <h4 id="biography">Biography:</h4> <p><b>Dr. Eric Green, M.D., Ph.D.</b>,  is the recently appointed Chief Medical Officer at Illumina. As Illumina’s medical leader, Dr. Green is responsible for guiding global efforts to advance the clinical application of genomics, expand access to precision medicine, and increase diversity in genomic data to improve healthcare for people worldwide.</p> <p>Prior to joining Illumina, Dr. Green was a genomics researcher and leader at the National Human Genome Research Institute (NHGRI) at the U.S. National Institutes of Health, including serving as the NHGRI Director for more than 15 years. Under his directorship, NHGRI became a driving force in integrating genomics into medicine and public health. Dr. Green was also the founding Director of the NIH Intramural Sequencing Center.</p> <p>For over two decades, Dr. Green directed a research program that included start-to-finish roles in the Human Genome Project; groundbreaking work on mapping, sequencing, and comparing mammalian genomes; discoveries about the genes involved in several rare genetic diseases; and efforts to accelerate applications of genomics in healthcare. Dr. Green earned his M.D. and Ph.D. in 1987 from Washington University in St. Louis; coincidentally, the word “genomics” was coined in that same year. Dr. Green’s awards include being elected to the National Academy of Medicine in 2023, honored with the 2025 Leadership Award by the American Society of Human Genetics, and designated a Fierce 50 Innovation Honoree of 2025 (which honors “Trailblazers Redefining Health, Science, &amp; Patient Care”).</p> <p><br/><br/></p> <img src="https://www.open-bio.org/img/2026/2026-03-09-Maryam-Zaringhalam.jpeg" alt ="Maryam Zaringhalam" style="width:50%"/> <h2 id="maryam-zaringhalam-center-for-open-science">Maryam Zaringhalam (Center for Open Science)</h2> <h3 id="talk-title-tbd">Talk title TBD</h3> <p><b>Maryam Zaringhalam, Ph.D.</b>, is the Senior Director of Policy at the <a href="https://www.cos.io/">Center for Open Science (COS)</a>. In that position, she leads COS’s policy efforts to increase openness, integrity, and trustworthiness of research.</p> <p>Prior to joining COS, Maryam served as the Data Science and Open Science Officer at the National Library of Medicine (NLM) at the National Institutes of Health (NIH), working to enhance capacity in the biomedical research community for data science and open science. From 2022 to 2024, she also served as the Assistant Director for Public Access and Research Policy at the White House Office of Science and Technology Policy (OSTP) where she oversaw federal policy development around public access, open science, and scientific integrity.</p> <p>Maryam is also a Senior Producer for the Story Collider, where she co-hosts the science policy podcast Science Soapbox, bringing true, personal stories of science to live audiences in Washington, DC. She received her PhD in Molecular Biology from the Rockefeller University.</p> <div class="well"> <h3 id="bosc-keynote-speaker-selection-process">BOSC keynote speaker selection process</h3> <p>BOSC usually includes two or three keynote talks given by prominent individuals or emerging leaders who are accomplished in areas relevant to the bioinformatics open source community and who represent a range of backgrounds and ideas. Please see our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker rubric</a> for more information about our keynote speaker selection process and criteria.</p> </div>https://www.open-bio.org/2026/03/05/event-fellowship-2026-1/Thu, 05 Mar 2026 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2026/03/05/event-fellowship-2026-1/<hr> <p>The call for applications for <strong>round 1</strong> of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> for 2026 is now open. <strong>The deadline for this round is 1 April 2026.</strong> You can submit your application through <a href="https://forms.gle/maZEJzCF4rifEJgz5">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://forms.gle/maZEJzCF4rifEJgz5">make a copy of this template</a>. <img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-Summit-group4-cropped.jpeg" alt="A team at the ESIIL Innovation Summit"></p> <p>The Open Bioinformatics Foundation (OBF)&rsquo;s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is April 1, 2026. (For those who want to apply for <a href="https://www.open-bio.org/events/bosc/">BOSC</a>, note that this is earlier than the BOSC/ISMB submission deadline of April 9.)</p> <p>We invite applications from candidates seeking financial support to attend relevant scientific events between May 2026 to April 2027. <em><strong>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</strong></em>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <h3 id="overview-of-the-overall-2025-rounds-of-obf-event-fellowship">Overview of the overall 2025 rounds of OBF Event Fellowship</h3> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 9th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>We changed the OBF event fellowship policy to say that the event that the applicant is applying to must be <strong>high-quality and not predatory</strong>. We also <strong>require</strong> the applicants and awardees write the application and blog draft themselves, and prohibit the use of AI/LLMs for this. These changes are now integrated in <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">travel_fellowship.md</a> and the <a href="https://forms.gle/xKBJqC9L5U2SAEKV8">OBF Event Fellowship application form</a>.</p> <p>Looking back at 2025, we received numerous applications, and <strong>nine applicants were selected</strong> from three rounds across 2025 to support their participation in various events. All OBF Event Fellowship awardees are required to write blog posts after their events; two of the people who were selected for awards in 2025 have not yet attended their events. <strong>Seven of them have written blog posts</strong> sharing their experiences at events that promote open science and open source bioinformatics, with the support of the OBF Event Fellowship. You can read their posts here:</p> <ol> <li>Ruby Krasnow: <a href="https://www.open-bio.org/2025/11/03/2025-11-03-Krasnow-ESIIL-Summit/">2025 ESIIL Innovation Summit: Collaborative and Open Environmental Data Science in Boulder</a></li> <li>Tayyaba Alvi: <a href="https://www.open-bio.org/2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/">ISMB 2025: A Week of Learning, Teaching, and Connecting in Liverpool</a></li> <li>Muhamad Haries Ramdhani: <a href="https://www.open-bio.org/2025/09/04/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025/">ISMB/ECCB 2025: Liverpool, LLMs and Lessons in Open Science</a></li> <li>Fatemeh Mirzadeh Sarcheshmeh: <a href="https://www.open-bio.org/2025/12/04/2025-12-04-Fatemeh-Elixir-BioHackathon-experience/">Elixir BioHackathon Experience</a></li> <li>Hetvi Jethwani: <a href="https://www.open-bio.org/2025/12/02/2025-12-02-Hetvi-J-BioHackathon-Europe-2025/">BioHackathon Europe 2025: A Week full of Brainstorming, Coding &amp; Collaboration</a></li> <li>Rafał Miłodrowski: <a href="https://www.open-bio.org/2026/02/03/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025/">BioHackathon Europe 2025: BUSCO genes, lakeside hacking, and open workflows</a></li> <li>David Kiragu Mwaura: <a href="https://www.open-bio.org/2026/02/23/2026-02-23-David-Mwaura-AIBBC2025/">Bridging Learning Gaps Through Open-Source Tools</a></li> </ol> <p>Congratulations to all of our awardees! We are delighted to help support their participation in open-source-related events with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and <a href="https://forms.gle/D31zSs558aRwj2ig9">apply for the fellowship</a> before 1 April 2026.</strong></p>https://www.open-bio.org/posts/financial-support-BOSC2026/Wed, 04 Mar 2026 02:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/posts/financial-support-BOSC2026/<p>BOSC is part of the big <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a> conference, so you need to register for ISMB to participate in BOSC.</p> <p>We recognize that the high price of travel and registration can be a barrier. Below are some ways to apply for financial assistance to attend ISMB / BOSC.</p> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/bosc2025-img/Iva%20Tutis%20by%20poster.jpeg" alt="Iva Tutis"></p> </div><div class="right"> <h2 id="obf-event-fellowships">OBF Event Fellowships</h2> <p>The Open Bioinformatics Foundation (OBF)&rsquo;s <a href="https://www.open-bio.org/event-awards/">Event Fellowships</a> are aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities&hellip;such as BOSC.</p> <p>Awards are made three times a year; the next <strong>deadline is April 1, 2026</strong> (note that this is earlier than the ISMB submission deadline of April 9).</p> </div><div style="clear:both"></div></div> <h2 id="bosc-registration-fee-support">BOSC Registration Fee Support</h2> <p><img src="https://www.open-bio.org/img/2025/bosc2025-img/CoFest%20-%20Carlo%2C%20Harry%2C%20other%20person%20working%20at%20table%20-%201.jpeg" alt="CoFest 2026 participants"></p> <p>Authors who <a href="https://www.open-bio.org/events/bosc-2026/submit/">submit their work to BOSC</a> can request ISMB registration fee support on the abstract submission form (these requests are not seen by reviewers). This initiative is funded by <a href="https://www.open-bio.org/events/sponsors/">sponsorships</a>.</p> <p>Only presenting authors whose abstracts are accepted for talk or poster presentation are eligible for this fee support, and not all requests will be granted.</p> <p>Requests from early-career applicants and people from underrepresented geographical areas will be given priority. Applicants will be notified about whether their request was granted shortly after abstract acceptance notifications go out in early May.</p> <h2 id="iscb-conference-fellowships">ISCB Conference Fellowships</h2> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/2025-03-11-Iscb_logo.png" alt="ISCB logo"></p> </div><div class="right"> <p>The ISCB (the organization that runs the ISMB conference) offers a limited number of <a href="https://www.iscb.org/ismb2026/general-info/conference-fellowships">conference fellowships</a> that cover the registration fee to help students and postdocs to present their work at ISMB.</p> <p>These fellowships are only open to those who have a <strong>Proceeding, Talk, or Poster (not late poster) accepted for presentation at ISMB</strong>. The application will be sent automatically to eligible people on May 5. The number of awards is limited; not all eligible applicants will receive awards. Please consult the <a href="https://www.iscb.org/ismb2026/general-info/conference-fellowships">ISMB page</a> for more information.</p> </div><div style="clear:both"></div></div> <h2 id="apply-to-be-event-staff-at-ismb">Apply to be Event Staff at ISMB</h2> <p><img src="https://www.iscb.org/images/banners/banner.ConferenceBanner.ISMB.2026.png" alt="ISCB logo"></p> <p>You can <a href="https://www.iscb.org/ismb2026/general-info/apply-to-be-event-staff">apply to work at ISMB 2026</a> for approximately 20-24 hours in exchange for free registration and time-based pay. (When you&rsquo;re not working, you can attend talks.) The <strong>application deadline is May 1, 2026</strong>.</p>https://www.open-bio.org/2026/02/23/2026-02-23-David-Mwaura-AIBBC2025/Mon, 23 Feb 2026 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2026/02/23/2026-02-23-David-Mwaura-AIBBC2025/<p>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. David Kiragu Mwaura,_an Assistant Research Scientist at the Kenya Institute of Primate Research, was awarded an OBF Event Fellowship to attend the <a href="https://www.aibbc-society.org/">2025 AIBBC conference</a>.</p> <p><img src="https://www.open-bio.org/img/2026-02-02-image-kiragu.jpg.png" alt="David Kiragu standing beside his mounted poster"></p> <h2 id="introduction">Introduction</h2> <p>My desire to share my masters’ research output in a real world demonstration had finally come to fruition. This was achieved by securing a competitive travel grant from the <strong>Open Bioinformatics Foundation Event Fellowship</strong>. Leaving the chilly landscapes of Glasgow, Scotland for the warm, tropical weather in my home country, Kenya, I was honored to attend the <a href="https://www.aibbc-society.org/">2025 African International Biotechnology and Biomedical Conference</a>, where scientists from around the world gather to exchange ideas that directly address Africa’s needs.</p> <h2 id="poster-presentation">Poster Presentation</h2> <p>My simple and urgent plan was to showcase that open-source educational tools are practical, fair, high-impact solutions and not just an alternative means to the huge learning gap created by expensive proprietary software, especially in resource-constrained environments like Africa. My core contribution was to demonstrate how freely available platforms, particularly R Shiny, can revolutionize learning. My poster, <strong>&ldquo;BRIDGING TECHNOLOGY AND GENETIC EDUCATION: AN OPEN SOURCE SHINY APPLICATION FOR TEACHING PATERNITY ANALYSIS&rdquo;</strong>, served as the definitive proof of concept.</p> <p>Standing proudly beside my poster, I highlighted the complexity of teaching kinship inference and presented our solution, <a href="https://github.com/KIRAGU-MWAURA/DadApp_Shiny_Web_App">DadApp</a>, the open source R shiny tool. I shared the successful results from the Kenya Institute of Primate Research (KIPRE) pilot study that described the increase of interest and confidence upon using DadApp as an active learning tool. The results were uniquely compelling to the audience which sparked the discussion among lecturers and researchers from many institutions across Africa, who recognized the immense value of such open source tools. They saw an accessible, validated tool that could be replicated and scaled here in Africa where technology is gradually accessible.</p> <p><img src="https://www.open-bio.org/img/2026-02-02-image-kiragu01.jpg.png" alt="Audience for the poster"></p> <p>However, what stood out was how diverse my audience was: Some asked what Open Source is and why it matters in the Biotechnology and Biomedical fields? Whereas some audience members were advanced to ask what license is the Shiny App released under and if it allows commercial use, modification and/or redistribution? The diverse audience validated the continuous need for sensitizing about the importance of Open Source tools and Open Science in general. One of the most satisfying highlights was having a Professor from one of the leading universities in Kenya appreciating the content of the poster and commenting that such Open Source tools are the future as they can help in enhancing flexibility in curriculum design. He further added that lecturers and those passionate in capacity development can tailor such tools to course goals especially in lessons that are mathematically and coding intensive.</p> <h2 id="final-thoughts">Final Thoughts</h2> <p>The AIBBC conference was a humbling experience because for the first time I got to see something that was once a thoughtful concept became a product that was exciting and appreciated by my peers to advanced scientists and lecturers from different scientific backgrounds. However, my greatest achievement was showing that advanced learning does not have to rely on expensive softwares but can also be achieved with an open source Shiny App like DadApp. Students/participants can utilize such open source tools to explore data, visualize results, and understand scientific principles that once felt out of reach. The sparked conversations, encouragement and collaborative opportunities ignited a strong desire amongst the audience to champion genuine scientific equity, and a recognition that every scientist has a role in bringing that future of Open Science to life.</p> <p>Looking back, the bridge from Glasgow to Kenya became one of ideas, innovation, and global learning. I hope the experience leaves a lasting impact on both myself and the audience long after the conference.</p> <pre><code> ‘When knowledge travels freely, learning knows no borders.’ </code></pre> <hr>https://www.open-bio.org/2026/02/03/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025/Wed, 04 Feb 2026 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2026/02/03/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025/<p>The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. I was awarded an OBF Event Fellowship to attend <a href="https://biohackathon-europe.org">BioHackathon Europe 2025</a>, held 3–7 November at the Esplanade Resort &amp; Spa in Bad Saarow, near Berlin, Germany. I am a PhD student at the Jagiellonian University in Kraków, working with insect genomes and large-scale comparative datasets. <a href="https://busco.ezlab.org">BUSCO</a> is part of my everyday toolkit, so spending a week contributing to a BUSCO-based phylogenomics workflow with an international team felt like a perfect fit. The fellowship covered my travel costs and made it possible for me to fully participate in the hackathon. <img src="https://www.open-bio.org/img/2026/2026-02-04-hotel.jpg" alt="View of Lake Scharmützelsee and the Esplanade Resort &amp; Spa from the lakeside promenade."></p> <h2 id="a-hackathon-by-the-lake">A hackathon by the lake</h2> <p>BioHackathon Europe took over a lakeside hotel that turned into a giant shared office for a week: meeting rooms full of laptops and whiteboards, and a steady flow of coffee and conversations. Mornings started with a short plenary, followed by focused hacking sessions in the project rooms. Evenings were more relaxed, with social activities, ad‑hoc debugging sessions, and lots of informal discussions about tools, data and careers.</p> <h2 id="project-03-benchmarking-busco-genes-for-phylogenomics">Project #03: benchmarking BUSCO genes for phylogenomics</h2> <p>I joined project #03, “Automatic workflow for benchmarking BUSCO genes for phylogenomics”. BUSCO lineage datasets are widely used to assess genome completeness and to extract putatively single-copy orthologs for phylogenetic analyses. However, once you look across many genomes at once, especially in groups with whole‑genome duplications, it quickly becomes clear that many BUSCO loci are not truly single copy. Our project aims to make this complexity visible and manageable. The goal for the week was to turn existing scripts and a prototype workflow into a robust Snakemake pipeline that starts from BUSCO output and ends with phylogenomic trees. The workflow includes steps for multiple‑sequence alignment and trimming, gene‑tree inference, detection of in‑ and out‑paralogs, and construction of concatenated supermatrices and species trees that explicitly account for paralogy.</p> <p><img src="https://www.open-bio.org/img/2026/2026-02-04-meeting.jpg" alt="Morning meeting on zoom and coding session."></p> <h2 id="my-role-testing-and-debugging">My role: testing and debugging</h2> <p>Coming from a background of running Snakemake pipelines on HPC systems, I focused on the “does this actually run for a new user?” side of the project. A surprising amount of hackathon time can disappear into environment issues, so as a team we invested early in getting a clean, reproducible setup with conda and Snakemake with clearly pinned software versions. My main contribution was to run the pipeline on a curated set of genomes and report back where things broke or behaved unexpectedly. This included checking intermediate outputs (alignments, gene trees, paralog reports), tracking down missing dependencies, and helping to standardise file naming conventions for genome FASTA files and BUSCO output directories. These details may sound minor, but they are crucial when scaling up to dozens or hundreds of genomes.</p> <p><img src="https://www.open-bio.org/img/2026/2026-02-04-pipeline.jpg" alt="Schema of the pipeline used in our project"></p> <h2 id="community-and-midweek-reporting">Community and mid‑week reporting</h2> <p>A highlight of the week was the mid‑week reporting session, where each project prepared a short poster and gave lightning updates. Walking around the room, it was impressive to see the variety of topics being tackled in parallel: workflows, training materials, AI‑readiness, data standards and more. Presenting our BUSCO project forced us to summarise why this workflow matters, not just how it works. The poster session also helped to connect with people from other projects who use BUSCO or phylogenomics in their own work. Several visitors were interested in applying the workflow to their clades, and their questions helped us clarify which configuration options and outputs will be most useful for future users.</p> <p><img src="https://www.open-bio.org/img/2026/2026-02-04-poster.jpg" alt="Photo of me and our mid‑week reporting poster."></p> <h2 id="takehome-messages">Take‑home messages</h2> <p>The week left me with a few key lessons:</p> <ul> <li><strong>Reproducible workflows are a collective effort.</strong> Agreeing on file naming, pinning software versions and writing documentation takes time, but doing it together during a hackathon pays off immediately.</li> <li><strong>“Single‑copy” genes are often more complicated than they look.</strong> The preliminary results we explored during the week highlight just how common paralogy is, even in supposedly universal BUSCO sets.</li> <li><strong>Hackathons are great for collaboration across time zones.</strong> Our work in Bad Saarow connected with contributions from an Australian outpost of the project, with progress passed back and forth through shared repositories and notes.</li> <li><strong>Open tools lower the entry barrier.</strong> By investing in a polished, documented workflow instead of a one‑off analysis, we make it easier for others to reuse and extend our work.</li> <li><strong>Pipelines live and grow in the open.</strong> The BUSCO phylogenomics pipeline we worked on is being developed in the open as the “buscophy” workflow on <a href="https://github.com/tbrown91/biohackathon-projects-2025/tree/main/03-automatic-workflow-for-benchmarking/buscophy">GitHub</a>. It takes BUSCO output from many genomes, aligns and trims the corresponding genes, builds gene trees, flags in- and out-paralogs, and then builds concatenated supermatrices and summary species trees from the filtered genes. Having all of this encoded in one reproducible pipeline means others can rerun exactly the same analysis, adapt it to their own taxa, or extend it with new methods.</li> </ul> <h2 id="what-comes-next">What comes next</h2> <p>The work we began at BioHackathon Europe 2025 will continue as the team refines the workflow, runs it on additional clades and prepares it for broader release. For my own research, I am excited to apply the BUSCO phylogenomics pipeline to insect genomes and to compare patterns of paralogy across groups with very different genome architectures. I expect this will directly improve the robustness of the phylogenies I use in my PhD.</p> <p><img src="https://www.open-bio.org/img/2026/2026-02-04-people.jpg" alt="Official BioHackathon Europe 2025 group picture in the courtyard."></p> <hr> <h2 id="acknowledgements">Acknowledgements</h2> <p>I am very grateful to the Open Bioinformatics Foundation for the Event Fellowship that made my participation in BioHackathon Europe 2025 possible, and to the organisers from ELIXIR for creating such a welcoming environment. I would also like to thank the BUSCO phylogenomics project leads and all my teammates for their patience, good humour and willingness to explain things one more time when the logs got confusing. Finally, I appreciate the support of my home institution and colleagues in Kraków, who made it easier for me to step away from local duties for a week of focused hacking. Thank you, OBF!</p> <hr>https://www.open-bio.org/2025/12/18/2026-keynote-community-comment/Thu, 18 Dec 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/12/18/2026-keynote-community-comment/<p><img src="https://www.open-bio.org/img/2025/bosc2025-img/Christine-Orengo-by-podium.jpeg" alt="Christine Orengo keynote - BOSC 2025"></p> <p>We thank our community for the excellent keynote speaker suggestions for <a href="https://www.open-bio.org/events/bosc">BOSC 2026</a>. The next phase of our selection process invites you to share any concerns about the suitability of the nominated individuals. Our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker selection process and criteria</a> outline the factors we consider when selecting speakers for BOSC 2026, including characteristics that will exclude a speaker.</p> <p>Please use <strong><a href="https://docs.google.com/forms/d/e/1FAIpQLSe3hUXZ5BQv2-I7DpL-SdEovAVh6Bq9wWgs93FMx5LylAC_Eg/viewform">this anonymous form</a></strong> to submit any concerns, including as much detail as you are comfortable providing, by <strong>Friday, January 9th, 2026</strong>.</p> <h3 id="this-years-nominees-are">This year’s nominees are:</h3> <ul> <li>Katy Börner</li> <li>Anne Carpenter</li> <li>Ishwar Chandramouliswaran</li> <li>Kyunghyun Cho</li> <li>Francis Collins</li> <li>Medha Devare</li> <li>Casey Greene</li> <li>Eric Green</li> <li>Susan Gregurick</li> <li>Lukas Heumos</li> <li>Mikhail Kolmogorov</li> <li>Heng Li</li> <li>Thomas Leitner</li> <li>Marcia McNutt</li> <li>Alondra Nelson</li> <li>Sandra Orchard</li> <li>Francis Oullette</li> <li>Cyril Pommier</li> <li>John Quackenbush</li> <li>Heidi Sofia</li> <li>Paul Thomas</li> <li>Kirstie Whitaker</li> <li>Maryam Zaringhalam</li> </ul> <p>The BOSC Organizing Committee will extend invitations for keynote speakers using the community-nominated list after the comment period closes. Since the Committee cannot guarantee a speaker&rsquo;s acceptance, they may need to consider individuals not on the original list without repeating the entire nomination process. However, the Committee remains open to community input if a speaker is believed not to meet the established standards.</p>https://www.open-bio.org/2025/12/02/2026-BOSC-keynote-nomination/Thu, 04 Dec 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/12/02/2026-BOSC-keynote-nomination/<p><img src="https://www.open-bio.org/img/2025/bosc2025-img/2025-mungall-keynote-wide.jpg" alt="Chris Mungall keynote - BOSC 2025"></p> <p><a href="https://www.open-bio.org/events/bosc">BOSC 2026</a> is planned for July 14-15, 2026, as part of ISMB 2026 in Washington, DC.</p> <p>We invite our community to <a href="https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform">nominate potential keynote speakers</a> who would be of interest to our community. You may submit as many nominations as you wish. The <a href="https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform">form</a> may be filled out multiple times. Please submit nominations by <strong>December 15, 2025</strong>.</p> <h3 id="why-this-matters">Why this matters</h3> <p>Keynote talks are always a highlight at BOSC. We traditionally open and close the conference with invited speakers—prominent contributors or emerging leaders whose work resonates with the bioinformatics open-source community.</p> <h3 id="about-the-selection-process">About the selection process</h3> <p>Prior to 2023, keynote selection was handled internally by the BOSC Organizing Committee. In 2023, we introduced a more consistent, transparent, and community-aligned process, including a public rubric for evaluating candidates. The results were excellent, and we are continuing this open nomination process for 2026. (See our selection rubric: <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md</a>)</p> <h3 id="key-dates">Key Dates</h3> <ul> <li>December 15, 2025 – Deadline for <a href="https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform">keynote speaker nominations</a></li> <li>December 19, 2025 – Nomination slate posted for community review</li> <li>January 9, 2026 – Deadline for community comments on the slate</li> </ul> <h3 id="nominate-a-keynote-speaker"><a href="https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform">Nominate a keynote speaker!</a></h3>https://www.open-bio.org/2025/12/04/2025-12-04-Fatemeh-Elixir-BioHackathon-experience/Thu, 04 Dec 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/12/04/2025-12-04-Fatemeh-Elixir-BioHackathon-experience/<p>The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Fatemeh Mirzade, a PhD researcher at the University of Antwerp, was awarded an OBF Event Fellowship to attend the BioHackathon Europe 2025 (<a href="https://biohackathon-europe.org/">https://biohackathon-europe.org/2025</a>). <img src="https://www.open-bio.org/img/2025/2025-11-03-Fatemeh-cover-image.jpg" alt="BioHackathon Europe 2025 group photo"></p> <h1 id="my-biohackathon-experience-contributing-to-open-science-in-proteomics">My BioHackathon Experience: Contributing to Open Science in Proteomics</h1> <p>From the 3rd to 7th of November 2025, I had an incredible opportunity that shaped my early PhD journey: participating in BioHackathon Europe 2025 as part of <strong>Project #29 on proteomics quality control</strong>. Thanks to the Open Bioinformatics Foundation (OBF) Event Fellowship, I joined a team of bioinformaticians and proteomics researchers working to solve a critical challenge in our field.</p> <p>🔗 Project #29 repository: <a href="https://github.com/MS-Quality-Hub/biohackathon2025">https://github.com/MS-Quality-Hub/biohackathon2025</a> 🔗 OBF on GitHub: <a href="https://github.com/OBF">https://github.com/OBF</a></p> <h2 id="why-i-joined">Why I Joined</h2> <p>As someone just starting their PhD, I was both nervous and excited to dive into this collaborative coding event. Our project aimed to build automated quality control frameworks for public proteomics repositories like PRIDE, which contains over 31,000 datasets. The problem? Without standardized quality metrics, researchers can&rsquo;t confidently reuse existing data, essentially flying blind when trying to assess if a dataset is suitable for their analysis.</p> <h2 id="my-contribution-making-sense-of-quality-metrics">My Contribution: Making Sense of Quality Metrics</h2> <p>I was assigned to create a formal taxonomy for QC metrics in mass spectrometry. When I first looked at the existing PSI-MS Controlled Vocabulary, I was overwhelmed. There were metrics scattered everywhere, categorized in ways that mixed fundamentally different information together.</p> <p>Working with the team, I helped develop a <strong>seven-dimensional classification system</strong> that describes each metric along orthogonal axes:</p> <ul> <li>workflow stage</li> <li>analytical dimension</li> <li>information dependency</li> <li>measurement scope</li> <li>acquisition strategy</li> <li>quality interpretation</li> <li>metric value type</li> </ul> <p><img src="https://www.open-bio.org/img/2025/2025-11-03-qc-workflow-sketch.jpg" alt="QC workflow sketch"></p> <p>I compiled and classified <strong>94 metrics</strong> from scientific literature, covering everything from chromatographic performance to identification confidence. For each one, I documented PSI-MS accession numbers, wrote descriptions, specified units, and noted applicability to different acquisition workflows. The work was tedious but deeply educational. By the end, I understood what “quality” actually means in proteomics.</p> <h2 id="what-open-source-contribution-feels-like">What Open Source Contribution Feels Like</h2> <p>This was my first real experience contributing to open-source infrastructure that will be used globally. The spreadsheet I created is now feeding directly into updates to the PSI-MS Controlled Vocabulary. The team used my work to add new relationship types to the ontology, enabling tools to automatically understand what each metric means.</p> <p>What struck me most was the collaborative nature of open science. I watched established researchers patiently explain concepts, saw consensus emerge through respectful debate, and learned that asking “stupid” questions often reveals important assumptions.</p> <p>Meanwhile, other team members built incredible tools:</p> <ul> <li>an <strong>mzQC export function for pMultiQC</strong></li> <li>an <strong>ID-free QC calculator using pyOpenMS</strong></li> <li>a <strong>web-based validator</strong> for our classification system</li> </ul> <p>These weren’t just internal prototypes but contributions to the broader proteomics ecosystem.</p> <h2 id="beyond-technical-skills">Beyond Technical Skills</h2> <p>Yes, I learned about mzQC formats, PSI-MS ontologies, and GitHub workflows. But the most valuable learning was about how open science actually functions. I experienced the generosity of researchers who take time to mentor newcomers, learned that technical decisions involve tradeoffs between elegance and practicality, and discovered that it&rsquo;s okay to feel out of your depth because that&rsquo;s where real learning happens.</p> <p>Coming in as a fresh PhD student, I felt intimidated by fast-moving technical discussions and unfamiliar acronyms. But that initial disorientation became exactly what made the experience valuable. I&rsquo;m leaving not just with new technical knowledge but with lasting connections to a community committed to collaborative infrastructure development.</p> <h2 id="why-this-matters">Why This Matters</h2> <p>We&rsquo;re building something that will help researchers worldwide make better use of public proteomics data. Imagine filtering datasets by quality before downloading terabytes, training machine learning models on curated high-quality data, or conducting meta-analyses that properly account for technical variation. That&rsquo;s the future we&rsquo;re working toward.</p> <p>This hackathon showed me what open science looks like in practice: people from different backgrounds coming together to tackle shared challenges, contributing their expertise freely, and building infrastructure that lifts the entire field.</p> <p>I&rsquo;m grateful to the Open Bioinformatics Foundation for making my participation possible and excited to continue contributing throughout my PhD.</p> <h2 id="want-to-explore-more">Want to Explore More?</h2> <p>❖ <strong>Full story on Medium:</strong> <a href="https://medium.com/@fatemehmirzadehsarcheshmeh/building-the-future-of-proteomics-quality-control-my-experience-at-biohackathon-europe-2025-8487191e170f">https://medium.com/@fatemehmirzadehsarcheshmeh/building-the-future-of-proteomics-quality-control-my-experience-at-biohackathon-europe-2025-8487191e170f</a></p> <p>❖ <strong>Project repo:</strong> <a href="https://github.com/MS-Quality-Hub/biohackathon2025">https://github.com/MS-Quality-Hub/biohackathon2025</a></p> <p>❖ <strong>OBF GitHub:</strong> <a href="https://github.com/OBF">https://github.com/OBF</a></p>https://www.open-bio.org/2025/12/02/2025-12-02-Hetvi-J-BioHackathon-Europe-2025/Tue, 02 Dec 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/12/02/2025-12-02-Hetvi-J-BioHackathon-Europe-2025/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Hetvi J,</em></strong> <em><strong>a PhD student at</strong></em> <em><strong>Imperial College London</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <strong><em><a href="https://biohackathon-europe.org/">BioHackathon Europe 2025</a></em></strong>.</p> <p>Thanks to the Event Fellowship from the Open Bioinformatics Foundation (OBF), I had the opportunity to attend BioHackathon Europe 2025 located in the beautiful city of Bad Saarow, Germany. I’m currently a 3rd year PhD student in Biostatistics and my work focuses on human mitochondrial genetics. Specifically, I construct statistical models to test whether the presence or absence of somatic mitochondrial variants is associated with gene expression changes indicative of stress and aging. As part of my PhD, I work with single-cell -omics data, and run bioinformatics pipelines over high performance computing systems. My broader interests in the fields of open-source scientific computing and bioinformatics motivated me to participate in this hackathon.</p> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-venue-biohack25.jpg" alt="The Location of the Hackathon"></p> <h2 id="background-on-the-hackathon">Background on the Hackathon</h2> <p>This event was a 5 day Hackathon with 31 projects, attended by 170+ in person and 200+ online. The hackathon began with presentations of each project &amp; we started working with our chosen teams on day 1. Every day, we had hacking sessions from 9am until 5:30pm &amp; the evenings were followed by social events to facilitate networking between people.</p> <p>During the hacking sessions, participants would work together with their project teams on assigned tasks &amp; make progress by co-working with team members. On the last day, we had final presentations detailing work done and future plans from the diverse range of projects.</p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-ppts-biohack25.jpg" alt="Final presentations"></p> <p>The projects are all in bioinformatics but spanning a variety of topics— everything from sustainable cluster computing to metadata standardization to building new pipelines. A full list of projects can be found here: <a href="https://biohackathon-europe.org/projects/">https://biohackathon-europe.org/projects/</a></p> <h2 id="brief-information-about-my-project">Brief information about my project</h2> <p>I was part of Project 4: <em>Beyond Beacons- Establishing genomic background in European and international biobanks</em>.</p> <p>We had 5 in person members and 1 online member working collaboratively on this project. The broad goal of this project was to assess the effect of genomic context as defined by haploblocks on the penetrance of mendelian variants.</p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-project-summary-biohack25.png" alt="Figure shows a visual summary of the pipeline created by us during this hackathon. Our pipeline begins with input VCF files which are clustered using mmseqs2 to obtain the population structure. We then combine information about the haploblocks, obtained clusters, and SNPs to generate binary encodings per individual and propose a simple linear model to associate these binary encodings with individual-level phenotypes."></p> <p>We segregated sequences from specific haploblocks that contain genes of interest and clustered them using mmseqs2 over 2600 individuals from the 1000 genomes project. Further, we developed a nomenclature system using binary strings to jointly-label the chromosomal, haploblock, cluster, and variant context per individual.</p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-brainstorm-biohack25.jpg" alt="A photo of the flipchart during one of our many brainstorming sessions for Project 4"></p> <p>We also made progress on sketching statistical models that would help associate these per-individual hashes with phenotypes. I contributed to building the nomenclature rules, and to model development and the codebase. More information on the project can be found at our Github repository. We will be releasing a Docker pipeline and a pre-print based on our work soon!</p> <p>Our Github: <a href="https://github.com/collaborativebioinformatics/Haploblock_Clusters_ElixirBH25">https://github.com/collaborativebioinformatics/Haploblock_Clusters_ElixirBH25</a></p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-team4-biohack25.jpg" alt="Project 4 - in-person team!"></p> <h2 id="social-events">Social events</h2> <p>The hackathon had some amazing social events I took part in.</p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-chain-biohack25.jpg" alt="Chain Reaction Obstacle Course"></p> <p>On Day 2, we had ‘Chain Reaction’ - an event where we made a creative obstacle course with all sorts of materials like wood or rubber ducks or even bubble machines to create a visual spectacle across 12 tables (the pictures will help!). A very unconventional but incredibly fun social activity- it was one of my favourite parts of the hackathon!</p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-poster-biohack25.jpg" alt="Poster Session"></p> <p>On Day 3, we had a mid-week progress update from each team through a Poster session. This was a great opportunity to learn about other projects in more detail and learn about their technical &amp; organizational approaches to the hackathon.</p> <p>Every day, we had walks at 6pm led by one of the hackathon organizers - which was a nice chance to see the lovely town of Baad Saarow with other participants.</p> <h2 id="learning-experiences">Learning experiences</h2> <p>Even with my limited background in the topic of recombination &amp; haploblocks— I was able to rapidly understand the project context &amp; make meaningful contributions through collaborating with others &amp; learning from them. It was also fun working collaboratively on a codebase.</p> <p>Moreover, getting a chance to interact with people from the wider bioinformatics community across sub-disciplines was very valuable for me. It was fascinating to hear about the interesting and diverse backgrounds other participants came from— my learnings from these conversations will definitely guide me as I progress in my career.</p> <p>Thanks again to OBF for enabling my participation in this project.</p> <!--- TODO: ADD IMAGE --> <p><img src="https://www.open-bio.org/img/2025/2025-12-02-boat-biohack25.jpg" alt="Photo of Bad Saarow Lake"></p>https://www.open-bio.org/2025/11/03/2025-11-03-Krasnow-ESIIL-Summit/Mon, 03 Nov 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/11/03/2025-11-03-Krasnow-ESIIL-Summit/<p><em><strong>The</strong></em> <a href="https://www.open-bio.org/travel-awards"><em><strong>Open Bioinformatics Foundation (OBF) Event Fellowship program</strong></em></a> <strong>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Ruby Krasnow, a PhD student at the University of Maine, was awarded an OBF Event Fellowship to attend the <a href="https://cu-esiil.github.io/Innovation-Summit-2025/">2025 ESIIL Innovation Summit</a></strong>. <img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-Summit-group4.png" alt="A group photo of six researchers (three men and three women) taken in a classroom. A draft food web is visible on the whiteboard behind them."> <em>My team (Group 4) from the 2025 ESIIL Innovation Summit.</em></p> <h2 id="introduction">Introduction</h2> <p>Thanks to the support of an OBF Event Fellowship, I attended the 2025 <a href="https://esiil.org/">Environmental Data Science Innovation &amp; Impact Lab</a> (ESIIL) <a href="https://cu-esiil.github.io/Innovation-Summit-2025/">Innovation Summit</a> in Boulder, Colorado. An annual event, this year’s ESIIL Summit had the following goals:</p> <ul> <li>Explore big data to understand environmental tipping points and transformations by identifying data synthesis opportunities and utilizing ESIIL cloud-compute capabilities.</li> <li>Promote best practices in ethical, open science by supporting accessibility and usability of environmental data by all stakeholders.</li> <li>Champion ethical practices in environmental science, and encourage the responsible use of AI.</li> <li>Support teams by establishing collaborations around data-inspired themes across different disciplines, sectors, and career stages.</li> </ul> <p><img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-Summit-everyone-small.jpg" alt="Summit participants stand on a staircase inside the Sustainability, Energy and Environment Community building at CU Boulder. A dinosaur skeleton is visible to the left of the stairs."> <em>Summit participants at the Sustainability, Energy and Environment Community (SEEC) building, part of the University of Colorado Boulder.</em></p> <p>The Summit was designed as an “unconference,” where much of the time was dedicated to forming teams that each tackled a specific research question related to understanding and predicting environmental tipping points and working in those teams to begin a collaborative project that ideally lasts far beyond the end of the in-person gathering. This event was a remarkable opportunity to meet and collaborate with other scientists from a variety of backgrounds.</p> <p>I learned a great deal about the conference theme as well as the open-source software tools that support the use of big data to answer questions related to the environmental transformations or disturbances. The topics chosen by the groups were extremely diverse, such as:</p> <ul> <li>Examining how hydrology, governance, and management interact within and across the Snake, Green, and Wind River Basins in the western U.S. - Synthesizing forest management and intervention strategies that can mitigate the impacts of linked disturbances (e.g., drought, windstorm, wildfire, and insect/pathogen disturbances).</li> <li>Creating a dashboard and interactive search tool for tribal decision-makers to access and understand meaningful information about extractive activities in the HeSapa (Black Hills) through &gt;2,400 Environmental Impact Statement/Assessment documents from the U.S. Forest Service, Bureau of Land Management, and other agencies.</li> <li>Evaluating how the order, duration, frequency, and intensity of disturbances affect the likelihood of regime shifts from forests to nonforests.</li> <li>Tackling broad questions about how to ensure greater data interoperability within the environmental data science community.</li> </ul> <p>My team chose to focus on environmental tipping points within freshwater food webs, exploring how the stability and resilience of food webs might be affected by—or serve as an early warning signal for—environmental tipping points or “regime shifts.” As an initial case study, we concentrated on Lake Champlain, a relatively data-rich system that one of our team members, <a href="https://www.plattsburgh.edu/academics/schools/arts-sciences/biological-sciences/faculty/gleichsner-alyssa.html">Dr. Alyssa Gleichsner</a>, knows well.</p> <p><img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-simple-foodweb.jpg" alt="Four-level trophic diagram composed of boxes labeled piscivorous fish, planktivorous fish, zooplankton, and phytoplankton, accompanied by cartoons of each organism. To the right of the hierarchy is a box containing images of a zebra mussel and Eurasian milfoil, labeled invasives."> <img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-moderate-foodweb.jpg" alt="Food web diagram for Lake Champlain, following the same general structure as the simplified diagram but with individual species labeled within the larger trophic groups."> <em>Preliminary drafts of a simplified food web of the Lake Champlain ecosystem, with more (left) or less (right) abstraction of individual species into trophic groups. Dates in parentheses in the right figure indicate the year of first appearance for invasive species.</em></p> <p>ESIIL staff encouraged us to use reproducible data analysis workflows from the very beginning of our project. Each team received a <a href="https://cu-esiil.github.io/stressors-food-web-connectivity-stability-innovation-summit-2025__4/">template GitHub repository</a> to track progress and share code, which we used when presenting our initial results during report-back sessions to all participants. Looking ahead, we plan to submit a proposal to form an ESIIL working group, which would provide additional support to expand this project’s scope and impact. Whether or not we receive funding, we aim to publish an open-access paper describing our results. In keeping with OBF and ESIIL’s open science ethos, we will publish our data and code alongside the paper so other researchers can reproduce, reuse, and extend our analysis to other freshwater systems.</p> <p>In addition to the time spent in working groups, the Summit featured several keynote presentations, including discussions on causal inference to identify climate impacts on ecological systems, predicting and managing ecological transformations in climate-adapted landscapes, and the use of AI in environmental data science. Perhaps the most meaningful aspect of the event was the emphasis on learning from and co-creating knowledge with the Indigenous peoples whose land we live and work on.</p> <p>It was impossible not to be moved by the words of the Indigenous leaders present at the Summit, who spoke about the deep connection we have to every part of the natural world and our responsibility to honor and protect the land, water, and life around us. Although I was aware in an academic sense of Traditional Ecological Knowledge (TEK) and efforts to incorporate TEK with traditional western science, the Summit was the first place I’ve experienced it in action, and it was very powerful to see how diverse ways of knowing can be weaved together to support environmental protection and management efforts.</p> <p><img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-mountains-small.jpg" alt="Sunrise over the mountains in Boulder, Colorado, visible in the distance beyond a field with trees."> <img src="https://www.open-bio.org/img/2025/2025-11-03-ESIIL-deer-small.jpg" alt="A mule deer standing in tall grass, eating leaves from a tree."> <em>Pictures of the mountains in Boulder and a grazing mule deer taken while walking to the University of Colorado Boulder East Campus, where the Summit was held.</em></p> <p>In many ways, the Summit showed me the value of diversity in scientific communities and the importance of community itself in maintaining hope and joy when facing immense challenges. Having learned more about ESIIL and its core values, I see many similarities with OBF, and I hope that OBF’s support of my participation in this ESIIL event will be only one of many examples of collaboration between the two organizations.</p> <h2 id="acknowledgements">Acknowledgements</h2> <blockquote> <p>&ldquo;Thank you to my Group 4 team members and to the OBF Event Fellowship for supporting my travel to the 2025 ESIIL Innovation Summit!&rdquo;</p> </blockquote> <hr>https://www.open-bio.org/2025/10/29/biopython-1-86-released/Wed, 29 Oct 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/10/29/biopython-1-86-released/<p>Biopython 1.86 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.86">PyPI</a>.</p> <p>This contains about nine months worth of updates, and is our first release with Python 3.14 support. See <a href="https://github.com/biopython/biopython/blob/biopython-186/NEWS.rst">change-log in the news file</a> (most of the changes are in <code>Bio.Align</code> and <code>Bio.PDB</code>). There have also been a few <a href="https://github.com/biopython/biopython/blob/biopython-186/DEPRECATED.rst">deprecations and removals of older code</a>.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors who were happy to be named:</p> <ul> <li>Rachel Stern (first contribution)</li> <li>Fabio Zanini</li> <li>Michiel de Hoon</li> <li>Oliver Wissett (first contribution)</li> <li>Peter Cock</li> <li>Samuel Prince (first contribution)</li> <li>Cassie Bastress (first contribution)</li> </ul>https://www.open-bio.org/events/bosc/sponsors/Wed, 22 Oct 2025 19:05:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc/sponsors/<div class="splitbox"><div class="left"> <h3 id="sponsoring-bosc">Sponsoring BOSC</h3> <p>Sponsorships from companies and non-profit organizations help enable us to provide free registration for some conference participants, offer honorariums to keynote speakers, and cover other expenses. Sponsors gain increased visibility and trust across the open source and open science ecosystem.</p> <br/> <h4 id="interested-in-sponsoring-bosc">Interested in sponsoring BOSC?</h4> <h4 id="please-contact-us-">Please contact us: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</h4> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Nomi-by-BOSC2024-poster.jpg" alt="Nomi by BOSC 2024 poster"></p> </div><div style="clear:both"></div></div> <br/> <div class="well"> <h2 id="2026-gold-sponsors">2026 Gold Sponsors:</h2> <p><a target="_new" href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/img/2026/2026-04-01-NIH-ODSS-logo.jpeg" style="width:55%" alt="NIH ODSS" /></a></p> <center><small>The NIH Office of Data Science Strategy (ODSS) leads the implementation of the NIH Strategic Plan for Data Science through scientific, technical, and operational collaboration with the institutes, centers, and offices that comprise NIH.</small></center> <br/> <p><a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/img/2026/2026-04-01-Seqera-logo.jpeg" style="width:45%" alt="Seqera" /></a></p> <center><small>Seqera, built by the creators of Nextflow, is the enterprise-first bioinformatics platform trusted by leading pharma and diagnostics companies to build, validate, and scale bioinformatics with confidence.</small></center> <br/> </div> <h2 id="what-is-bosc">What is BOSC?</h2> <p>BOSC is an annual meeting organized by the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation (OBF)</a>, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>Each BOSC ​includes keynote ​talks,​ talks chosen from submitted abstracts, ​poster​ ​sessions,​ ​panel, and ​lots​ ​of​ ​opportunities​ ​for​ ​networking. It is followed by​ ​collaborative​ ​working​ ​sessions​ ​at the <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a>.​ ​These​ ​events​ ​bring​ ​together​ ​software​ ​engineers,​ ​bioinformaticians,​ ​and​ ​researchers​ ​to collaborate​ ​on ​open​ ​source​ ​bioinformatics​ ​tools and frameworks and approaches to open science.</p> <p>Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB), which typically attracts over 2000 participants.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt="Panel at BOSC 2015"></p> <p>BOSC​ ​participants​ ​come​ ​from​ ​a​ ​wide​ ​variety​ ​of​ ​research​ ​environments​ ​and​ ​backgrounds:</p> <ul> <li>Biological​ ​researchers,​ ​students,​ ​and​ ​post-docs​</li> <li>Power​ ​bioinformatics​ ​users</li> <li>Bioinformatics​ ​tool​ ​and​ ​workflow​ ​developers</li> <li>Bioinformatics​-focused​ ​principal​ ​investigators​ ​and​ ​researchers</li> <li>Sequencing​ ​core​ ​facility​ ​staff</li> <li>Industry​ ​scientists​ ​and​ ​bioinformaticians</li> <li>Data​ ​scientists</li> </ul> <h2 id="previous-events">Previous Events</h2> <p>BOSC​ has been held <a href="https://www.open-bio.org/events/bosc/about/">every​ ​year​ ​since​ ​2000</a>.​ Most years, BOSC is part of the large Intelligent Systems for Molecular Biology meeting (ISMB).</p> <p>In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>. In July 2020, BOSC again joined forces with GCC to form the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>. Held online, BCC2020 attracted over 600 participants from 62 countries.</p> <p><a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> was part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, and took place July 29-30, 2021 (followed by a two-day <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest</a>).</p> <p><a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> was held July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> in person in Madison, Wisconsin, USA, and simultaneously online.</p> <p><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a> took place July 24-25, 2023 as part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> in Lyon, France and online. Like the previous year, we joined forces with Bio-Ontologies for part of a day!</p> <p><a href="https://www.open-bio.org/events/bosc-2024/">BOSC 2024</a>, the 25th annual Bioinformatics Open Source Conference, took place July 15-16, 2024 as part of <a href="https://www.iscb.org/ismb2024/home">ISMB 2024</a> in Montreal, Canada and online. It was followed by <a href="https://www.open-bio.org/events/bosc-2024/ismb-collaborationfest-2024/">CoFest 2024</a>.</p> <p><a href="https://www.open-bio.org/events/bosc-2025/">BOSC 2025</a> took place in Liverpool, UK, as part of the large <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a> conference, which attracted a record 2238 participants. For the first time, <a href="https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/">CollaborationFest</a> was part of the main ISMB/ECCB conference.</p> <p><a href="https://www.open-bio.org/events/bosc/">BOSC 2026</a> will be held in Washington, DC (with an online participation option) July 14-15, 2026 as part of <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a>.</p> <p><a href="https://www.open-bio.org/events/bosc/about" class="btn btn-lg btn-primary">More about BOSC</a></p> <br/> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Seqera-booth-2024.jpg" alt="Seqera booth at BOSC 2024"></p> <h2 id="benefits-of-sponsorship">Benefits of Sponsorship</h2> <p>Sponsoring BOSC increases your visibility in the bioinformatics community. We acknowledge our sponsors before, during and after the event in multiple ways:</p> <ul> <li>We list our sponsors on the BOSC website</li> <li>Sponsors are thanked and named in the introduction/closing slides during the meeting</li> <li>We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area</li> <li>The sponsors are thanked in selected emails to our mailing list and social media posts (with your logo) that go out before, during and after the event</li> <li>The sponsors are listed in our published reports after the meeting, e.g., <a href="https://f1000research.com/articles/7-1309/v1">https://f1000research.com/articles/7-1309/v1</a></li> <li>Platinum sponsors can show a short video before the first keynote</li> <li>Gold sponsors can show a short video some time during the conference</li> <li>We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <h2 id="how-sponsorships-help-bosc">How sponsorships help BOSC</h2> <p>We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to</p> <ul> <li>offer free registration to some BOSC participants</li> <li>support the <a href="https://www.open-bio.org/event-awards/">OBF&rsquo;s Event Fellowship program</a>, increasing participation from underrepresented groups</li> <li>provide child care at the conference</li> <li>underwrite the cost of conference events such as dinners or refreshments at poster sessions</li> <li>help defray the cost of videography</li> <li>provide space and catering at the CollaborationFest</li> <li>offer honoraria to keynote speakers</li> <li>pay for captioning and translations</li> </ul> <div class="well"> <p>In 2021, sponsorships enabled us to offer free registration to 20 participants from all over the world! <iframe loading="lazy" src="https://www.google.com/maps/d/embed?mid=1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width="640" height="480"> </iframe> </p> </div> <h1 id="sponsors-from-previous-years">Sponsors from previous years</h1> <h2 id="2025-platinum-sponsor">2025 Platinum Sponsor:</h2> <p><a target="_new" href="https://chanzuckerberg.com/science/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:45%" alt="CZI" /></a></p> <center>The aim of CZI's Open Science program is the universal and immediate open sharing of all scientific knowledge, processes, and outputs. </center> <br/> <h3 id="2025-gold-sponsor">2025 Gold Sponsor:</h3> <p><a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" style="width:30%" alt="Seqera" /></a></p> <center><small>Seqera, developed by the creators of Nextflow, empowers researchers to develop and deploy scalable bioinformatics pipelines faster</small></center> <p align="center"><iframe src="https://drive.google.com/file/d/1V1BbVcCPQHWN-8eMr4-yZ19xAK1p0Tfd/preview" width="640" height="480" allow="autoplay" ></iframe></p> <p><strong>2025 Silver Sponsor:</strong></p> <p><a target="_new" href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" style="width:20%" alt="GigaScience" /></a></p> <br/> <h2 id="2024-platinum-sponsors">2024 Platinum Sponsors:</h2> <p><a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" style="width:45%" alt="Seqera" /></a></p> <center>Seqera makes complex data analysis accessible at any scale</center> <p><a target="_new" href="https://chanzuckerberg.com/science)"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:45%" alt="CZI" /></a></p> <div class="splitbox"><div class="left"> <br/> <p><strong>2024 Gold Sponsor:</strong></p> <p><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Data Science"></a></p> </div><div class="right"> <br/> <p><strong>2024 Silver Sponsor:</strong></p> <div class="splitbox"><div class="left"> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a></p> </div><div class="right"> </div><div style="clear:both"></div></div> </div><div style="clear:both"></div></div> <br/> <h2 id="bosc-2023-platinum-sponsor">BOSC 2023 Platinum Sponsor</h2> <p><a target="_new" href="https://chanzuckerberg.com/science)"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:45%" alt="CZI" /></a></p> <h3 id="bosc-2023-silver-sponsors">BOSC 2023 Silver Sponsors</h3> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" style="width:20%" alt="GigaScience" /></a> <a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" style="width:20%" alt="Genevia" /></a> <a href="https://www.software.ac.uk/"><img src="https://www.open-bio.org/wp-content/uploads/2023/04/SSI_PRIMARY-LOGO-300x96.png" style="width:20%" alt="SSI logo" /></a></p> <h2 id="bosc-2022-platinum-sponsors">BOSC 2022 Platinum Sponsors</h2> <p><a target="_new" href="https://chanzuckerberg.com/science"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:35%" alt="CZI" /></a></p> <br/> <p><a target="_new" href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" style="width:25%" alt="AWS" /></a></p> <h2 id="bosc-2022-gold-sponsors">BOSC 2022 Gold Sponsors</h2> <p><a target="_new" href="https://www.broadinstitute.org/data-sciences-platform"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/Broad-DSP-logo-1.png" style="width:30%" alt="Broad" /></a></p> <p><a target="_new" href="https://datascience.nih.gov"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/NIH-ODSS_Horizontal_1Color-653.jpg" style="width:35%" alt="NIHODSS" /></a></p> <h3 id="bosc-2022-silver-sponsors">BOSC 2022 Silver Sponsors</h3> <p><a href="https://arvados.org"><img src="https://www.open-bio.org/wp-content/uploads/2022/05/ArvadosCurii.png" style="width:20%" alt="Arvados, supported by Curii" /></a> <a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" style="width:20%" alt="Gigascience" /></a></p> <br/> <div class="well"> <center> <h3 id="if-you-are-interested-in-becoming-a-bosc-sponsor-please-contact-us-at-">If you are interested in becoming a BOSC sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</h3> </center> </div>https://www.open-bio.org/2025/10/07/event-fellowship-2025-3/Mon, 06 Oct 2025 21:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/10/07/event-fellowship-2025-3/<p>The call for applications for <strong>round 3</strong> of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> for 2025 is now open. <strong>The deadline for this round is 1 December 2025.</strong> You can submit your application through <a href="https://forms.gle/D31zSs558aRwj2ig9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">make a copy of this template</a>.</p> <p>The Open Bioinformatics Foundation (OBF)&rsquo;s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is December 1, 2025.</p> <p>We invite applications from candidates seeking financial support to attend relevant scientific events between January 2026 to December 2026. <em><strong>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</strong></em>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <h3 id="overview-of-the-second-2025-round-of-the-obf-event-fellowship">Overview of the Second 2025 round of the OBF Event Fellowship</h3> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In the second round of 2025 (August 2025), we received numerous applications, and five applicants were selected for funding to support their participation in various events. <strong>Congratulations to the following recipients</strong>:</p> <ol> <li>David Kiragu Mwaura - Africa International Biotechnology and Biomedical Conference</li> <li>Elminah - Systems biology: from large datasets to biological insight</li> <li>Fatemeh Mirzadeh Sarcheshmeh - BioHackathon Europe 2025</li> <li>Hetvi Jethwani - BioHackathon Europe 2025</li> <li>Rafał Miłodrowski - BioHackathon Europe 2025</li> </ol> <p>Notably, the OBF Events Fellowship sponsored three participants at the BioHackathon Europe 2025.</p> <p>We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:</p> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/2025-08-25-TA4.png" alt="OBF Event awardee Tayyaba Alvi at the ISMB/ECCB2025"></p> </div><div class="right"> <p><strong>Tayyaba Alvi</strong> (left) attended the ISMB/ECCB2025 Conference, supported by OBF Event Fellowships. <a href="https://www.open-bio.org/2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/">Read about their experience here</a>.</p> </div><div style="clear:both"></div></div> <p>Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and <a href="https://forms.gle/D31zSs558aRwj2ig9">apply for the fellowship</a> before 1 December 2025.</strong></p>https://www.open-bio.org/events/bosc-2026/Mon, 06 Oct 2025 20:29:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2026/<p><img src="https://www.open-bio.org/img/2025/2025-07-BOSC-room.png" alt="The audience at BOSC 2025"></p> <div class="well"> <p>Since 2000, BOSC has covered all aspects of open source bioinformatics and open science. <strong>BOSC 2026</strong>, the 27th annual Bioinformatics Open Source Conference, will take place <strong>July 14-15 in Washington, DC</strong>, as part of <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a>. We are excited to announce our two <a href="https://www.open-bio.org/events/bosc-2026/bosc-2026-keynotes/">keynote speakers, <strong>Eric Green and Maryam Zaringhalam</strong></a>, and two <a href="https://www.open-bio.org/events/bosc-2026/panels/">panels</a> on important and timely topics: <em>Policies and Strategies for Resilient Open Science</em> and <em>Open Source in the Age of AI</em>. We will again join forces with <a href="https://www.bio-ontologies.org.uk/">Bio-Ontologies and Knowledge Representation (BOKR)</a> for half a day.</p> </div> <div class="well"> <h2 id="bosc-2026-key-dates">BOSC 2026 Key Dates</h2> <div class="splitbox"><div class="left"> <ul> <li>April 1: <a href="https://www.open-bio.org/event-awards/">OBF Event Award application deadline</a></li> <li><strong>April 9: Abstract submission deadline (talks and posters) - submit your abstract <a href="https://www.open-bio.org/events/bosc-2026/submit/">here</a>!</strong></li> <li>May 5: Talk/poster acceptance notifications</li> <li>May 7: Late poster submission deadline</li> <li>July 12-16: <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a> (Washington, DC and online)</li> <li><strong>July 14-15:</strong> <strong>BOSC 2026</strong> (part of ISMB 2026)</li> <li>July 17-18: CollaborationFest (more info coming soon!)</li> </ul> <p></div><div class="right"> <img src="https://www.open-bio.org/img/2025/bosc2025-img/CoFest%20-%203%20people%20working%20at%20table.jpeg" alt="Three people at CoFest 2025"></p> </div><div style="clear:both"></div></div> </div> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/bosc2025-img/Maggie%20Fu%20by%20poster.jpeg" alt="Maggie Fu by poster at BOSC 2025"> <br/></p> </div><div class="right"> <h3 id="topics">Topics</h3> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Data Access and Visualization</li> <li>Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Outreach and Training</li> <li>Open AI/ML</li> <li>Sustainable Data</li> <li>&hellip;and more!</li> </ul> </div><div style="clear:both"></div></div> <br/> <div class="well"> <h3 id="registration-and-financial-assistance">Registration and Financial Assistance</h3> <p>To participate in BOSC 2026 or the ISMB CollaborationFest, you will need to register for <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a>. Those who submit abstracts to BOSC can request a fee waiver on the submission form. You can also apply for an <a href="https://www.open-bio.org/event-awards/">OBF Event Award</a>; the deadline is April 1.</p> <p><img src="https://www.open-bio.org/img/2025/bosc2025-img/BOSC%20orgs%20-%20Jason%20Moni%20Nomi%20Karsten%20Herve.jpeg" alt="BOSC 2025 organizing committee"></p> </div> <h2 id="sponsorships">Sponsorships</h2> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/2025-gigascience-sponsors.jpg" alt="Scott Hunter and Nomi Harris point to BOSC 2024 poster"></p> </div><div class="right"> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from companies and non-profit organizations help to defray some of our costs and support our outreach efforts. Thanks to our sponsors, we were able to grant free registration to 12 BOSC 2025 participants and cover travel expenses of some keynote speakers and panelists.</p> <p>Interested in sponsoring BOSC 2026? Please see our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors page</a>!</p> </div><div style="clear:both"></div></div> <h3 id="2025-gold-sponsors">2025 Gold Sponsors</h3> <div class="splitbox"><div class="left"> <p><a target="_new" href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/img/2026/2026-04-01-NIH-ODSS-logo.jpeg" alt="NIH ODSS" /></a></p> <center><small>The <b><a target="_new" href="https://datascience.nih.gov/">NIH Office of Data Science Strategy (ODSS)</a></b> leads the implementation of the NIH Strategic Plan for Data Science through scientific, technical, and operational collaboration with the institutes, centers, and offices that comprise NIH.</small></center> <p></div><div class="right"> <a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/img/2026/2026-04-01-Seqera-logo.jpeg" alt="Seqera" width="90%"/></a></p> <center><small><a target="_new" href="https://seqera.io/"><b>Seqera</b></a>, built by the creators of Nextflow, is the enterprise-first bioinformatics platform trusted by leading pharma and diagnostics companies to build, validate, and scale bioinformatics with confidence.</small></center> </div><div style="clear:both"></div></div> <br/> <div class="well"> <h2 id="bosc-2026-organizing-committee">BOSC 2026 Organizing Committee</h2> <div class="splitbox"><div class="left"> <p><em><strong>Chair: Nomi L. Harris</strong></em> (Lawrence Berkeley National Laboratory)</p> <ul> <li>Karsten Hokamp (Trinity College Dublin)</li> <li>Jessica Maia (BD)</li> <li>Hervé Ménager (Institut Pasteur)</li> <li>Mónica Muñoz Torres (Univ. of Colorado Anschutz)</li> <li>Tazro Ohta (Chiba University)</li> <li>Van Truong (University of Pennsylvania)</li> <li>Deepak Unni (SIB, Swiss Institute of Bioinformatics)</li> <li>Jason Williams (Cold Spring Harbor Laboratory)</li> </ul> </div><div class="right"> <p><img src="https://www.open-bio.org/img/2026/2026-02-05-bosc-2026-org-committee-square.png" alt="BOSC 2025 Organizing Committee"></p> </div><div style="clear:both"></div></div> <h4 id="bosc-2025-review-committee-2026-list-coming-soon">BOSC <em>2025</em> Review Committee (2026 list coming soon)</h4> <p>Aziz Khan*, Bastian Greshake Tzovaras*, Bhavesh Patel, Christopher Fields*, Damien Goutte-Gattat*, Daniel Korn, Deepak Unni, Fortune Ogo-Ndah Awala, Gayathri Jonnalagadda, J. Harry Caufield*, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov, Luis Pedro Coelho, Monica C Munoz-Torres, Naouel Karam, Nomi Harris, Olawumi Olasunkanmi, Peter Cock, Rafael Gonçalves, Sayali Talware, Sepideh Mazrouee*, Tanya Berardini, Tazro Ohta*, Tyrone Chen, Van Truong, Yuvanesh Vedaraju</p> <p>* indicates reviewers who did extra reviews</p> </div> <h3 id="about-bosc">About BOSC</h3> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since 2000, BOSC has covered all aspects of open source bioinformatics and open science. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow and sustain open source communities.</p> <p>Last year&rsquo;s conference, <a href="https://www.open-bio.org/events/bosc-2025/">BOSC 2025</a>, took place July 21-22, 2025 in Liverpool, UK (as part of <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a>). Read our <a href="https://f1000research.com/articles/14-887/v1">BOSC 2025 report on F1000Research</a>! BOSC 2025 included two days of <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/">keynote talks</a>, talks from submitted abstracts, a <a href="https://www.open-bio.org/events/bosc-2025/panel">panel discussion on data sustainability</a>, and posters. It also featured a <a href="https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025">joint session</a> with the <a href="https://www.bio-ontologies.org.uk/2025-meeting">Bio-Ontologies and Knowledge Representation (BOKR)</a>, which opened with a <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/">joint keynote by Chris Mungall</a> followed by talks on some of our favorite topics, including open data and reusable and reproducible science. The full lineup of BOSC 2025 talks and posters, including links to talk videos, is available on our <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/">Schedule page</a>.</p> <p><img src="https://www.open-bio.org/img/2025/bosc2025-img/Carlo%20Moni%20Deepak%20Nomi%20-%20CoFest%20table.jpeg" alt="BOSC 2025 organizing committee"></p> <p>BOSC is usually preceded or followed by <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a> (CoFest for short), a two-day collaborative work session. This is an opportunity for anyone interested in open science, biology or programming to meet, talk and work collaboratively. In 2025, CollaborationFest was part of ISMB/ECCB.</p> <p><a href="https://www.open-bio.org/events/bosc/about" class="btn btn-lg btn-primary">More about BOSC</a></p> <p>&nbsp;<br/></p> <div class="well"> <h4 id="code-of-conduct">Code of Conduct</h4> <p>As part of ISMB 2026, BOSC 2026 is covered by the <a href="https://www.iscb.org/about-iscb/policy-statements-bylaws-and-legal-documents/code-of-ethics-and-professional-conduct">ISCB Code of Ethics and Professional Conduct</a>.</p> </div>https://www.open-bio.org/2025/09/30/2025-09-30-gigascience/Tue, 30 Sep 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/09/30/2025-09-30-gigascience/<p>To begin something is difficult; to keep something going is a different challenge. Even when it is the right thing to do, if it does not yield economic benefit in the short term, it may be difficult to sustain. Open science, including open-source software development and open data, is precisely such an example. Everyone agrees these are of great importance, yet when confronted with the immediate demands of an academic career or the short-term profit of a company, putting in the extra work to make all of the code and data publicly accessible and reusable may not be a priority. That is why individuals and organizations that not only embrace these principles but also persist with them over long periods are worthy of being recognized. They act not merely for themselves, but for the whole of human society. <img src="https://www.open-bio.org/img/2025/2025-gigascience-cake.jpg" alt="Photo at GigaScience Birthday Party 2025 - Scott cutting the cake"></p> <p>One of these organizations is the <a href="https://academic.oup.com/gigascience">GigaScience journal</a>. Since its founding, GigaScience has been at the forefront of open data science. Its initiative to build its own data repository, to assign curators, and to archive the data underlying accepted articles was truly pioneering, and other journals followed. Unlike traditional journals operated solely by editorial boards, GigaScience is, in effect, equivalent to establishing a full-fledged data center.</p> <p>The recent news concerning GigaScience’s owners, BGI, laying off the entire editorial, software and curation team in Hong Kong on short notice, has filled us with both surprise and deep disappointment. They are the very people who established the journal’s identity and direction and made it an essential journal in biomedical informatics. Departing Editor in Chief Scott Edmunds wrote a passionate article sharing a retrospective on <a href="https://doi.org/10.59350/hzfr4-z0881">15 years of innovation at GigaScience</a> [1].</p> <p>GigaScience’s work is not only about selecting manuscripts, but also about validating the underlying data and recording the necessary metadata for preservation. These time-consuming steps might appear to exceed what an ordinary editorial office is supposed to do. Yet, if we reflect upon the true role of research articles, that of sharing the latest scientific results, we must admit that it is the conventional journal that has become outdated. The age of handwritten letters and printed texts has passed; now is the age of computation. The work that GigaScience does to make sure that not just publications, but the data they are reporting on, is truly what the scientific community has long needed.</p> <p>GigaScience has been a longtime sponsor of the Bioinformatics Open Source Conference (BOSC). Members of its editorial office have participated in BOSC and the encompassing Intelligent Systems for Molecular Biology (ISMB) conference for many years, at times giving talks and serving in discussion panels (for example, Scott was on the <a href="https://www.open-bio.org/events/bosc-2025/panel/">2025 Data Sustainability panel</a>). Beyond their financial contributions and their support and hard work on behalf of open science, the people at GigaScience are our friends.</p> <p>We sincerely hope that under its new management, the assets that were so painstakingly constructed will be preserved and further developed for years to come. And to those talented and brilliant members who were let go — Scott, Nicole, Chris, Peter, Mary Ann, Bastien, and Ken — we wish you bright and fortunate opportunities ahead. From our hearts, we hope that we may once again see you at scientific meetings, still burning with a passionate commitment to open science and open publication.</p> <p>Reference:</p> <blockquote> <p>Edmunds, S. (2025, September 17). And it&rsquo;s goodbye from me. GigaBlog. <a href="https://doi.org/10.59350/hzfr4-z0881">https://doi.org/10.59350/hzfr4-z0881</a></p> </blockquote> <p>Signed by the following, many of whom are or have been members of the BOSC organizing committee or Open Bioinformatics Foundation, including board members. You can add your name via a pull request:</p> <ul> <li>Tazro Ohta</li> <li>Nomi Harris</li> <li>Peter Cock</li> <li>Mónica Muñoz Torres</li> <li>Chris Fields</li> <li>Bastian Greshake Tzovaras</li> <li>Deepak Unni</li> <li>Hervé Ménager</li> <li>Hilmar Lapp</li> </ul> <p>Post-publication signatories (chronological, please <a href="https://github.com/OBF/OBF.github.io/edit/main/content/posts/2025-09-30-gigascience.md">make a pull request</a> by the end of October if you wish to add your name):</p> <ul> <li>J. Harry Caufield</li> <li>Nicola Soranzo</li> <li>Daniel Mietchen</li> <li>Mark A. Jensen</li> <li>Lane Rasberry</li> <li>Hans-Rudolf Hotz</li> <li>Maryann Martone</li> </ul> <p><img src="https://www.open-bio.org/img/2025/2025-gigascience-party.jpg" alt="Photo at GigaScience Birthday Party 2025"> <img src="https://www.open-bio.org/img/2025/2025-online-bcc.jpg" alt="Sreenshot of BCC online conference"> <img src="https://www.open-bio.org/img/2025/2025-gigascience-cake.jpg" alt="Photo of Moni and Scott on-stage during BOSC 2025 panel"> <img src="https://www.open-bio.org/img/2025/2025-gigascience-sponsors.jpg" alt="Photo highlighging GigaScience&rsquo;s BOSC 2025 sponsorship"> <img src="https://www.open-bio.org/img/2025/2025-cavern-club-outside.jpg" alt="Small group photo outside the Cavern Club, Liverpool, after BOSC 2025"> <img src="https://www.open-bio.org/img/2025/2025-cavern-club-inside.jpg" alt="Photo of Moni and Scott inside the Cavern Club, Liverpool, after BOSC 2025"></p>https://www.open-bio.org/2025/09/24/2025-09-24-BOSC2025-report-and-videos/Wed, 24 Sep 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/09/24/2025-09-24-BOSC2025-report-and-videos/<p><img src="https://www.open-bio.org/img/2025/2025-07-BOSC-room.png" alt="A full room at BOSC 2025"></p> <p>Whether you attended BOSC 2025 or missed it, you can read about it (with lots of photos!) in our <a href="https://f1000research.com/articles/14-887">report published in F1000Research</a>.</p> <p>We are also pleased to announce that videos of the BOSC 2025 talks are now available on our <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/">schedule page</a>, as well as on our <a href="https://www.youtube.com/@OBFBOSC/videos">YouTube channel</a>. Enjoy!</p>https://www.open-bio.org/2025/09/04/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025/Thu, 04 Sep 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/09/04/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025/<p><strong><em>The</em></strong> <a href="https://github.com/OBF/OBF.github.io/blob/main/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Muhamad Haries Ramdhani,</em></strong> <strong><em>a PhD Student at the</em></strong> <strong><em>University of Aberdeen</em></strong>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <a href="https://www.iscb.org/ismbeccb2025"><strong><em>ISMB/ECCB 2025</em></strong></a>. <img src="https://www.open-bio.org/img/2025/2025-09-04-haries-ramdhani-1.png" alt="Keynote speakers and DREAM challenges talks at the ISMB/ECCB"></p> <h3 id="the-journey-to-liverpool"><strong>The Journey to Liverpool</strong></h3> <p>I had heard about ISMB before, but I wasn&rsquo;t entirely clear on its joint conference format with ECCB. What I did know was that ISMB/ECCB is arguably the biggest conference for computational biology in the world. For months, my attendance felt uncertain, as I initially didn&rsquo;t know if the 2025 edition would be held in the UK. When the location was confirmed as Liverpool, it was a huge relief. Being a UK-based student meant I was fortunate enough to avoid a lengthy and often stressful visa application process.</p> <p>As a PhD student, attending my first major international conference was a significant goal. My research focuses on benchmarking and cell-to-cell communication and the ISMB/ECCB program felt perfectly aligned with my work. I was particularly drawn to the <strong>DREAM Challenges</strong> track, as it offered a chance to see a wide variety of approaches to benchmarking, which is central to my own projects. Furthermore, the conference provided an ideal venue to present my own poster and receive feedback from experts in the field. Beyond the formal sessions, I was very excited about <strong>CollaborationFest</strong>. The opportunity to contribute directly to open-source projects and network with the developers behind the tools we use every day was a major motivation for me to apply and attend.</p> <h3 id="navigating-a-massive-conference"><strong>Navigating a Massive Conference</strong></h3> <p>Upon arriving, I realised the main conference didn&rsquo;t formally kick off until Monday. Sunday&rsquo;s schedule was composed mostly of tutorials and the student council symposium, both of which required extra payment to attend. However, the scientific energy began to build that evening with an incredible opening keynote from Nobel Prize winner <strong>Dr. John Jumper</strong>. In his talk, &ldquo;Predicting the universe of biomolecular interactions with artificial intelligence,&rdquo; Dr. Jumper walked attendees through the evolution of the AlphaFold project. He shared insights into the technical and conceptual milestones behind each generation of AlphaFold, including innovations like rawMSA masked language models, Evoformer modules and the importance of self-distillation. He emphasised that no single breakthrough carried the project, instead, AlphaFold’s success came from a steady accumulation of improvements and a methodology rooted in biological intuition and empirical iteration.</p> <p>From Monday onwards, the conference was in full swing and the buzzing atmosphere truly hit. I have never been in a building with so many people. With over 2300 attendees, it was incredible to be surrounded by peers who all share a deep interest in computational biology. The sheer scale of the event was an experience in itself, requiring constant movement between auditoriums to attend the specific talks that aligned with my interests. My primary focus areas were the tracks for MLCSB, the NIH Track on GenAI, Cyberinfrastructure, Digital Twins and Quantum Computing and the DREAM Challenges. As my own research is in benchmarking, I spent the most time at the DREAM Challenge sessions. It was really nice to see the different and creative approaches people were taking to benchmark complex biological problems. I also made a point to attend talks in the Sysmod track, mainly because I was in a Systems Biology lab during my undergrad and the field still piques my interest.</p> <p>The keynotes each provided a masterclass in a different corner of our field:</p> <ul> <li> <p><strong>Amos Bairoch</strong>, in his talk <em>&ldquo;Plus ça change, plus c’est la même chose&hellip;&rdquo;</em>, delivered a powerful history lesson on 45 years of biocuration. He charted the field&rsquo;s course from manually typing protein sequences in 1980 to leading the first Swiss-Prot release in 1986. Bairoch’s central message was a crucial paradox: despite incredible technological progress, the foundational work of expert curation still faces the same core challenges of being underfunded, undervalued, and wrongly assumed to be replaceable.</p> </li> <li> <p><strong>James Zou</strong>, the 2025 Overton Prize winner, explored the transformative potential of AI agents in his talk, &ldquo;Computational biology in the age of AI agents.&rdquo; He presented a compelling vision of AI &ldquo;scientists&rdquo; like the Virtual Lab, which can autonomously design research and CellVoyager, which reanalyses complex genomic data. His closing point emphasized that the future is not about replacement but a powerful synergy between AI&rsquo;s scale and human creativity.</p> </li> <li> <p><strong>Charlotte Deane</strong> offered a dose of critical realism in her keynote, &ldquo;Building the future of AI-driven structure-based drug discovery,&rdquo; examining both the hype and the hurdles. While showcasing powerful tools from her own lab, she cautioned that the field is hampered by biased training data and flawed benchmarks. Her talk served as a crucial reminder that new AI models do not always outperform traditional methods on realistic test sets, raising serious questions about their true ability to generalize.</p> </li> </ul> <h3 id="posters-serendipity-and-collaboration"><strong>Posters, Serendipity and Collaboration</strong></h3> <p><img src="https://www.open-bio.org/img/2025/2025-09-04-haries-ramdhani-2.png" alt="From left to right: Haries and his poster, Collaboration Fest and the code Haries was working on for Schema.science during the Collaboration Fest"></p> <p>The poster sessions were immense, with what I estimated to be around 500 posters presented each day in a massive venue. I came prepared with a list of posters I wanted to see and enjoyed many engaging conversations with the authors. The hall was also a hub of serendipitous networking. While wandering the aisles, I met a new friend, a fellow PhD student from Indonesia who is now at Nottingham.</p> <p><img src="https://www.open-bio.org/img/2025/2025-09-04-haries-ramdhani-3.png" alt="Haries’ Collaboration Fest project working on the automation of generating training guides using LLM"></p> <p>The final day brought an event I had been looking forward to with great anticipation: <strong>Collaboration Fest</strong>. I have always wanted to join a Collaboration Fest and I was very excited for the opportunity to engage directly with the community in a hands-on setting dedicated to advancing open-source projects. It represented the perfect way to cap off a week of intense learning, shifting the focus from listening to actively participating and networking with developers to contribute to the tools that are so vital to our field. In Collaboration Fest, I worked with Phil Reed from schemas.science which is an initiative to improve the findability on the web of scientific research data, products and resources. <a href="https://github.com/schemas-science/schemas-science.github.io/tree/ismbeccb2025-cofest">I worked on improving the process of generating training guides for domain-agnostic schemas.science using LLM</a>. I also had the chance to present my own poster on <a href="https://github.com/MorganResearchLab/benccchmarker">benCCChmarker</a>, which is a software to benchmark multiple single-cell RNA-seq cell-to-cell communication algorithms. benCCChmarker provides an easy to use framework to compare different algorithms using simulated cell-to-cell communication single-cell RNA-sequencing data and curated data. I received a very interesting visit from people who work directly in the field, which led to a fantastic discussion about my work.</p> <h3 id="lessons-learned-and-reflections"><strong>Lessons Learned and Reflections</strong></h3> <p>Attending ISMB/ECCB 2025 was an invaluable experience that taught me several key lessons:</p> <ol> <li><strong>The Scale of Community is Motivating</strong>: There is a unique energy that comes from being in a space with over 2300 people who share your specific scientific interests. The &ldquo;buzz&rdquo; in the venue was a powerful reminder that we are all part of a large, collaborative and global effort to advance science.</li> <li><strong>AI is a Tool, Not a Panacea</strong>: The keynotes collectively painted a realistic picture of AI in biology. It is a transformative tool, but its success depends entirely on thoughtful model design, rigorous evaluation and most importantly, robust, well-curated data. Professor Deane’s talk was a particularly important reminder to remain critical and avoid being biased by hype.</li> <li><strong>Foundational Work is Irreplaceable</strong>: Professor Bairoch’s talk was a crucial counterpoint to the focus on cutting-edge AI. It underscored that foundational resources built on expert human curation are the bedrock upon which new technologies stand. This work is vital, yet it continues to be undervalued and underfunded.</li> <li><strong>Embrace Serendipity</strong>: While I had a schedule, some of the most memorable interactions were unplanned, like bumping into an old friend or starting a conversation at a poster. These moments are where new ideas and collaborations often begin.</li> </ol> <p>This conference broadened my perspective on the challenges and opportunities in computational biology and gave me new ideas to apply to my own research. It was an intense, exhausting but ultimately rewarding week.</p> <h3 id="acknowledgements"><strong>Acknowledgements</strong></h3> <p>I am thankful to the OBF Event Fellowship for the travel award which allowed me to attend ISMB/ECCB 2025. My thanks also go to the University of Aberdeen for funding my PhD research and to my mentor, Dr. Michael Morgan, for his invaluable guidance and wisdom.</p> <h3 id="links-and-resources-to-open-science"><strong>Links and Resources to Open Science</strong></h3> <ul> <li>Schemas.science branch that I worked on during Collaboration Fest <a href="https://github.com/schemas-science/schemas-science.github.io/tree/ismbeccb2025-cofest">https://github.com/schemas-science/schemas-science.github.io/tree/ismbeccb2025-cofest</a></li> <li>benCCChmarker <a href="https://github.com/MorganResearchLab/benccchmarker">https://github.com/MorganResearchLab/benccchmarker</a></li> </ul>https://www.open-bio.org/2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/Mon, 25 Aug 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Tayyaba Alvi,</em></strong> <em><strong>a PhD student at</strong></em> <em><strong>Fritz Lipmann Institute on Aging</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <strong><em><a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB2025</a></em></strong>. <img src="https://www.open-bio.org/img/2025/2025-08-25-TA4.png" alt="David Baker on the screen on the left, and me with my poster on the right"></p> <p>Thanks to the Event Fellowship from the Open Bioinformatics Foundation (OBF), I had the chance to attend the 33rd Conference on Intelligent Systems for Molecular Biology (ISMB 2025) in Liverpool. It’s the annual meeting of the International Society for Computational Biology (ISCB) and the biggest conference in the field. This year, it brought together over 2,000 researchers from all over the world at ACC Liverpool, a beautiful venue right by the Albert Dock.</p> <p><img src="https://www.open-bio.org/img/2025/2025-08-25-TA1.png" alt="ACC Liverpool on the left, and a view of the main auditorium from the back, on the right"></p> <h2 id="day-1-teaching-and-kicking-things-off">Day 1: Teaching and Kicking Things Off</h2> <p>The conference started with workshops and tutorials, along with the ISCB Student Council Symposium. I was excited (and a little nervous!) to help organize and lead a tutorial on Mendelian Randomization (MR), together with two colleagues from my group. We had around 17 participants from different backgrounds and career stages join us for an interactive session on causal inference. We covered key assumptions, common pitfalls like pleiotropy, and hands-on examples in R. It was really rewarding to see people engage, ask questions, and reflect on how these methods might apply to their own work. If you are interested, you can find the tutorial slides and other information on the <a href="https://donertas-group.github.io/ismb2025_mr_tutorial/">Tutorial Page</a>.</p> <p><img src="https://www.open-bio.org/img/2025/2025-08-25-TA3.png" alt="Ongoing Tutorial on Causal Inference"></p> <p>In the evening, we heard a fantastic keynote from John Jumper, who shared the story behind AlphaFold. He walked us through the ups and downs of building such a groundbreaking method, and how many of their ideas came from trial and error. It was fascinating and also really encouraging to hear how persistence and curiosity shaped their success.</p> <p><img src="https://www.open-bio.org/img/2025/2025-08-25-TA2.png" alt="Janet Thornton introducing the keynote speaker, John Jumper"></p> <h2 id="day-24-talks-posters-and-conversations">Day 2–4: Talks, Posters, and Conversations</h2> <p>The second day opened with a keynote from Amos Bairoch, who spoke about the ongoing challenges in biocuration. With so much biological data being generated, his talk highlighted just how important curated, high-quality data resources are, and how we need to keep investing in them. After that, the days were packed with talks across different tracks and COSIs. I attended sessions from:</p> <ul> <li>GenComp (Comparative Genomics)</li> <li>DREAM</li> <li>BOSC (Bioinformatics Open Source Conference)</li> <li>And MICROBIOME, which had some especially interesting talks on Tuesday and Thursday</li> </ul> <p>There was a lot to take in—talks ranged from methods development to applications in systems biology, single-cell data, and microbiome analysis. One of the talks that really stood out to me was James Zou’s keynote, where he introduced the idea of a virtual AI lab. He talked about how AI agents and language models are starting to help with experiment planning, literature synthesis, and even idea generation. It felt like a sneak peek into how computational biology might look just a few years from now.</p> <p>Outside the talks, the poster sessions and coffee breaks were great for meeting people. I had lots of interesting conversations, some about research, others just about navigating PhD life or sharing career advice. Chatting with poster presenters also helped me learn about tools and approaches I hadn’t seen before. Those casual exchanges were honestly one of the best parts of the week.</p> <p>The conference wrapped up with a conversation with David Baker, who shared his insights on protein design and creative science, followed by a final keynote from Fabian Theis. His talk focused on atlas-scale data integration and the Human Cell Atlas, a huge and ongoing effort to map cell types across tissues and conditions. It was a powerful reminder of how large-scale collaboration can really push the field forward.</p> <h2 id="exploring-liverpool">Exploring Liverpool</h2> <p>In between conference sessions, I made sure to explore a bit of Liverpool. The dockside area near the venue was lovely to walk around—full of history, great views of the Mersey, and a surprisingly peaceful vibe despite all the conference hustle.</p> <p><img src="https://www.open-bio.org/img/2025/2025-08-25-TA5.png" alt="John Lennon Peace Monument on the left, and the Wheel of Liverpool on the right"></p> <hr> <h2 id="final-thoughts">Final Thoughts</h2> <p>ISMB 2025 was a really full and energizing week. Between leading a tutorial, hearing inspiring talks, and connecting with scientists from all over, I came away with lots of new ideas and a deeper appreciation for the community we&rsquo;re part of. I’m super grateful to OBF for supporting my attendance. It made it possible for me to not only learn from the best in the field but also contribute something back through our tutorial. I&rsquo;m excited to take these experiences into my own research and hopefully return to ISMB again in the future.</p> <hr>https://www.open-bio.org/2025/07/15/event-fellowship-2025-2/Tue, 15 Jul 2025 21:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/07/15/event-fellowship-2025-2/<p>The call for applications for <strong>round 2</strong> of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> for 2025 is now open. <strong>The deadline for this round is 1 August 2025.</strong> You can submit your application through <a href="https://forms.gle/D31zSs558aRwj2ig9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">make a copy of this template</a>.</p> <p>The Open Bioinformatics Foundation (OBF)&rsquo;s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is August 1, 2025.</p> <p>We invite applications from candidates seeking financial support to attend relevant scientific events between September 2025 to August 2026. <em><strong>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</strong></em>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <h3 id="overview-of-the-first-2025-round-of-the-obf-event-fellowship">Overview of the First 2025 round of the OBF Event Fellowship</h3> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In the first round of 2025 (April 2025), we received numerous applications, and four applicants were selected for funding to support their participation in various events. <strong>Congratulations to the following recipients</strong>:</p> <ol> <li>Ruby Krasnow 2025 ESIIL Innovation Summit September 23-25, 2025</li> <li>Tayyaba Alvi International conference on Intelligent Systems for Molecular Biology (ISMB) 20-24 July, 2025</li> <li>Seun Olufemi RSECon25 9-11 September 2025</li> <li>Muhamad Haries Ramdhani ISMB/ECCB 2025 20th July 2025 - 24th July 2025</li> </ol> <p>We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:</p> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-02.jpg" alt="OBF Event awardee Kyra Feuer at the 2025 International Statistical Genetics Workshop"></p> </div><div class="right"> <p><strong>Masturina Binti Md Mansor</strong> (left) attended the 2025 International Statistical Genetics Workshop, supported by OBF Event Fellowships. <a href="https://www.open-bio.org/2025/04/30/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop/">Read about their experience here</a>.</p> </div><div style="clear:both"></div></div> <p>Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and <a href="https://forms.gle/D31zSs558aRwj2ig9">apply for the fellowship</a> before 1 August 2025.</strong></p>https://www.open-bio.org/events/bosc-2025/panel/Fri, 30 May 2025 16:50:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2025/panel/<h1 id="data-sustainability">Data Sustainability</h1> <p>In the rapidly evolving landscape of bioinformatics, research data is the bedrock of discovery, innovation, and progress. But how secure is this foundation for the future? This panel will examine the critical challenge of Data Sustainability: the proactive and principled approach to ensuring that valuable research data, along with the necessary infrastructure, funding, expertise, and governance, remains findable, accessible, interoperable, reusable (FAIR), and ethically managed throughout its entire life cycle and for future generations. It is about transforming data from a transient output into a durable asset that continues to yield scientific insights and maximize return on investment over decades.</p> <p>The imperative to responsibly manage and preserve our collective digital knowledge has never been more acute. Enabling data to be efficiently preserved, shared, and reused accelerates discovery, decreases redundancy, and safeguards the substantial investments made in research. In a challenging funding landscape where critical biomedical datasets can be at risk of being deprioritized, censored, or lost, the need to champion sustainable data practices is paramount. Lost or inaccessible data represents a setback to scientific advancement, leading to wasted resources and the costly repetition of already completed research and analyses.</p> <p>This panel will bring together a variety of perspectives to explore the challenges and possible solutions for achieving data sustainability. We will discuss practical strategies and address pressing questions on the topics of FAIR and CARE principles in action (and their limitations for sustainability), sustainable funding and infrastructure models, the role of open source and open science in long-term sustainability, data lifecycle management and stewardship, technical and scalability challenges, and ethical considerations.</p> <h1 id="panelists">Panelists</h1> <h3 id="tony-burdett">Tony Burdett</h3> <div class="splitbox"><div class="left"> <p>Tony Burdett is the Director of <a href="https://biofair.uk/">BioFAIR</a>, a UKRI-funded federated digital research infrastructure for UK life sciences. He has more than 20 years experience in life sciences and bioinformatics research infrastructure, and has been a long-standing advocate for FAIR data and the corresponding culture change that is needed to promote sustainable, open, data-driven research. His background is medical, biological and software engineering: he has a BSc in Biomedical Science and an MRes in Bioinformatics. Across his career, Tony has built up extensive experience of leading teams that run large scale, FAIR-enabling biological data management solutions, public repositories, and research infrastructure.</p> </div><div class="right"> <img src="https://www.open-bio.org/img/2025/2025-06-18_Tony-Burdett.jpg" alt ="Tony Burdett" style="width:90%"/> </div><div style="clear:both"></div></div> <h3 id="nicky-mulder">Nicky Mulder</h3> <div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/img/2025/2025-06-18_Nicky-Mulder.jpg" alt ="Nicky Mulder" style="width:90%"/> </div><div class="right"> <p>Nicola (Nicky) Mulder, PhD, is Professor and head of the Computational Biology (CBIO) division at the University of Cape Town, and Principal investigator of the Harnessing Data Science for Health in Africa eLwazi Open Data Science Platform. For 12 years, she led <a href="https://www.h3abionet.org/">H3ABioNet</a>, a Pan-African bioinformatics network for H3Africa, which built bioinformatics capacity on the continent. Her group provides bioinformatics services and develops new algorithms for the analysis of complex African genetic data. Prof. Mulder is actively involved in bioinformatics capacity development globally and sits on a number of international scientific advisory boards, including the board of directors of the International Society for Computational Biology (ISCB),</p> </div><div style="clear:both"></div></div> <h3 id="varsha-khodiyar">Varsha Khodiyar</h3> <p><div class="splitbox"><div class="left"> Dr. Varsha Khodiyar is a recognised leader in data curation and open science, with over 25 years shaping best practices in data sharing. Her contributions span from her early roles with the Human Gene Nomenclature Committee and the Gene Ontology project to leading initiatives as Data Curation Manager at Springer Nature, including the <a href="https://masterclasses.nature.com/online-course-in-managing-data/18365540">Nature Research Academies on data management</a>. She currently serves on the Scientific Advisory Committee of the <a href="https://globalbiodata.org/">Global Biodata Coalition (GBC)</a> and as Executive Advisor to <a href="https://fairsharing.org/">FAIRsharing.org</a>, providing governance to these important components of the international data repository infrastructure.</p> </div><div class="right"> <img src="https://www.open-bio.org/img/2025/2025-06-06_Varsha-Khodiyar.png" alt ="Varsha Khodiyar" style="width:90%"/> </div><div style="clear:both"></div></div> <h3 id="chris-mungall">Chris Mungall</h3> <div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/img/2025/2025-03-26-Chris-Mungall-2022-square.jpg" alt ="Chris Mungall" style="width:90%"/> </div><div class="right"> <p>Dr. Chris Mungall, a Senior Scientist at Berkeley Lab, has led the creation of key biological ontologies for the integration of resources covering gene function, anatomy, phenotypes and the environment, including the Gene Ontology, the Uberon anatomy ontology, the Cell Ontology (CL), and the Mondo disease ontology. His research centers around the capture, computational integration, and dissemination of biological research data, and the development of methods for using this data to elucidate biological mechanisms underpinning the health of humans and of the planet. For decades, he has been a strong advocate for open-source bioinformatics software, open standards, and open science.</p> </div><div style="clear:both"></div></div> <h3 id="scott-edmunds">Scott Edmunds</h3> <div class="splitbox"><div class="left"> <p>Dr Scott Edmunds is Editor in Chief of <a href="https://academic.oup.com/gigascience">GigaScience</a>, the Hong Kong based Open Science journal that publishes data and software papers (and which launched at ISMB in 2012). After PhD and postdoctoral research experience in Cancer Molecular Pathology, he has spent nearly 20 years working in open access publishing and open data. He has co-founded Citizen Science organisations Bauhinia Genome and CitizenScience.Asia, and is on the Board of Directors of the Dryad Digital Repository and Make Data Count. He has also taught data management and curation at Hong Kong University.</p> </div><div class="right"> <img src="https://www.open-bio.org/img/2025/2025-07-15_Scott-Edmunds.png" alt ="Scott Edmunds" style="width:90%"/> </div><div style="clear:both"></div></div> <h3 id="moderator-monica-munoz-torres">MODERATOR: Monica Munoz-Torres</h3> <div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/wp-content/uploads/2022/05/Monica_Munoz-Torres-2.jpeg" alt ="Monica Munoz-Torres" style="width:75%"/> </div><div class="right"> <p>Dr. Munoz-Torres is an Associate Professor at the University of Colorado Anschutz Medical Campus. She leads the Standards Team and is the Co-chair of the Steering Committee for the NIH-funded Bridge to Artificial Intelligence (Bridge2AI) Program. She is also Co-Lead of the Clinical &amp; Phenotypic Data Capture Work Stream of the Global Alliance for Genomics and Health (GA4GH). Dr. Munoz-Torres&rsquo;s expertise spans genomics, biocuration, knowledge representation, and data harmonization, as well as the development of software tools and standards to advance these fields.</p> </div><div style="clear:both"></div></div> https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/Tue, 27 May 2025 00:09:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/<div class="well"> <h2 id="bosc-2025-keynote-speakers"><a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/">BOSC 2025 keynote speakers</a></h2> <div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/img/2025/2025-03-26-Chris-Mungall-2022-square.jpg" alt ="Chris Mungall" style="width:60%"/> <p><a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes">KEYNOTE: Chris Mungall</a> <br /> Open Knowledge Bases in the Age of Generative AI</p> </div><div class="right"> <img src="https://www.open-bio.org/img/2025/2025-05-12-Christine-Orengo-square.png" alt ="Christine Orengo" style="width:60%"/> <p><a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes">KEYNOTE: Christine Orengo</a> <br /> Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED</p> </div><div style="clear:both"></div></div> </div> <div class="well"> <h2 id="panel-data-sustainability"><a href="https://www.open-bio.org/events/bosc-2025/panel/">Panel: Data Sustainability</a></h2> <img src="https://www.open-bio.org/img/2025/2025-07-16-panel-ribbon.png" alt ="Panelists" style="width:90%"/> </div> <h2 id="bosc-2025-schedule-at-a-glance">BOSC 2025 Schedule at a Glance</h2> <p>(Keep scrolling to see the full schedule of talks and posters!)</p> <div style="position: relative; padding-top: 90%;"> <iframe style="position: absolute; top: 0; left: -5; width:102%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vTzyut-NfEtyeZ6jVgRJbi1ug8uua_OH7eXmZLUXeM7pJBxoEcu0mCMo6DevvFeHTx1mMCN3Zc93xSn/pubhtml?gid=0&amp;single=true&amp;widget=true&amp;headers=false" allowfullscreen="allowfullscreen" frameborder="0"></iframe> </div> <h2 id="schedule-of-talks">Schedule of Talks</h2> <div style="position: relative; padding-top: 90%;"> <iframe style="position: absolute; top: 0; left: -20; width:120%; height:100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vTzyut-NfEtyeZ6jVgRJbi1ug8uua_OH7eXmZLUXeM7pJBxoEcu0mCMo6DevvFeHTx1mMCN3Zc93xSn/pubhtml?gid=1729310258&amp;single=true&amp;widget=true&amp;headers=false" allowfullscreen="allowfullscreen" frameborder="0"></iframe> </div> <h2 id="schedule-of-posters">Schedule of Posters</h2> <p>Please see the <a href="https://www.iscb.org/ismbeccb2025/programme-agenda/posters">ISMB/ECCB poster page</a> for more information, including poster abstracts. BOSC posters will be up for both days of BOSC. Each presenter is assigned to present their poster during Session A or B on Monday, July 21, or Tuesday, July 22, respectively.</p> <p>⏺ <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2025/posters.php?track=BOSC&amp;session=A#search">Session A: July 21 at 10:00-11:20 and 16:00-16:40</a> <br /> ⏺ <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2025/posters.php?track=BOSC&amp;session=B#search">Session B: July 22 at 10:00-11:20 and 16:00-16:40</a> <br /> ⏺ <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2025/posters.php?track=BOSC&amp;session=E#search">Virtual posters</a></p> <div style="position: relative; padding-top: 90%;"> <iframe style="position: absolute; top: 0; left: -20; width:122%; height:100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vTzyut-NfEtyeZ6jVgRJbi1ug8uua_OH7eXmZLUXeM7pJBxoEcu0mCMo6DevvFeHTx1mMCN3Zc93xSn/pubhtml?gid=1094351563&single=true&amp;widget=true&amp;headers=false" allowfullscreen="allowfullscreen" frameborder="0"></iframe> </div>https://www.open-bio.org/2025/04/30/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop/Wed, 30 Apr 2025 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/04/30/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop/<p>Thanks to the Event Fellowship from Open Bioinformatics Foundation (OBF), I was privileged to attend the <a href="https://www.colorado.edu/ibg/workshop-2025">2025 International Statistical Genetics Workshop (ISG)</a>. ISG is an intensive, week-long workshop held annually in Boulder, Colorado that provides hands-on training in the principles and application of over a dozen open-access bioinformatics tools for analysis of genomic data. This workshop has been running since 1987 and boasts a faculty of world-renowned experts in statistical genetics from around the globe. The curriculum switches annually between family-based and population-based genetic studies. The focus this year was on the theory, performance, and interpretation of genome-wide association studies (GWAS) and their downstream analyses.</p> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-01.jpg" alt="Images of the workshop welcome sign and the room in which the workshop took place"> <em>The workshop was a combination of lectures and collaborative hands-on practicals</em></p> <p>The schedule was intensive and jam-packed with learning. Each day we gathered from 8am-5pm for a combination of lectures and hands-on practicals. We covered various aspects of genome-wide association studies, from the theory and principles behind the analyses, to the logistics of running them, to how to perform downstream analyses to investigate biological mechanisms. We learned how to perform analyses on multiple platforms including the terminal, RStudio, and Jupyter. On Monday we learned about classic and modern statistical approaches for genetic modeling; population genetics; how to generate, QC, and impute data using <a href="https://www.cog-genomics.org/plink/2.0/">plink</a>; and how to perform principal components analysis using plink and <a href="https://yanglab.westlake.edu.cn/software/gcta/#Overview">GCTA</a>. Topics on Tuesday included how to access different data, including recruiting participants for your own studies and accessing biobanks; theory and performance of GWAS association tests using <a href="https://github.com/weizhouUMICH/SAIGE">SAIGE</a>; meta-analysis of multiple GWAS using <a href="https://github.com/statgen/METAL">METAL</a>; and calculation of polygenic risk scores using <a href="https://github.com/zhilizheng/SBayesRC">SBayesR</a>. Wednesday was a relatively light day, with a only a few sessions which were focused on calculating SNP heritability and genetic correlations with <a href="https://github.com/bulik/ldsc">LD score regression</a>. We also had a poster session on Wednesday, during which I presented my work on using the open-access tool <a href="https://github.com/getian107/PRScsx">PRS-CSx</a> for improving polygenic risk score prediction for severe mental illness in diverse populations.</p> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-02.jpg" alt="Images of myself and others at the poster session"> <em>The tabletop poster session - I presented a poster on using the open-source algorithm PRS-CSx</em></p> <p>On Thursday we continued with post-GWAS analyses, including additional SNP heritability calculations with <a href="https://yanglab.westlake.edu.cn/software/gcta/#GREML">GREML</a>; pathway analysis with <a href="https://cncr.nl/research/magma/">MAGMA</a>; eQTL analysis with <a href="https://www.sanger.ac.uk/tool/peer/">PEER</a> and <a href="https://github.com/andreyshabalin/MatrixEQTL">MatrixEQTL</a>; and fine mapping and colocalization with <a href="https://github.com/stephenslab/susieR">SUSIE</a> and <a href="https://github.com/chr1swallace/coloc/">coloc</a>. Finally, on Friday we went through statistical power and how to calculate it with R and online tools; identifying causal and confounding factors with Mendelian Randomization in R; and performing rare variant analyses using <a href="https://github.com/hail-is/hail">Hail</a>.</p> <p>A huge benefit of this workshop, besides the technical skills it imparted, was the ability to network with such an experienced and diverse group of people in an intimate setting. We had direct face time with world leaders in the statistical genetics field, who headed off any intimidation we might have felt by reminding us in the very first lecture that we were all colleagues and insisting that we call them by their first names. In addition to being extremely knowledgeable, they were friendly, warm, and happy to answer one-on-one questions and give advice. Meeting and working with the other attendees - many of whom were from across the country or the world - was also fantastic, and was an opportunity I would have never had otherwise. I was even able to meet some of my own collaborators from the PsycheMERGE consortium, who I had only previously met over Zoom, in person for the first time!</p> <p>When the workshop wasn’t in session, I visited as many places in Boulder as I could. The hotel was located steps from the historic Pearl Street Mall which is home to tons of restaurants and shops. My favorite visits were to the Piece, Love &amp; Chocolate shop for some rich sipping chocolate; BarTaco for some scrumptious tacos, Gemini for some refined and delicious tapas; and The Attic for arcade games and satisfying American food. My favorite eatery was Rosetta Hall, an upscale food hall steps from the hotel with diverse, beautiful culinary options and live music. I also had a delightful visit to the Boulder Bookstore, which had 20,000 square feet of space and three floors containing over 100,000 books of every genre imaginable.</p> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-03.jpg" alt="Images of cusisine from Rosetta Hall"> <em>Enjoying some delicious cuisine at Rosetta Hall</em></p> <p>Perhaps the best part of Boulder was its natural beauty. The hotel was located near the Boulder foothills which contain the famed Flatirons formation. This view was a stunning backdrop that we were able to enjoy during lunch, networking sessions, and on a group hike on Wednesday.</p> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-04.jpg" alt="Images of the view of the Flatirons from the hotel and the Open Space park"> <em>The workshop was a short walk away from the stunning Flatirons and the Open Space park</em></p> <p>I also found some time to take an Uber up into the mountains to visit the incredible Lost Gulch Overlook, which boasts views of the forest and snow-capped peaks of the Continental Divide. The combination of the stunning view, the peaceful silence, and the crisp, cold air was otherworldly.</p> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-05.jpg" alt="Images of the view from the Lost Gulch Overlook"> <em>Breaktaking views from the Lost Gulch Overlook</em></p> <p>The week was over before I knew it. I left with new connections, the knowledge and confidence to conduct my own GWAS analyses, and the ability to pass on my knowledge to my colleagues. The best part: all of the materials, including the code, from recent ISG workshops are freely available online on <a href="https://www.colorado.edu/ibg/workshop">ISG’s website</a>! Additionally, the workshop will be virtual next year to help accommodate a wider range of attendees. I highly encourage you to go!</p> <p><img src="https://www.open-bio.org/img/2025/2025-04-30-Kyra-Feuer-06.jpg" alt="Image of all of the ISG 2025 attendees"> <em>All of the ISG 2025 attendees</em></p> <p>THANK YOU OBF!!!</p>https://www.open-bio.org/posts/2025-04-02-archiving-obf-posts/Wed, 02 Apr 2025 14:49:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/posts/2025-04-02-archiving-obf-posts/<p>The websites and blog posts of the OBF go back a long way, with the first posts having been published all the way back in June 2001. Keeping them accessible and findable under stable links is not an easy feat, especially given that since 2001 we&rsquo;ve changed the way we create and serve those pages more than once, <a href="https://www.open-bio.org/posts/2025-03-04-new-website/">most recently in March of this year</a>. And while we have successfully managed to do so, we thought it would be nice to have some backup plans in place.</p> <p>Which is why this blog is now also archived for the long-term with the help of <a href="https://rogue-scholar.org/"><em>Rogue Scholar</em></a>, to ensure that our blog posts remain part of the extended scholarly record. <em>Rogue Scholar</em> makes use of open technologies to both archive the full-text of our blog posts itself, but also makes sure that they are archived in <a href="https://web.archive.org/">The Wayback Machine</a> of the Internet Archive semiannually.</p> <p>To ensure the long-term findability, <em>Rogue Scholar</em>&rsquo;s archive contains rich metadata and also assigns a DOI for each blog post enlisted. Thanks to this, blog posts don&rsquo;t only have a stable identifier that can perpetually link to the correct places, this also means that our blog posts will have a stable and <strong>citable identifier</strong>, which allows them to become objects that are more easily citable within the scientific record.</p> <p>In the future, we plan to expose those DOIs more easily through our blog itself, but <a href="https://rogue-scholar.org/communities/obf/records?q=&amp;l=list&amp;p=1&amp;s=10&amp;sort=newest">already now you can find all of our posts listed on Rogue Scholar</a>.</p>https://www.open-bio.org/posts/financial-support-BOSC2025/Sun, 30 Mar 2025 02:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/posts/financial-support-BOSC2025/<p>We recognize that the high price of travel and registration can make it hard for some people to attend BOSC/ISMB. Below are some ways to apply for financial assistance to present your work at BOSC 2025.</p> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/2025-03-11-Ruth-Nanjala-OBF-travel-awardee.png" alt="OBF Event awardee Ruth Nanjala and her poster at ICHG 2023"></p> </div><div class="right"> <h2 id="obf-event-fellowships">OBF Event Fellowships</h2> <p>The Open Bioinformatics Foundation (OBF)&rsquo;s <a href="https://www.open-bio.org/event-awards/">Event Fellowships</a> are aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities.</p> <p>Awards are made three times a year; the next <strong>deadline is April 1, 2025</strong> (note that this is earlier than the ISMB/ECCB submission deadline of April 17).</p> <p><strong><a href="https://www.open-bio.org/2025/03/02/event-fellowship-2025-1/">More info about applying for an OBF Event Fellowship</a></strong></p> <p><em>Left: <a href="https://www.open-bio.org/2023/03/21/ruth-nanjala-experience-at-the-ichg-2023-conference/">Awardee Ruth Nanjala and her poster at ICHG 2023</a></em></p> </div><div style="clear:both"></div></div> <h2 id="bosc-registration-fee-waiver">BOSC registration fee waiver</h2> <div class="splitbox"><div class="left"> <p>Authors who <a href="https://www.open-bio.org/events/bosc-2025/submit/">submit their work to BOSC</a> can request ISMB registration fee support on the abstract submission form (these requests are not seen by reviewers). This initiative is funded by <a href="https://www.open-bio.org/events/sponsors/">sponsorships</a>.</p> <p>Only presenting authors whose abstracts are accepted for talk or poster presentation are eligible for this fee waiver, and depending on the number of applicants, not all requests will be granted.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/img/2025/2025-03-11-Beatrice-Mihalache-with-BOSC-poster.jpg" alt="Beatrice Mihalache presenting a poster at BOSC 2024"></p> </div><div style="clear:both"></div></div> <p>Requests from early-career applicants and people from underrepresented geographical areas will be given priority. Applicants will be notified about whether their fee waiver request was granted around the same time that abstract acceptance notifications go out (May 14).</p> <br/> <div class="splitbox"><div class="left"> <h2 id="iscb-conference-fellowships">ISCB Conference Fellowships</h2> <p>The ISCB (the organization that runs the ISMB conference) offers a limited number of <a href="https://www.iscb.org/ismbeccb2025/general-info/conference-fellowships">conference fellowships</a> for students and postdocs to present their work at ISMB.</p> <p>Rules for the ISCB conference fellowships (these are not BOSC-specific):</p> </div><div class="right"> <br/> <p><img src="https://www.open-bio.org/img/2025/2025-03-11-Iscb_logo.png" alt="ISCB logo"></p> </div><div style="clear:both"></div></div> <ul> <li>Eligibility is limited to students or postdocs, plus early career researchers from Low through Upper-Middle Economic countries. Postdocs and employees of any US federal agency are not eligible.</li> <li>Only open to those who have a <strong>Proceeding, Talk, or Poster (not late poster) accepted for presentation at ISMB/ECCB</strong>.</li> <li>The applicant must be the presenting author of the work.</li> <li>Applicant must be a current ISCB member</li> <li>Applicant must be able to pay all expenses of attending the conference up front, including conference registration fee, travel, accommodations, and meals.</li> <li><strong>The application will be sent automatically to eligible people on May 14</strong> (the day after talk/poster acceptances go out).</li> <li>The number of awards is limited; not all eligible applicants will receive awards.</li> </ul> <h2 id="apply-to-be-event-staff-at-ismbeccb">Apply to be Event Staff at ISMB/ECCB</h2> <p><img src="https://www.open-bio.org/img/2025/banner.ConferenceBanner.ISMBECCB.2025.png" alt="ISCB logo"></p> <p>You can <a href="https://www.iscb.org/ismbeccb2025/general-info/apply-to-be-event-staff">apply to work at ISMB/ECCB 2025 for approximately 20-24 hours</a> in exchange for free registration and time-based pay. (When you&rsquo;re not working, you can attend talks.) The <strong>application deadline is May 9, 2025</strong>. Note that Event Staff have to already be ISCB members.</p>https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/Wed, 26 Mar 2025 04:29:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/<img src="https://www.open-bio.org/img/2025/2025-03-26-Chris-Mungall-2022-square.jpg" alt ="Chris Mungall" style="width:50%"/> <h3 id="chris-mungall-lawrence-berkeley-national-laboratory">Chris Mungall (Lawrence Berkeley National Laboratory)</h3> <h4 id="open-knowledge-bases-in-the-age-of-generative-ai"><em>Open Knowledge Bases in the Age of Generative AI</em></h4> <h4 id="keynote-talk-for-joint-boscbokr-session">(Keynote talk for <a href="https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/">joint BOSC/BOKR session</a>)</h4> <h4 id="talk-video"><a href="https://www.google.com/url?q=https://www.youtube.com/watch?v%3DLz7I2nB4Q5k&amp;sa=D&amp;source=editors&amp;ust=1760741772335658&amp;usg=AOvVaw2c9PAHMKhy_6LSqyRljd__">Talk video</a></h4> <p>ABSTRACT: The scientific and clinical community relies on the active development of a wide range of interlinked knowledge bases in order to plan experiments, interpret omics data, and to help with the diagnosis and treatment of disease. These knowledge bases make use of expert curation and the use of community ontologies in order to provide accurate and structured information that can be used algorithmically. The advent of generative AI and agentic methods presents fantastic opportunities for accelerating curation, increasing the breadth and depth of coverage. Open knowledge bases also present opportunities to generative AI, in the form of a trusted backbone of knowledge that can mitigate the hallucinations that plague large language models. However, the pace of development of AI, combined with misunderstandings about both strengths and weaknesses, poses significant dangers. In this talk, I will present our recent work on the use of agentic AI to assist with manual knowledge base tasks, particularly those involving complex ontology development and maintenance tasks. I will present a realistic picture of challenges we face, but also strategies to mitigate them, and a path towards a future where agents, curators, and others can work together to leverage and integrate open source tools and data along with the combined knowledge of the scientific community.</p> <br/> <p><i><strong>Dr. Chris Mungall</strong> is a Senior Scientist at Berkeley Lab, where he heads the <a href="https://biosciences.lbl.gov/egsb/biosystems-data-science/">Biosystems Data Science department</a> in the Environmental Genomics and Systems Biology Division. Chris’s research interests center around the capture, computational integration, and dissemination of biological research data, and the development of methods for using this data to elucidate biological mechanisms underpinning the health of humans and of the planet. He and his team have led the creation of key biological ontologies for the integration of resources covering gene function, anatomy, phenotypes and the environment, including the the Uberon anatomy ontology, the Cell Ontology (CL), and the Mondo disease ontology. He is also one of the cofounders of the <a href="https://obofoundry.org/">OBO Foundry</a>. For decades, he has been a strong advocate for open-source bioinformatics software, open standards, and open science.</p> <p>Chris, who has a PhD in bioinformatics from the University of Edinburgh, is a PI on the <a href="http://geneontology.org/">Gene Ontology</a> (GO), the <a href="https://monarchinitiative.org/">Monarch Initiative</a>, the <a href="https://www.alliancegenome.org/">Alliance of Genome Resources</a>, <a href="https://biosciences.lbl.gov/2020/10/08/phenomics-first-project-receives-10m-to-unite-genetic-disease-data/">Phenomics First</a>, and the <a href="https://ncats.nih.gov/translator">NCATS Biomedical Data Translator</a>, as well as metadata lead for the <a href="https://microbiomedata.org/">National Microbiome Data Collaborative</a> (NMDC). In 2017, Chris was the first person to be awarded the <a href="https://www.biocuration.org/2017-biocuration-awards/">Exceptional Contributions to Biocuration Award</a> by the International Society for Biocuration. In 2020, he received a Berkeley Lab Early Scientific Career Director’s Award.</i></p> <br/> <img src="https://www.open-bio.org/img/2025/2025-05-12-Christine-Orengo-square.png" alt ="Christine Orengo" style="width:50%"/> <h3 id="christine-orengo-university-college-london">Christine Orengo (University College London)</h3> <h4 id="working-together-to-develop-promote-and-protect-our-data-resources-lessons-learnt-developing-cath-and-ted"><em>Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED</em></h4> <h4 id="talk-video-1"><a href="https://www.google.com/url?q=https://www.youtube.com/watch?v%3DmHxr4oUCsNQ&amp;sa=D&amp;source=editors&amp;ust=1760741772319332&amp;usg=AOvVaw0RgpvcUJoizEGILRiCq8CW">Talk video</a></h4> <p>ABSTRACT: The CATH protein domain structure classification was the vision of the pioneering computational scientist Janet Thornton. Algorithms developed by Orengo and Taylor in the lab of Willie Taylor enabled the analyses that laid the foundations for CATH. Since then, the Orengo team have taken CATH forward in many ways. Working closely with the protein sequence, structural and evolutionary biology communities provided the focus and feedback to shape the resource. Maintaining the value and integrity of CATH has necessitated continuously embracing new types of data as it became relevant and developing the appropriate tools for this. For example, CATH was recently expanded &gt;400-fold with predicted structures from AlphaFold Database (AFDB) using novel AI-based tools. CATH is also a partner resource in InterPro and was used by the Structural Genomics Consortia in the US for more than 15 years to probe novel fold and function space. All CATH data and tools are publicly available. The talk will present landmark developments and describe how the resource has benefitted from extensive collaborations with the wider community to handle the data expansions and to provide accurate data needed by the community. It will also draw on CATH experience to reflect on strategies for supporting open data and open source. <br/></p> <p><i><strong>Dr. Christine Orengo</strong> is a Professor of Bioinformatics at University College London (UCL). Her research focuses on the development of algorithms to capture relationships between protein structures, sequences and functions. She has built one of the most comprehensive protein classifications, <a href="https://www.cathdb.info/">CATH</a>. CATH structural and functional data for hundreds of millions of proteins has enabled studies that revealed essential universal proteins and their biological roles, and extended characterisation of biological systems implicated in disease e.g. in cell division, cancer and aging. <a href="https://data.niaid.nih.gov/resources?id=zenodo_10788941">The Encyclopedia of Domains (TED)</a> is a joint effort by CATH (Orengo group) and the Jones group at University College London to identify and classify protein domains in AlphaFold2 models from AlphaFold Database version 4, covering over 188 million unique sequences and 365 million domain assignments.</p> <p>Dr. Orengo received her PhD from University College London. She is currently a Vice President of the International Society of Computational Biology (ISCB) and was previously the ISCB&rsquo;s first female President. She is a Fellow of the Royal Society (FRS), an Elected Member of EMBO since 2014, and a Fellow of ISCB since 2016. Dr. Orengo is a strong supporter of FAIR and open data and data sharing practices.</i></p> <br/> <div class="well"> <h3 id="bosc-keynote-speaker-selection-process">BOSC keynote speaker selection process</h3> <p>BOSC usually includes two or three keynote talks given by prominent individuals or emerging leaders who are accomplished in areas relevant to the bioinformatics open source community and who represent a range of backgrounds and ideas. Please see our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker rubric</a> for more information about our keynote speaker selection process and criteria.</p> </div>https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/Mon, 17 Mar 2025 00:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/<p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/BOSC2023-crowded-room-Bastian-1-1.png" alt="Crowded room in the joint BOSC/Bio-Ontologies session in 2023"></p> <p>We are pleased to announce that <a href="https://www.open-bio.org/events/bosc/">BOSC</a> and the newly-renamed <a href="https://www.bio-ontologies.org.uk/2025-meeting">Bio-Ontologies and Knowledge Representation (BOKR)</a> will join forces for a day at ISMB/ECCB 2025! The joint session will include talks chosen from abstracts submitted to BOSC or BOKR, plus a keynote speaker who is well known in both the ontology and open science communities (stay tuned for an announcement soon!).</p> <div class="splitbox"><div class="left"> <p>BOSC and BOKR are two of the longest-running COSIs (Communities of Special Interest) at ISMB: <a href="https://www.open-bio.org/events/bosc/about/">BOSC started in 2000</a> and BOKR (then called Bio-Ontologies) in 1998. BOKR focuses on the FAIR development and application of ontologies and other Linked Open Data resources and the organization, presentation and dissemination of knowledge in biomedicine and the life sciences. BOSC covers the full spectrum of open source, open science, open data and open standards in the life sciences.</p> <p><em>(Right: Melissa Haendel was the keynote speaker at the BOSC/Bio-Ontologies joint session in 2022.)</em></p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/07/Melissa-at-podium.jpeg" alt="Previous joint keynote speaker Melissa Haendel at BOSC/Bio-Ontologies joint session in 2022"></p> </div><div style="clear:both"></div></div> <p>You can <a href="https://www.open-bio.org/events/bosc-2025/submit">submit relevant abstracts</a> to either BOSC or BOKR (please do not double-submit the same abstract). The Program Chairs of both COSIs will consider appropriate abstracts for the joint session.</p> <p>BOSC 2025 will take place July 21-22, and BOKR will be July 22-23. The joint session will be part or all of the day on July 22.</p>https://www.open-bio.org/2025/02/26/ISMB-CollaborationFest-2025/Fri, 07 Mar 2025 01:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/02/26/ISMB-CollaborationFest-2025/<p><a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest 2025</a> will be a two-day collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. Bring your own project ideas or come ready to collaborate with others on their projects!</p> <p><a href="https://www.open-bio.org/events/bosc/collaborationfest/"><img src="https://www.open-bio.org/wp-content/uploads/2025/01/CoFest-gallery.png" alt="CoFest gallery"></a></p> <p>BOSC has held CollaborationFests (aka CoFests) every year before or after ISMB since 2010. This year, we decided to hold the CollaborationFest as part of ISMB/ECCB and open it to all registered ISMB/ECCB participants. It will take place during the last two days of ISMB/ECCB.</p> <p><a href="https://www.open-bio.org/events/bosc/collaborationfest/">ISMB CollaborationFest 2025</a> is co-organized by volunteers from four COSIs:</p> <ul> <li>Bioinformatics Open Source Conference (BOSC)</li> <li>Bio-Ontologies and Knowledge Representation (BOKR)</li> <li>Function COSI</li> <li>3DSig</li> </ul> <p>Due to space constraints, participation in CollaborationFest is limited. To indicate your interest in participating, <strong><a href="https://www.iscb.org/ismbeccb2025/register">register for ISMB/ECCB 2025</a> by June 20 and sign up for CollaborationFest as an “add-on”</strong> during the registration process. We will contact you by June 23 to request a few pieces of information to help us organize the event. Last-minute walk-ins may be possible for ISMB participants if we are not at capacity.</p> <p>A limited number of ISMB registration waivers will be available for trainees (students and postdocs) who would like to participate in the CollaborationFest and are willing to work as volunteers during the first two days of ISMB. <a href="https://www.iscb.org/ismbeccb2025/general-info/apply-to-be-event-staff">More info here about applying to volunteer at ISMB</a>.</p> <p>Limited remote participation in CollaborationFest will be possible, but the amount of interaction that is possible will be highly dependent on the people and projects active on the day. We expect to have a video feed from the room available; joining will require you to have <a href="https://www.iscb.org/ismbeccb2025/register">registered as a (virtual or in-person) ISMB/ECCB attendee</a>.</p>https://www.open-bio.org/posts/2025-03-04-new-website/Tue, 04 Mar 2025 18:23:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/posts/2025-03-04-new-website/<p><img src="https://www.open-bio.org/img/2025-03-04-hugo.svg" alt="the hugo logo"></p> <p>Over the past few weeks, we have been working behind the scenes to migrate our website, resulting in the page that you currently have in front of you! Our pages are now generated by the <a href="https://gohugo.io/"><em>Go</em>-based, open source static site generator <em>Hugo</em></a>, and are stored on <a href="https://github.com/OBF/OBF.github.io">GitHub</a>. All old URLs should continue working as before, but <strong>if you run into any missing pages or other issues, please let us know by <a href="https://github.com/OBF/OBF.github.io/issues/new">submitting an issue</a> or contacting us via the channels linked in the page footer</strong>.</p> <p>Until recently, the OBF websites and blog ran on <em>Wordpress</em>, the most common, PHP-based Content Management System, which overall has served us well over the years (and which itself was a migration from the previous <em>MediaWiki</em>-based setup). Beyond the <a href="https://www.theverge.com/2024/9/27/24256361/wordpress-wp-engine-drama-explained-matt-mullenweg">recent governance issues with Wordpress</a>, we also decided to move towards a static site system due to being easier to maintain in the long-term.</p> <p>Keeping up with the security patches for WP itself, the plugins we used and keeping it compatible with our custom theme required a lot of effort. As a small, all-volunteer-run organisation, we decided that it&rsquo;s both a better use of our time and more sustainable in the long-term to use a simpler static site generator. Ultimately, the output of the static site generator is just a collection of HTML files that can easily be moved between hosts and are mostly self-contained.</p> <p>For our use-case, <em>Hugo</em> and its ecosystem have the benefit that <a href="https://github.com/ashishb/wp2hugo"><em>wp2hugo</em></a> provides an easy way to migrate an existing blog from Wordpress to Hugo! Using an <em>XML dump</em> that Wordpress can generate, Hugo can create all the markdown files and even get the necessary static files like images in the right place. If you&rsquo;re considering moving away from Wordpress, this might be worthwhile alternative to look at!</p>https://www.open-bio.org/2025/03/02/event-fellowship-2025-1/Mon, 03 Mar 2025 21:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/03/02/event-fellowship-2025-1/<p>The call for applications for <strong>round 1</strong> of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> for 2025 is now open. <strong>The deadline for this round is 1 April 2025.</strong> You can submit your application through <a href="https://forms.gle/D31zSs558aRwj2ig9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">make a copy of this template</a>.</p> <p>The Open Bioinformatics Foundation (OBF)&rsquo;s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is April 1, 2025. (For those who want to apply for BOSC, note that this is earlier than the BOSC/ISMB submission deadline of April 17.)</p> <p>We invite applications from candidates seeking financial support to attend relevant scientific events between May 2025 to April 2026. <em><strong>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</strong></em>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <h3 id="overview-of-the-third-2024-round-of-the-obf-event-fellowship">Overview of the third 2024 round of the OBF Event Fellowship</h3> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In the third round of 2024 (December 2024), we received numerous applications, and four applicants were selected for funding to support their participation in various events. <strong>Congratulations to the following recipients</strong>:</p> <ol> <li>Jacqueline Wahura: the Royal Entomological Society Conference 2024.</li> <li>Kyra Feuer: 2025 International Statistical Genetics Workshop.</li> <li>Zoé Pochon: ISBA11 (International Symposium on Biomolecular Archaeology) and SPAAM7 (Standards, Precautions, and Advances in Ancient Metagenomics) in Turin, Italy</li> </ol> <p>We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:</p> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic6.1.jpg" alt="OBF Event awardee Masturina Binti Md Mansor at their APBJC2024 poster"></p> </div><div class="right"> <p><strong>Masturina Binti Md Mansor</strong> (left) attended the 1st Asia &amp; Pacific Bioinformatics Joint Congress 2024, supported by OBF Event Fellowships. <a href="https://www.open-bio.org/2024/11/19/masturina-experience-at-apbjc2024/">Read about their experience here</a>.</p> <p><strong>Erin Krichilsky</strong> received the award to attend the 27th International Congress of Entomology (ICE2024 Kyoto) and shared <a href="https://www.open-bio.org/2024/11/21/erin-rin-krichilsky/"><strong>their story here</strong></a>.</p> <p><strong>Jacqueline Wahura</strong> attended the Royal Entomological Society Conference 2024, virtually. They reported <a href="https://www.open-bio.org/2025/01/07/jacqueline-wahura-ento24-experience/"><strong>their experience here</strong></a>.</p> </div><div style="clear:both"></div></div> <p>Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and <a href="https://forms.gle/D31zSs558aRwj2ig9">apply for the fellowship</a> before 1 April 2025.</strong></p>https://www.open-bio.org/events/bosc-2026/collaborationfest/Sun, 16 Feb 2025 09:35:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2026/collaborationfest/<div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/img/2025/bosc2025-img/CoFest%20-%203%20people%20working%20at%20table.jpeg" alt="Participants at CoFest 2025"></p> </div><div class="right"> <p>CollaborationFest 2026 will be a collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you. Bring your own project ideas or come ready to collaborate with others on their projects!</p> <p>BOSC has organized CollaborationFests (aka CoFests) every year before or after ISMB since 2010. The 2026 CoFest will start the day after ISMB 2026, in a nearby location in Washington, DC.</p> </div><div style="clear:both"></div></div> <h3 id="dates-and-location">Dates and Location</h3> <p>Friday July 17 to Saturday July 18 (right after ISMB 2026), 9:00am - 5:00pm both days.</p> <p>The location is in central Washington DC. The address will be shared with those who register.</p> <div class="splitbox"><div class="left"> <h3 id="how-to-sign-up">How to sign up</h3> <p>Due to space constraints, participation in CollaborationFest is limited. Participation is free, but registration is mandatory. A registration link will be available shortly.</p> <p>We encourage you to register for ISMB, but the CoFest itself is free. Three easy steps to sign up:</p> <ul> <li>add yourself to this <a href="https://docs.google.com/spreadsheets/d/1HvB9nHCBiCrSLWR9BNG5ypMecEbn7MOOnWIZxagQwRo/edit?usp=sharing">spreadsheet</a> to help us gauge interest, coordinate topic groups and logistics</li> <li>add your project ideas to this <a href="https://docs.google.com/document/d/1x7h4Tx3Y8IrcDSkSs_LylVFzQhjNKmQpwAbizQnyxYQ/edit?tab=t.0">document</a> if you have something in mind</li> <li>join the #cofest2026 channel in the <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-3va3bz5qa-hR9nKXHXO9GmrkddIpJXcQ">OBF Slack</a>!</li> </ul> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/CoFest2023-lunch-1-736x1024.png" alt="Lunch at CoFest 2023"></p> </div><div style="clear:both"></div></div> <h3 id="cost">Cost</h3> <p>CoFest is free to attend, but no food or drinks will be provided.</p> <h3 id="collaborationfest-news-and-activities">CollaborationFest News and Activities</h3> <p>As we get closer to BOSC 2026 and the CollaborationFest, we will add relevant news and activities here. Note that some of these activities are on dynamically updated Github pages, and will only be fully ready &ldquo;the day of&rdquo;, or shortly before.</p> <h3 id="sponsors">Sponsors</h3> <p>Thanks to Computercraft for generously providing the space for this event; we appreciate their support in making it possible.</p> <h3 id="code-of-conduct">Code of Conduct</h3> <p>As an OBF-organized event, CollaborationFest 2026 is covered by the <a href="https://github.com/OBF/obf-docs/blob/master/code-of-conduct/CODE_OF_CONDUCT.md">OBF Code of Conduct</a>.</p>https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/Sun, 16 Feb 2025 09:35:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/<p>ISMB CollaborationFest 2025 will be a collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you. Bring your own project ideas or come ready to collaborate with others on their projects!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/cofest2024-1.jpeg" alt="Participants at CoFest 2024"></p> <p>BOSC has organized CollaborationFests (aka CoFests) every year before or after ISMB since 2010 (see, for example, <a href="https://open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/">the 2024 CoFest page</a>.). This year, we are excited to hold <strong>CollaborationFest as part of ISMB/ECCB, opening it to all registered ISMB/ECCB participants</strong>. The organizers are affiliated with four different COSIs: BOSC, Bio-Ontologies and Knowledge Representation (BOKR), Function COSI, and 3DSIG.</p> <h3 id="dates">Dates</h3> <p>Wednesday July 23 to Thursday July 24 (the last two days of ISMB/ECCB 2025).</p> <h3 id="how-to-sign-up">How to sign up</h3> <div class="splitbox"><div class="left"> <p>Due to space constraints, participation in CollaborationFest is limited. To indicate your interest, <a href="https://www.iscb.org/ismbeccb2025/register">register for ISMB/ECCB 2025</a> by June 20 and <strong>sign up for CollaborationFest as an “add-on” during the registration proces</strong>s. We will contact you by June 23 to gather additional information to help organize the event. Last-minute walk-ins may be possible if space allows.</p> <p>Limited remote participation will be possible, but engagement opportunities will depend on the people and projects active on the day. A video feed from the room will be available, but joining will require you to be a registered (virtual or in-person) ISMB/ECCB participant.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/CoFest2023-lunch-1-736x1024.png" alt="Lunch at CoFest 2023"></p> </div><div style="clear:both"></div></div> <h3 id="collaborationfest-news-and-activities">CollaborationFest News and Activities</h3> <p>As we get closer to ISMB/ECCB 2025 and the CollaborationFest, we will add relevant news and activities here. Note that some of these activities are on dynamically updated Github pages, and will only be fully ready &ldquo;the day of&rdquo;, or shortly before.</p> <h4 id="1-genomic-safe-harbor-sites-in-zebrafish">1. Genomic Safe Harbor Sites in Zebrafish</h4> <p>This challenge invites participants to identify potential genomic safe harbor (GSH) sites in the zebrafish genome using an integrative omics approach.</p> <p><a href="https://github.com/parnaljoshi/gsh-zebrafish-hackathon">https://github.com/parnaljoshi/gsh-zebrafish-hackathon</a></p> <h4 id="2-how-much-funding-per-protein">2. How much funding per protein?</h4> <p>Quantifying the financial investment in specific areas of biomedical research is challenging. While NIH funding is extensive, directly attributing grant dollars to individual proteins studied is non-trivial. Approximating the dollar amount of funding allocated to the proteins help us to:</p> <ul> <li>Assess funding distribution across different biological targets.</li> <li>Identify potentially under-funded or over-concentrated areas of protein research.</li> <li>Track the financial trajectory of research on specific proteins over time.</li> <li>Provide researchers and funding agencies with data about financial resource allocation at the protein level.</li> </ul> <p><a href="https://github.com/anphan0828/funding-per-protein-hackathon">https://github.com/anphan0828/funding-per-protein-hackathon</a></p> <h4 id="3-enhancing-protein-knowledge-curation-using-gene-ontology-annotations-and-large-language-models-for-community-literature-submissions">3. Enhancing Protein Knowledge Curation using Gene Ontology Annotations and Large Language Models for Community Literature Submissions</h4> <p>Data-driven biomedical discovery depends on effective data curation - a time-consuming process that involves identifying relevant literature, extracting experimental knowledge, and validating information into structured formats suitable for databases like UniProt.</p> <p>The emergence of generative AI and large language models (LLMs) presents new opportunities to assist human-driven data curation workflows. These technologies can support curators in searching ontologies and extracting knowledge from scientific literature, potentially streamlining the entire curation process.</p> <p><strong>Objective</strong></p> <p>Learn how to manually assign Gene Ontology terms or develop innovative approaches using LLM tools to enhance the curation workflow, enabling efficient and accurate extraction of experimental data from scientific literature.</p> <p><a href="https://github.com/anphan0828/ISMB_CollaborationFest_EBI">https://github.com/anphan0828/ISMB_CollaborationFest_EBI</a></p> <h4 id="4--biopython-gpu-accelerate-biopython-msa-gpu-protein-aligner">4. BioPython-GPU: Accelerate BioPython MSA-GPU Protein Aligner</h4> <p>Integrate drop in GPU-accelerated MMseq2 into biopython for acceleration.</p> <p><a href="https://github.com/collaborativebioinformatics/GPU_MSA_Integration">https://github.com/collaborativebioinformatics/GPU_MSA_Integration</a></p> <h4 id="5-integrate-icn3d-viewer-with-jalview-msa">5. Integrate iCn3D viewer with Jalview MSA</h4> <p>Jalview shows MSA and structure alignment with Jmol. Jalview could also link to iCn3D to show MSA together with structure alignment. <a href="https://github.com/jiywang3/Integrate-iCn3D-viewer-with-Jalview-MSA">https://github.com/jiywang3/Integrate-iCn3D-viewer-with-Jalview-MSA</a></p> <h4 id="6-the-worlds-biomedical-knowledge-in-less-than-a-gram-introducing-the-pgp-incubator">6. The world’s biomedical knowledge in less than a gram: introducing the PGP incubator</h4> <p>The PGPincubator is an effort to create a distribution of open data, tools, workflows, AI models, and learning materials that support validation, benchmarking, and education in bioinformatics and biomedicine for precision health and (pre-clinical) biomedical AI. In addition, the incubator is a distributed network of physical computing infrastructure used to test components included in the distribution, such as validating genomics workflows or benchmarking AI models.</p> <p>To help hatch this network, PGPincubator is creating a network (using Tailscale) of “h-grams.” A h-gram is 1-4 microSD cards (3-4 weigh about a gram!) each flashed with a bootable operating system image and pre-loaded with data and tools. The PGPincubator open source project develops and maintains the scripts, process documentation and data resources required to build/test the h-gram image. These h-grams can then be booted on compatible commodity PC hardware. The operating system (Ubuntu) is pre-configured to act as a server suitable for home, office or lab and is accessed by other devices through a browser. Each h-gram will be pre-loaded with hundreds of gigabytes of openly licensed infrastructure software, bioinformatics tools, genomic datasets, AI models, and learning resources, making them ideal for education, validation, and benchmarking in biomedical research.</p> <p>We&rsquo;ll be demoing how to use the PGPincubator live! <a href="https://github.com/PGPinformatics/PGPincubator">https://github.com/PGPinformatics/PGPincubator</a></p> <h4 id="7-collaborative-development-of-grinn-get-residue-interaction-energies-and-networks-for-interaction-energy-based-analysis-of-biomolecular-simulation-trajectories">7. Collaborative development of gRINN (get Residue Interaction Energies and Networks) for interaction energy based analysis of biomolecular simulation trajectories</h4> <p>This project focuses on enhancing gRINN, a Python tool for analyzing protein energy networks from molecular dynamics simulations. gRINN calculates amino acid interaction energies from GROMACS trajectories and constructs Protein Energy Networks to identify key residues in protein communication pathways.</p> <p>We invite contributors to test the tool with diverse protein systems, identify bugs, develop tutorials, and optimize performance. Testers, developers, and documentation contributors at all skill levels are welcome.</p> <p><a href="https://github.com/osercinoglu/grinn-ismb-2025">https://github.com/osercinoglu/grinn-ismb-2025</a></p> <h4 id="8-improving-how-we-describe-and-discover-bioinformatics-tools">8. Improving how we describe and discover Bioinformatics tools</h4> <p>Bioconductor hosts over 3,000 R packages, but finding the right one can be challenging. biocEDAM is an experimental tool that uses large language models and the EDAM ontology to suggest meaningful package tags.</p> <p>At CoFest, we’ll work on integrating Gemini (a free, key‑free option) and testing the tool on more packages. We also welcome input on Model Context Protocols (MCPs), exploring how they might help surface package metadata in the future.</p> <p>Who should join: R developers, ontology experts, LLM/NLP enthusiasts, and anyone with domain knowledge keen to improve software discoverability.</p> <p><a href="https://github.com/mblue9/biocedam-cofest-2025">https://github.com/mblue9/biocedam-cofest-2025</a></p> <h3 id="9--extracting-metadata-from-proteomics-publications">9. Extracting metadata from proteomics publications</h3> <p>Many proteomics studies share raw data, but their experimental details remain buried in free-text methods and supplementary tables, making reuse and meta-analysis difficult. This project invites you to build models or pipelines that extract structured metadata—like organism, instrument, or disease—from paper abstracts and methods sections, using a gold-standard training set and clear evaluation tools.</p> <p>You&rsquo;ll work with a curated training set of 100+ annotated papers and compare your results to a GPT-o4-mini baseline. In the second phase, test your model on recent, unannotated publications to assess generalizability.</p> <p>Ideal for: NLP practitioners, proteomics researchers, or anyone interested in making scientific metadata more accessible and machine-readable.</p> <p><a href="https://github.com/SparkyDaBear/Intelligent_MetaData_ISMB_collaboration_fest_2025">https://github.com/SparkyDaBear/Intelligent_MetaData_ISMB_collaboration_fest_2025</a></p> <h3 id="code-of-conduct">Code of Conduct</h3> <p>As part of ISMB/ECCB 2025, CollaborationFest 2025 is covered by the <a href="https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct">ISCB Code of Ethics and Professional Conduct</a>.</p>https://www.open-bio.org/2025/01/18/2025-keynote-community-comment/Sat, 18 Jan 2025 00:19:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/01/18/2025-keynote-community-comment/<p>We invited our community to nominate potential keynote speakers for BOSC, and we were delighted with the many excellent suggestions received. In the next stage of this process, we&rsquo;re providing you with an opportunity to express any concerns regarding the suitability of any nominated individuals as BOSC Keynote Speakers.</p> <p>Our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker selection process and criteria</a> include examples of potential reasons for exclusion. <strong>If you have concerns about any of the individuals on our list, please share them (with as much detail as you feel comfortable providing) through <a href="https://docs.google.com/forms/d/e/1FAIpQLSe3hUXZ5BQv2-I7DpL-SdEovAVh6Bq9wWgs93FMx5LylAC_Eg/viewform">this anonymous form</a> by Friday, January 24, 2025.</strong></p> <p><strong>And the nominees are…</strong></p> <ul> <li>Aitana Neves</li> <li>Alondra Nelson</li> <li>Aviv Regev</li> <li>Catalina Lopez-Correa</li> <li>Chris Mungall</li> <li>Christine Orengo</li> <li>Dorrie Main</li> <li>Francis Ouelette</li> <li>Guanming Wu</li> <li>Heidi Sofia</li> <li>Helen Parkinson</li> <li>Joslynn Lee</li> <li>Kari Jordan</li> <li>Lincoln Stein</li> <li>Lisa Bowleg</li> <li>Mallory Freeberg</li> <li>Robert Aboukhalil</li> <li>Rowland Mosbergen</li> <li>Susanna Sansone</li> <li>Susheel Varma</li> <li>Sushma Naithani</li> <li>Tanya Berardini</li> <li>X. Shirley Liu</li> </ul> <p>Following the close of the community comment period, the BOSC Organizing Committee will use this list as a starting point for extending invitations to potential keynote speakers. As we cannot predict which speakers will accept the invitation, we may need to consider individuals beyond those nominated. In such cases, we will not repeat this nomination process. However, community members are always encouraged to inform the Organizing Committee if they believe a speaker does not align with our established standards.</p>https://www.open-bio.org/2025/01/09/nominate-keynotes-bosc2025/Thu, 09 Jan 2025 06:33:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/01/09/nominate-keynotes-bosc2025/<p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/ISMB-bosc-2025-banner.png" alt=""></p> <h2 id="we-invite-you-to-join-us-for-bosc-2025-a-vibrant-gathering-at-the-forefront-of-open-source-bioinformatics-and-open-science">We invite you to join us for BOSC 2025, a vibrant gathering at the forefront of open-source bioinformatics and open science!</h2> <ul> <li><strong>Location</strong>: Liverpool, UK, and virtual</li> <li><strong>Dates:</strong> July 21-22, 2025</li> <li><strong>Website</strong>: <a href="https://www.open-bio.org/events/bosc/">/events/bosc/</a></li> <li><strong>LinkedIn</strong>: <a href="https://www.linkedin.com/groups/14344023/">https://www.linkedin.com/groups/14344023/</a></li> <li><strong>Bluesky</strong>: <a href="https://bsky.app/profile/bosc.bsky.social">https://bsky.app/profile/bosc.bsky.social</a></li> <li><strong>Slack</strong>: <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew</a></li> </ul> <p><strong>Key Dates</strong></p> <ul> <li><strong>January 16, 2025: Deadline for community nominations of keynote speakers</strong></li> <li>April 17: Deadline for submitting talk/poster abstracts</li> <li>May 13: Talk/poster acceptance notifications</li> <li>May 15: Late poster submission deadline</li> <li>July 20-24: ISMB/ECCB 2025</li> <li>July 21-22: BOSC 2025 (the first two full days of ISMB/ECCB 2025)</li> <li>July 23-24: ISMB CollaborationFest</li> </ul> <p><strong>About BOSC</strong></p> <p>Since 2000, BOSC has provided a forum for sharing ideas and results in open-source bioinformatics and open science. Our annual two-day program includes keynote talks, talks chosen from submitted abstracts, posters, a panel discussion, and more!</p> <h2 id="exciting-news-for-2025"><strong>Exciting news for 2025</strong>:</h2> <p>BOSC 2025 will include a <strong>joint session with the newly renamed Bio-Ontologies and Knowledge Representation COSI!</strong></p> <p>Plus, our popular <strong>collaborative work event (CollaborationFest, or CoFest) will be held as part of ISMB,</strong> with participation open to all. Don&rsquo;t miss this great opportunity to connect with fellow researchers, contribute to groundbreaking projects, and shape the future of bioinformatics!</p> <p><strong>Nominate a keynote speaker!</strong></p> <p>We would like to assemble a diverse list of potential BOSC 2025 keynote speakers <strong>(see <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">our open selection process and rubric</a>).</strong> We invite the community to nominate keynote speakers using <a href="https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform">this form</a> by January 16. After that, we will share our list and solicit comments from the community prior to finalizing the speakers.</p> <p><strong>Submit an abstract! (But not yet!)</strong></p> <p>Abstract submission will open around the end of January. We encourage you to <strong>submit abstracts (due April 17</strong>– no extensions) on any topic relevant to open-source bioinformatics or open science. Some abstracts will be selected for lightning talks, longer talks, or posters.</p> <p><strong>BOSC topics include</strong> (but are not limited to):</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Open Approaches to Translational Bioinformatics</li> <li>Open Science</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach, and Training</li> <li>AI/ML: open approaches</li> </ul> <p>Registration fee assistance is available (more info on that soon).</p> <p>We hope to see you (in person or virtually) at BOSC 2025!</p>https://www.open-bio.org/2025/01/07/jacqueline-wahura-ento24-experience/Tue, 07 Jan 2025 15:12:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2025/01/07/jacqueline-wahura-ento24-experience/<p><em>The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Jacqueline Wahura Waweru, a PhD researcher at the University of Cape Town and International Center of Insect Physiology and Ecology, was awarded an OBF Event Fellowship to attend the annual <a href="https://www.royensoc.co.uk/event/ento24-online/">Royal Entomological Society Conference (Ento24)</a>.</em></p> <p>I was privileged to virtually attend the annual Royal Entomological Society conference Ento24 ( <a href="https://www.royensoc.co.uk/event/ento24-in-person/">Ento24: In-person - Royal Entomological Society</a>), which took place on 10th to 12th September at the University of Liverpool, UK. The theme of the conference was insect science. Diverse speakers spanning various sub-themes, including pest and natural enemies, host microbiome interactions, genetics and genomics, vector surveillance and control, among others were present. This being the first broad range insect conference that I have ever attended, the diversity in the range of sub-themes covered at the conference made me fully appreciate the diversity in research and interests in the various insect species being presented. Each speaker was eligible to give a 15-minute presentation on their work.</p> <p>The conference started with a keynote talk on Conservation Biology by Prof Michael Samways from Stellenbosch University, who is the author of the recently published “Conservation of Dragonflies”. This talk was very insightful in highlighting the challenges in protecting species from extinction. In addition, he highlighted some of the drivers of insect species extinction and the challenge that has on the ecosystem. With the threat that climate change presents, and the effect of human activities on the ecosystem, insect species must be protected to protect biodiversity and the gains that come with having insects in the environment, such as offering pollination services to plants used for human food.</p> <p>During the pests and natural enemies session, I was excited to hear a diverse range of strategies being employed to control pests and natural enemies including the use of insect endosymbionts. It was exciting to hear of symbiosis research in insects like aphids, given that symbiosis is a theme on which my current research focuses, albeit in a different insect model, the mosquito. In addition, there were talks on controlling the Fall armyworm insect, which is a major pest in maize, through intercropping and push pull technology.</p> <p>It was during the host microbiome interaction session that I was privileged to do my presentation titled “An influential insider: <em>Microsporidia MB</em> influences the gut microbiota composition in <em>Anopheles arabiensis</em> mosquitoes” ( <a href="https://docs.google.com/presentation/d/1jBiuFXzYOAiqq9pdW3Me567AZmgmTVFEFfzIJKzWgEM/edit#slide=id.g321fbe3a0ce_2_363">RES_annual_conference_JWahura</a>). <em>Microsporidia MB</em> is an insect endosymbiont in <em>Anopheles arabiensis</em> mosquitoes that was shown to impair the transmission of <em>Plasmodium falciparum</em>. In my talk, I highlighted my key findings that <em>Microsporidia MB</em> influenced the gut microbiota in infected mosquitoes to favor microbes with the <em>Plasmodium</em> transmission blocking phenotype. I outlined the steps followed in my methods and provided a GitHub link to the audience detailing the steps I followed in analyzing the gut microbiota data. It was interesting to see how my research, which is still in its infancy, stirred interest in the audience, and I received feedback on considerations I ought to take in my analysis pipeline as well as research gaps to consider filling.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/12/image.png" alt=""></p> <p>Other interesting talks during the host microbiome interaction session included those of the effect of different environmental variables on the gut microbiota of mosquitoes, the effect of endosymbionts in aphids on the host microbiome and the protective effect of microbiomes in insects such as ants on fruits such as apples.</p> <p>The second day of the conference started with a keynote talk on tsetse fly ecology and control by Prof Steve Torr from Liverpool School of Tropical Medicine. During this talk, we were brought to speed on the history of the tsetse fly and the burden of the disease associated with it. In addition, he highlighted all the control strategies that have been developed to reduce the burden associated with the disease and the outlook of gaps to be addressed in the future.</p> <p>The genetics and genomics session was highly exciting to me as it aligns with my interests in bioinformatics. Various interesting talks on topics such as reproductive manipulation of insects for massive field releases, understanding the genetic drivers of polyphagy in plant pests and talks on genome assemblies formed the basis of this session. The range of talks during this session provided insight into the breadth of genomics research and the scale of adoption of open science practices in insect science. Additionally, there was a strong highlight on the application of insect endosymbionts such as <em>Wolbachia</em> in managing key vectors, including <em>Anopheles gambiae</em> and <em>Aedes aegypti,</em> during the vector surveillance session.</p> <p>The last keynote talk on the last day was on “Co-evolution in social parasites and their hosts” by Prof Suzanne Foltzik from Johannes Gutenberg, University of Mainz. She did an excellent talk spanning genomics, microbiomes and proteomics and showcased the progress they have made in understanding the co-evolution of parasites and their host ants and bees.</p> <p>This conference was one of a kind to me in helping me gain a broad perspective on insects and the dynamic range of ongoing research on various insect models. I was also able to gain new insights on alternative niches I could explore in my work by attending this conference. Although I was attending the conference virtually, I managed to get the emails of some attendees with whom I was interested in having follow up discussions on potential avenues of collaboration. It was also exciting to see how different scientists and students are embracing open science globally and also how they are contributing to developing open-source tools.</p> <p>I am sincerely thankful to the Open Bioinformatics Foundation (OBF) for supporting my attendance at the Royal Entomological Society’s Ento24 conference and for allowing me to contribute to open science by sharing my approaches to malaria transmission blocking using insect endosymbionts.</p>https://www.open-bio.org/events/bosc-2025/Tue, 17 Dec 2024 23:29:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2025/<p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/BOSC2023-crowded-room-Jason-standing-1.png" alt="Part of the audience of BOSC 2023"></p> <div class="well"> <p><a href="https://www.open-bio.org/events/bosc/">BOSC 2026</a> will take place in Washington, DC, as part of <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a>, July 12-16, 2026. We hope you will join us!</p> </div> <p>Since 2000, BOSC has covered all aspects of open source bioinformatics and open science.</p> <p>BOSC 2025, the 26th annual Bioinformatics Open Source Conference, took place July 21-22, 2025 in Liverpool, UK (as part of <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a>). Read our <a href="https://f1000research.com/articles/14-887/v1">BOSC 2025 report on F1000Research</a>!</p> <p>BOSC 2025 included two days of <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/">keynote talks</a>, talks from submitted abstracts, a panel discussion, and posters. The full lineup of talks and posters is available on our <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/">schedule page</a>. The talk videos are linked from our <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/">schedule page</a> as well as on our <a href="https://www.youtube.com/@OBFBOSC/videos">YouTube channel</a>.</p> <p>BOSC 2025 included a <a href="https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025">joint session</a> with the <a href="https://www.bio-ontologies.org.uk/2025-meeting">Bio-Ontologies and Knowledge Representation (BOKR)</a>. It featured a <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-keynotes/">joint keynote by Chris Mungall</a> and talks on some of our favorite topics, including open data and reusable and reproducible science. The program concluded with a <a href="https://www.open-bio.org/events/bosc-2025/panel/">panel discussion on Data Sustainability</a>.</p> <br/> <div class="well"> <h2 id="bosc-2025-key-dates">BOSC 2025 Key Dates</h2> <div class="splitbox"><div class="left"> <ul> <li>April 17: Abstract submission deadline (talks and posters)</li> <li>May 15: Late poster submission deadline</li> <li>July 20-24, 2025: <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a> (Liverpool, UK, and online)</li> <li><strong>July 21-22, 2025:</strong> <strong>BOSC 2025</strong> (part of ISMB/ECCB 2025)</li> <li>July 22 (second day of BOSC): <a href="https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025">Joint session with Bio-Ontologies and Knowledge Representation (BOKR)</a></li> <li>July 23-24: <a href="https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/">ISMB CollaborationFest</a> (collaborative work event)</li> </ul> <p></div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2025/01/Thomas-Mboa-on-panel.jpeg" alt="Thomas Mboa during BOSC 2024"></p> </div><div style="clear:both"></div></div> </div> <h3 id="topics">Topics</h3> <p><div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/wp-content/uploads/2024/08/Larry-and-Melanie-in-BOSC-audience-1.jpeg" alt="Larry Hunter and Melanie Courtot at BOSC 2024"> <br/></p> </div><div class="right"> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Data Access and Visualization</li> <li>Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Outreach and Training</li> <li>Open AI/ML</li> <li>Sustainable Data</li> <li>&hellip;and more!</li> </ul> </div><div style="clear:both"></div></div> <br/> <h3 id="registration-and-financial-assistance">Registration and Financial Assistance</h3> <p>To participate in BOSC 2025 or the ISMB CollaborationFest, you will need to <a href="https://www.iscb.org/ismbeccb2025/register">register for ISMB/ECCB 2025</a>. Those who <a href="https://www.open-bio.org/events/bosc-2025/submit/">submit abstracts to BOSC</a> can request a fee waiver on the submission form. You can also apply for an <a href="https://www.open-bio.org/event-awards/">OBF Event Award</a>; the deadline is April 1.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/08/BOSC-org-committee-Montreal-1.jpeg" alt="BOSC 2024 organizing committee"></p> <h2 id="sponsorships">Sponsorships</h2> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/12/Beatrice-Mihalache-with-BOSC-poster.jpg" alt="Beatrice Mihalache presenting a poster at BOSC 2024"></p> </div><div class="right"> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from companies and non-profit organizations help to defray some of our costs and support our outreach efforts. Thanks to our sponsors, we were able to grant free registration to 15 participants at BOSC 2024, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you&rsquo;re interested in sponsoring BOSC 2025, please see our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors page</a>!</p> </div><div style="clear:both"></div></div> <h3 id="2025-platinum-sponsor">2025 Platinum Sponsor:</h3> <p><a target="_new" href="https://chanzuckerberg.com/science/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:65%" alt="CZI" /></a></p> <div class="splitbox"><div class="left"> <br/> <p><strong>2025 Gold Sponsor:</strong></p> <p><a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" style="width:95%" alt="Seqera" /></a></p> <p></div><div class="right"> <br/> <strong>2025 Silver Sponsor:</strong></p> <div class="splitbox"><div class="left"> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a></p> </div><div class="right"> </div><div style="clear:both"></div></div> </div><div style="clear:both"></div></div> <div class="well"> <h3 id="about-bosc">About BOSC</h3> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow and sustain open source communities.</p> <p>BOSC is usually preceded or followed by <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a> (CoFest for short), a two-day collaborative work session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. In 2025, CollaborationFest will be part of ISMB/ECCB!</p> <p><a href="https://www.open-bio.org/events/bosc/about" class="btn btn-lg btn-primary">More about BOSC</a></p> </div> <div class="well"> <h3 id="bosc-2025-organizing-committee">BOSC 2025 Organizing Committee</h3> <div class="splitbox"><div class="left"> <p><em><strong>Chair: Nomi L. Harris</strong></em> (Lawrence Berkeley National Laboratory)</p> <ul> <li>Karsten Hokamp (Trinity College Dublin)</li> <li>Deepak Unni (SIB, Swiss Institute of Bioinformatics)</li> <li>Jessica Maia (BD)</li> <li>Tazro Ohta (Chiba University)</li> <li>Jason Williams (Cold Spring Harbor Laboratory)</li> <li>Monica Munoz-Torres (Univ. of Colorado Anschutz Medical Campus)</li> <li>Hervé Ménager (Institut Pasteur)</li> </ul> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/12/BOSC-2025-org-committee-square.png" alt="BOSC 2025 Organizing Committee"></p> </div><div style="clear:both"></div></div> <h4 id="bosc-2025-review-committee">BOSC 2025 Review Committee</h4> <p>Aziz Khan*, Bastian Greshake Tzovaras*, Bhavesh Patel, Christopher Fields*, Damien Goutte-Gattat*, Daniel Korn, Deepak Unni, Fortune Ogo-Ndah Awala, Gayathri Jonnalagadda, J. Harry Caufield*, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov, Luis Pedro Coelho, Monica C Munoz-Torres, Naouel Karam, Nomi Harris, Olawumi Olasunkanmi, Peter Cock, Rafael Gonçalves, Sayali Talware, Sepideh Mazrouee*, Tanya Berardini, Tazro Ohta*, Tyrone Chen, Van Truong, Yuvanesh Vedaraju</p> <ul> <li>indicates reviewers who did extra reviews</li> </ul> </div> <h4 id="code-of-conduct">Code of Conduct</h4> <p>As part of ISMB/ECCB 2025, BOSC 2025 is covered by the <a href="https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct">ISCB Code of Ethics and Professional Conduct</a>.</p>https://www.open-bio.org/2024/11/21/erin-rin-krichilsky/Thu, 21 Nov 2024 15:54:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/11/21/erin-rin-krichilsky/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Erin (Rin) Krichilsky, a PhD researcher at Columbia University and the American Museum of Natural History, was awarded an OBF Event Fellowship to attend the <a href="https://ice2024.org/">27th International Congress of Entomology (ICE2024 Kyoto)</a></em>.</p> <p>This year, I had the privilege to co-host the symposium “Bee diversity in East and Southeast Asia: Systematics and Status of the Fauna” at the International Congress of Entomology (ICE) in Kyoto, Japan. The symposium hosted eight researchers from Korea, Malaysia, Taiwan, China, Singapore, Thailand, and Nepal working in universities and government institutions. Each researcher gave a 15-minute presentation about bee studies in their region. Open data was a central theme, as many novel findings are discovered through DiscoverLife and the community science platform iNaturalist, and project results are posted to the Global Biodiversity Information Facility (GBIF) and the International Union for the Conservation of Nature (IUCN).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/figure1-1-1024x366.png" alt=""></p> <p>Figure 1. Images of bees from insect collections in Taiwan</p> <p>It is estimated that bee species records are lacking for 79-90% of the global land area outside North America and Western Europe. However, those numbers are based on what is published online and do not reflect the reality of efforts beyond those two regions. The goal of our symposium was to create a network of researchers working on bees in Asia, as there are many projects with overlapping objectives, as well as unite ideas on how to use open data to mitigate biodiversity loss and improve faunistic understanding.</p> <p>ICE only takes place once every four years, with a changing location. This year, it was estimated that there were over 4,000 attendees from 83 countries. Additionally, this was the fourth time in the near one hundred year history that the conference was held in Asia. We wanted to seize the opportunity of location to connect bee researchers in the region and show a global audience the many research projects happening there.</p> <p>In addition to the symposium, we hosted a gathering where the presenters and those not participating in the event but conducting research on bees in Asia could meet. This event gathered nearly 20 individuals from ten different countries.</p> <p>I am an Entomologist and PhD student studying the evolution and diversity of bees and apoid wasps. Before starting my degree, I lived in Taiwan, working with and learning from colleagues on a national checklist of the bee species there, Dr. Sheng Shan Lu and Wen-Chi Yeh of the Taiwan Forestry Research Institute and Dr. I-Hsin Sung of Chiayi University. We <a href="https://www.gbif.org/project/BIFA6_033/a-bilingual-open-source-checklist-and-digitization-of-taiwans-bee-fauna">received funding</a> from GBIF called the data mobilization grant to digitize bees in all national collections, which resulted in open source species and distribution data. Open data is essential for establishing a baseline biodiversity list, as it reveals novel information on species’ biology, range, and/ or morphology, as well as undescribed taxa. Dr. Sung presented our research, his talk “A Bilingual Open-Source Checklist and Digitization of Taiwan’s Bee Fauna&quot; and others in the symposium showcased how platforms like GBIF, IUCN, DiscoverLife, and iNaturalist are critical for bee studies in the region. Additionally, since many bee groups have a taxonomy that has not been revised in up to a century, being able to see label data, images, and maps of fauna from neighbouring countries helps progress local efforts.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/Screenshot-2024-11-20-at-1.19.20-PM-1024x789.png" alt=""></p> <p>Figure 2. Digitization images of bee specimens from Taiwan and their label data. Notice the range in collection dates from 1910 to 2019!</p> <p>Publicly available field and natural history collection data brings awareness and efforts to bee studies globally. The ICE symposium provided the opportunity for bee researchers to network and discuss projects, collaborations, and best practices for open-source tools. I am endlessly grateful to the Open Bioinformatics Foundation (OBF) for supporting my attendance at ICE, allowing me to enact our goals to contribute to open science by sharing our approaches and ideas to mitigate gaps in bee biodiversity knowledge. ICE has by far been my favorite conference I have ever attended! In addition to the success of the symposium, I was selected to receive a Presentation Award for Young Scientists (PAYS), all thanks to OBF. I highly encourage applications to the OBF Event Fellowship, as without their generosity, I would not have been able to meet such an important and inspiring group of researchers.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/figure3-1024x748.png" alt=""></p> <p>Figure 3. Symposium speakers, organizers, and attendees at ICE 2024.</p>https://www.open-bio.org/2024/11/19/masturina-experience-at-apbjc2024/Tue, 19 Nov 2024 16:11:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/11/19/masturina-experience-at-apbjc2024/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Masturina Binti Md Mansor, a PhD student at the Universiti Putra Malaysia, was awarded an OBF Event Fellowship to attend <a href="https://www.apbjc.asia/">Asia &amp; Pacific Bioinformatics Joint Congress 2024</a></em>.</p> <p>I flew in to Okinawa, Japan, from Kuala Lumpur, Malaysia on 21st October 2024 for the first ever Asia Pacific Bioinformatics Joint Conference 2024 (APBJC). It was my first international conference as a PhD candidate, a memorable milestone that I will cherish as I push forth in my research journey. This APBJC was successfully brought together by the big houses of bioinformatics in the region, namely the Japanese Society for Bioinformatics (JSBi), the Asia-Pacific Bioinformatics Network (APBioNET), the International Society for Computational Biology (ISCB), the Genome Informatics Workshop (GIW), and the Asia-Pacific Bioinformatics Conference (APBC). Digital advertisements flashed through the streets of Kokusai Dori in Naha in anticipation of the 4-day event (22nd October - 25th October) as the city welcomed around 700 participants from all around the world, bringing together researchers, scientists, academicians, industry players and other science/tech enthusiasts alike. The conference took place at the Naha Cultural Arts Theatre (NAHart), off the main street of Kokusai Dori.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic4.1.jpg" alt=""><em>Digital adverts along Kokusai Dori welcoming APBJC2024</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic10-768x1024.jpg" alt=""><em>Digital adverts along Kokusai Dori welcoming APBJC2024</em></p> <p>With the generous funding from the Open Bioinformatics Foundation (OBF), I was able to gain exposure to the different trends in bioinformatics, and network with other bioinformaticians in the field. Not only were researchers and academicians present, but industry players like Amazon, Megazone and Alafia also provided luncheon seminars on integrating their services in bioinformatics and healthcare. One thing I have noticed about being in the bioinformatics/computational biology field, is the exponential pace trends and new ideas are generated. This conference was a great opportunity for me to not only learn from other bioinformaticians, but also for me to gain feedback on my research as well.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic6.1.jpg" alt=""><em>Me with my poster on the ‘Structure and Function of Aquaporin from Antarctic Pseudomonas’</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic14-1024x684.jpg" alt=""><em>Engaging with another poster presenter on her research</em></p> <p>The focus this year oriented around the integration of AI in bioinformatics and healthcare research. It was interesting to see how most oral and poster presenters integrated AI into their research. From protein structure prediction to omics data analytics, and to those who were complimenting computational work with experimental methods, AI was a big theme everywhere. It also gave me ideas on how to better leverage open source tools and other best practices for reproducible science, which I am eager to share with my colleagues back home in Malaysia. Being able to converse and exchange knowledge with other participants in APBJC on how AI would help us advance bioinformatics research was especially enlightening to me. It felt like the future was already here!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic13-1024x576.jpg" alt=""><em>Seminars and workshops</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic12-1024x768.jpg" alt=""><em>Seminars and workshops</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic16-1024x684.jpg" alt=""><em>Together with the members of APBioNet</em></p> <p>Whilst my journey to Okinawa was primarily to attend APBJC, I could not help but notice the charm and allure of the island. Even the airport was set at a picturesque background, with the turquoise waters of the sea visible from the airport terminal as I landed. It is a land rich in natural beauty, food, culture and welcoming people. The city was a unique mix of modern and old design, giving it that Okinawan identity.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic17.jpg" alt=""><em>A backdrop of the sea at the airport terminal</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic9.jpg" alt=""><em>Exploring the streets of Naha, Okinawa</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic3.jpg" alt=""><em>Exploring the streets of Naha, Okinawa</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic2.jpg" alt=""><em>Enjoying an authentic Omakase dining</em></p> <p>Overall, the first APBJC was a huge success, of which I am grateful to have had the opportunity to be part of. It was truly a hallmark moment for the bioinformatics community in Asia and Pacific, coupled with Okinawa’s warm hospitality and welcome. I am hopeful this pivotal event will pave the way for more to come over the years as we endeavour together to advance and make science and technology accessible. Till we meet again next time!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/pic18-1024x684.jpg" alt=""><em>A group picture with some of the organisers, volunteers and participants before the networking session</em></p>https://www.open-bio.org/2024/11/07/apbjc-2024-tanakamol-mahawans/Thu, 07 Nov 2024 13:09:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/11/07/apbjc-2024-tanakamol-mahawans/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Tanakamol Mahawan, a PhD student at the Institute of Systems, Molecular and Integrative Biology , University of Liverpool, was awarded an OBF Event Fellowship to attend <a href="https://www.apbjc.asia/">Asia &amp; Pacific Bioinformatics Joint Congress 2024</a></em>.</p> <p>This year’s Asia &amp; Pacific Bioinformatics Joint Conference (APBJC 2024) in Okinawa was a special milestone for me; it was the first conference I attended since moving back to Thailand from the UK. Now a new lecturer at a Thai university, I felt a unique excitement and gratitude stepping into this event, thrilled by the chance to reconnect with the vibrant bioinformatics community in Asia Pacific and meet others passionate about advancing open science.</p> <h4 id="falling-in-love-with-okinawa"><strong>Falling in Love with Okinawa</strong></h4> <p>From the moment I landed at Naha Airport, I was charmed by Okinawa. The warm weather was a welcome reminder of home, and as I walked toward my hotel, I found myself surrounded by the sights and sounds of the Okinawa Traditional Eisa Festival, a lively celebration filled with rhythmic drumming and dance. The island’s beauty was undeniable—pristine beaches, lush landscapes, and a culture that exudes warmth. Walking through the streets, I saw the incredible fusion of Okinawan tradition and modernity, from the traditional shisa lion statues guarding doorways to bustling markets selling both local delicacies and modern treats. Okinawa instantly felt like the perfect setting for an international gathering focused on innovation and collaboration.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXfne2LM6pDaBtSrsLdpdiWmF3RpU0qrrN5L5b49zibnpF3QFGs5YxEr2IZ8sP4juKkGV-QgFdrkxqHh9MW3fC7fl_zTHj1hdy1DJ0e19aROynUIYhkPXCSvbtvpqVO2u-Qm1RacvDq70zernQ7_cCc5S3O7?key=gk1eoygKHJXhv5ZPn_sDJA" alt=""><em>Pic 1 :  Okinawa Traditional Eisa Festival 2024</em></p> <p><strong>The Science of Batch Effect Correction</strong></p> <p>At the conference, I had the opportunity to present my research, “A Comprehensive Approach to Batch Effect Correction in Machine Learning: A Case Study Using Pancreatic Cancer RNA-Seq Data.” This was a moment I had been working toward, sharing insights from my PhD on tackling one of the core challenges in omics data analysis. I highlighted the importance of open science principles—transparency, reproducibility, and community collaboration—all of which are essential in bioinformatics.</p> <p>It was encouraging to see a strong interest in my poster, with attendees eager to discuss the nuances of batch effect correction. We discussed  why quality checks are crucial before using any batch-corrected data in downstream analyses—a topic that resonated with many who had experienced the complexities of multi-source data integration firsthand. As part of my commitment to open science, I shared the link to my <a href="https://github.com/Victormah/ML_PDACBiomarker">GitHub repository</a>, where others can access the code and workflow I developed for batch correction. This, I believe, contributes to a collective effort in making bioinformatics research reproducible and accessible to all.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/image-763x1024.jpeg" alt="">P <em>ic 2 : Poster presentation</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/image-3-1024x768.jpeg" alt=""><em>Pic 3 : Workshop on Drug Response Prediction and Graph Neural Network(GNN)</em></p> <h4 id="building-quality-connections"><strong>Building Quality Connections</strong></h4> <p>One of the most enriching parts of the conference was meeting new friends and potential collaborators. A memorable group of PhD students from Osaka, Hokkaido and Oxford brought fresh perspectives and infectious enthusiasm, making our post-conference discussions both lively and enlightening. We shared experiences and stories over local food, discussing everything from research challenges to future aspirations.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/image-2-1024x768.jpeg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/11/image-1-1024x576.jpeg" alt=""><em>Pic4 -5 : A group of friends from  Osaka , Hokkaido and Oxford</em></p> <p>Another exciting connection was Dr. Nok, a researcher from Singapore and a senior in machine learning research. We bonded over our shared interests and began brainstorming ideas for a potential collaborative project. Meeting these brilliant minds underscored how bioinformatics is more than just science—it connects researchers across borders, allowing us to work together towards common goals.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXcOmPAAuIH9fvxEnM8l-sbu9qC9KHzZFcsne1GgajF4KW1YTtPEseOBlHoUpEZp1Z3rIwANzMUog8OjEwRmjACbBEJ1jtGlsi2hLVdWlL_DLWcx26rYoU2dDROgmnx3sFJWNHg58Cy97uKf9dJ0NEBkvjH9?key=gk1eoygKHJXhv5ZPn_sDJA" alt=""><em>Pic 6 : Dr. Chayaporn Suphavilai (Nok), My future collaboration in Machine Learning projects</em></p> <h4 id="embracing-open-science-and-representing-thailand"><strong>Embracing Open Science and Representing Thailand</strong></h4> <p>My participation in APBJC 2024 was more than just a chance to present my work; it was an opportunity to promote open-source bioinformatics and open science, fields where transparency and accessibility are essential. My research, part of which has been published in BMC Medical Informatics and Decision Science, is available on GitHub, where I’ve shared tutorials and workflows aimed at making complex analyses more accessible. This commitment to open science is something I hold close, as it embodies the collaborative spirit that drives meaningful progress in bioinformatics.</p> <p>Attending APBJC 2024 also held a personal significance for me. As a Thai researcher in the relatively underrepresented field of bioinformatics in my region, I am passionate about bringing a unique perspective from Thailand to the global stage. This conference allowed me to represent Thailand, contributing to diversity in the open science community while fostering interdisciplinary connections.</p> <p>In the end, APBJC 2024 was much more than a scientific gathering—it was an inspiring experience highlighting bioinformatics&rsquo;s collaborative essence. I left Okinawa with a renewed sense of purpose, new friendships, and the excitement of upcoming projects. I look forward to continuing this journey and, hopefully, inspiring the next generation of scientists from Thailand and beyond. Thank you APBJC 2024, for arranging the wonderful event and OBF Event Fellowship for giving me this great opportunity.</p>https://www.open-bio.org/2024/11/04/open-science-in-computational-virology-eccb2024/Mon, 04 Nov 2024 11:26:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/11/04/open-science-in-computational-virology-eccb2024/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Li Chuin Chong, a PhD student at the TWINCORE Centre for Experimental and Clinical Infection Research GmbH &amp; Medizinische Hochschule Hannover, Germany, was awarded an OBF Event Fellowship to attend <a href="https://eccb2024.fi/">23rd European Conference on Computational Biology (ECCB2024)</a></em>.</p> <p>I sincerely offer my gratitude to Open Bioinformatics Foundation (OBF) for the partial support, which allowed me to participate in the 23rd European Conference on Computational Biology (ECCB2024) in Turku, Finland. This was a milestone in my academic journey, as it marked my first international bioinformatics conference as a PhD candidate and my first-ever visit to Finland. This enabled me to share our findings from my PhD project, besides offering a platform to meet and interact with computational scientists from worldwide.</p> <p>This 5-days conference with the theme of ‘Data and Algorithms for Health and Science’ was well attended by over 750 participants from 50 countries, featuring around 90 talks and 400 poster presentations. ECCB2024 offered five keynote talks and even a lively scientific debate. One talk that particularly stood out to me was by Peer Bork, who delivered an engaging presentation on planetary metagenomics. He discussed SPIRE (Searchable, Planetary-scale Microbiome Resource), a groundbreaking database that compiles microbiome data on a global scale. This resource allows for extensive mining of microbiome information, enabling researchers to identify novel baseline findings through meta-analysis. Bork’s team demonstrated how SPIRE is advancing data-driven discoveries, offering a transformative tool for microbiome studies, with wide-ranging applications in ecology, health, and global biodiversity.</p> <p>Apart from the interesting talk, ECC2024 gave me an invaluable opportunity to present my research work, entitled “Towards quantifying zoonotic spillover risks of RNA viruses: A comprehensive approach using next-generation sequencing data”. My presentation focused on the identification of novel flaviviruses and coronaviruses, analyzing their hosts and assessing the potential for spillover events. I introduced our open-source software tool, virushunter-virusgatherer (available on GitHub: <a href="https://github.com/lauberlab/VirusHunterGatherer">https://github.com/lauberlab/VirusHunterGatherer</a>), which facilitates novel virus identification, showcasing how it integrates with other bioinformatics tools to provide a robust framework for RNA virology. This opportunity sparked meaningful discussions on the importance of open science and the role of interoperable frameworks in predicting zoonotic events, aligning with the core principles of the OBF. On the last day of the conference, I was excited to receive a free book from Oxford University Press titled ‘An editor’s guide to writing and publishing science’, which will undoubtedly be a valuable resource in my academic journey.</p> <p>Lastly, I am very grateful to my supervisor, Prof. Dr. Chris Lauber for supporting my attendance at this conference. Again, I thank the OBF for awarding me a travel fellowship to partially cover my travel expenses, and extend my appreciation to the CoViPa consortium, which supports this project. Their support has been instrumental in making my participation at ECCB2024 possible.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXegAJldskVt2TbsCkcd_VCu6oueyFbzCqTwvsPZqnWK0YJLCSJ-cifViqeKuxHtdyPAIIAE_AQ3nuvBQ-YOrLpqs6tiw-Hy5Qm0Y34WMeZiyIHCndz30MuPqTUeNoyxqM5w0FKN2q_E4FT90Qo4z93bYqBoab5pKFWRajV76g?key=cDoeJpbBYNOq_K7Ook9MWw" alt=""></p> <p>Memories from ECCB2024 – Sharing insights from my research and discussing the open science perspective, while connecting with new colleagues from around the world.</p>https://www.open-bio.org/2024/10/24/bioinformatics-spain-and-i/Thu, 24 Oct 2024 10:20:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/10/24/bioinformatics-spain-and-i/<p><em>The</em> <a href="https://www.open-bio.org/travel-awards"><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></a> <em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Jacob González Isa,</em> a PhD student at the University of Cambridge (started October 2024) and formerly an MSc student at the Technical University of Madrid, <em>was awarded an OBF Event Fellowship to attend</em> <em>the</em> first <a href="https://congresosebibc.com/">Congress of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC)</a>.</p> <p>From October 16 to 18, 2024, Valencia hosted the first Congress of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC), which I attended thanks to the Event Fellowship awarded by the Open Bioinformatics Foundation (OBF).</p> <p>This was set to be a turning point for me—and not only because SEBiBC debuted and brought together over 300 attendees—an impressive feat for a society less than three years old. It was something else. Something personal. It was like a bittersweet farewell. This congress took place right in the middle of a professional transition: I finished my bachelor&rsquo;s and master&rsquo;s degrees in Spain and am now moving abroad to pursue a PhD.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/10/GaLEJPhXEAEbGvH-1.jpeg" alt="">Family picture at the end of the 1st Congress of the SEBiBC.</p> <p>Let me tell you about three aspects of my experience at this conference and why it was so important to me:</p> <p><strong>1. First time as a symposium organiser</strong></p> <p>It was the first time I organised a Networking session at the Student Symposium as a member of <a href="https://www.rsg-spain.iscbsc.org/">RSG</a> (the Regional Student Group in Spain of the <a href="https://www.iscb.org/">ISCB</a>). We created a sort of card game in which the participants, during lunch, had to assemble a bioinformatic pipeline combining their cards. It was so gratifying to see how this &ldquo;nerdy&rdquo; twist on networking helped foster connections and spark discussions among the attendees!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/10/WhatsApp-Image-2024-10-18-at-17.58.18_0c17272e-1-768x1024.jpg" alt="">Jacob explaining the rules of the &ldquo;Pipeline Assembly&rdquo; networking activity.</p> <p><strong>2. The commitment to Open Science</strong></p> <p>Open and FAIR bioinformatics was omnipresent during the congress. Christine Orengo, from the University College of London (UCL), told us about their latest work, The Encyclopedia of Domains (TED) into CATH (<a href="https://www.cathdb.info/">https://www.cathdb.info/</a>) and its relevance beyond structural Bioinformatics. Jaime Huerta-Cepas, leader of important work in open software and databases like ETE and EggNOG, shared their FESNov catalogue (<a href="https://novelfams.cgmlab.org/)">https://novelfams.cgmlab.org/)</a>, with Álvaro Rodríguez as first author, which compiles more than 400,000 novel gene families unique to uncultivated microorganisms. Christine and Jaime had a common view on the cruciality of the open bioinformatics tools and databases they have used, such as Foldseek, MMseqs2, ETE, GMGC, ColabFold and Merizzo. Without these accessible resources and the community’s efforts, their groundbreaking work simply would not have been possible.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/10/image-2-1024x569.png" alt="">Jaime Huerta-Cepas emphasises the importance of the open-source tools and community behind his work. Image taken from @SEBiBC_es</p> <p>In this congress, I understood the excellence of Spanish bioinformatics and its commitment to open science and reproducibility. The list of accomplishments and initiatives is impressive. From digital twins projects led by the Barcelona Supercomputing Center, home to one of the world’s most powerful supercomputers, MareNostrum 5, to cutting-edge tools like SQANTI3 for long-read transcriptomics developed by the Ana Conesa lab, Treeprofiler by Ziqi Deng, ETE4 by Jordi Burguet and CAASTools by Fabio Carteri, and many more that I don’t have space to mention. More than 100 posters filled the room with innovative tools. Everything is open and accessible.</p> <p>On a 1000-fold smaller scale, I was excited to present my M.Sc thesis work with a poster, where I developed a pipeline called MetEOr to mine enzymes of biotechnological interest. The feedback I received was incredibly helpful and will guide me in refining the documentation and improving how I share my work moving forward.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/10/WhatsApp-Image-2024-10-19-at-16.01.44_8a05ebe1-1-768x1024.jpg" alt="">During the poster session, I presented my tool MetEOr (<a href="https://github.com/jacgonisa/MetEOr">https://github.com/jacgonisa/MetEOr</a>) and the results derived from it with the plastic-degrading enzyme family.</p> <p><strong>3. Where I come from and where I go</strong></p> <p>To be fair, six years ago, I could have never imagined being in an event like this and starting to feel like a scientist. I am a first-generation university graduate who grew up and studied in a very humble background in one of the poorest regions in Spain, Andalusia. My home city has one of the highest youth unemployment rates in Europe.</p> <p>In 2023, I found an incredible opportunity in Madrid and joined the Jaime Huerta-Cepas group, where I’ve learned more than I ever have in my entire life. While there, I also discovered RSG, SEBiBC, and Spain&rsquo;s longstanding commitment to open bioinformatics. It was there that I truly found my place in the bioinformatics community.</p> <p>However, life has exciting, unexpected turns, and another fantastic opportunity came my way that I couldn&rsquo;t pass up… So, I packed my bags and started a PhD in October at the University of Cambridge.</p> <p>I have never hidden that I am scared of going abroad for long periods, but experiences like the one I had this week in Valencia inspire me to kick off a career in bioinformatics internationally with confidence and enthusiasm.</p> <p>I can&rsquo;t envisage my professional journey without Spain. This congress in Valencia was so important to me because I believe it’s essential to represent the Spanish (and Andalusian) community while I’m in the UK. Even as I embark on my PhD abroad, I wish to have strong roots in Spain, with tangible connections with people that I can call friends. I want to bring the best Bioinformatics from Spain to the UK and vice versa.</p> <p>In Valencia, I learnt that bioinformatics is an especially interconnected, transversal discipline, perhaps due to the huge set of crosscutting skills we develop and the fact that international mobility is commonplace. It was inspiring to see foreign researchers thriving in Spain and Spanish scientists like Luz García Alonso (another keynote speaker and a bioinformatician at the Sanger Institute) doing great science abroad.</p> <p>The Open Bioinformatics Foundation has helped me lay the first stone in the bridge I want to build between Spain and England, and I couldn&rsquo;t be more grateful.</p> <p>¡Gracias y hasta pronto!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/10/image.png" alt="">After three tiring and overwhelming days, I deserved a delicious dish of paella! Fun fact: paella originated in Valencia, so it is actually more a regional, Valencian dish than a Spanish one.</p>https://www.open-bio.org/2024/10/15/open-source-and-open-minds-tbnss-2024/Tue, 15 Oct 2024 07:25:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/10/15/open-source-and-open-minds-tbnss-2024/<p><em>The</em> <a href="https://www.open-bio.org/travel-awards"><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></a> <em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Keerthana Padmanabhan,</em> a PhD researcher at the National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, INDIA, <em>was awarded an OBF Event Fellowship to attend</em> <em>the</em> <a href="https://nenckiopenlab.org/tbnss2024/">Transatlantic Behavioral Neuroscience Summer School 2024 (TBNSS 2024)</a>.</p> <p>In September 2024, I had the wonderful opportunity to attend the <a href="https://nenckiopenlab.org/tbnss2024/">Transatlantic Behavioral Neuroscience Summer School 2024 (TBNSS 2024)</a> conducted in Mikolajki, Poland, from September 9th to 20th 2024 by the Nencki Open Lab, Nencki Institute of Experimental Biology PAS, Poland. First and foremost, this was made possible by the travel fellowship granted to me by the Open Bioinformatics Foundation, for which I am extremely grateful.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXdvZDIeHR5Gegera5ClPE4hs9LLTwFoJ1jCfBYzLwCJoO-XYbGnQ_tr_gZWc1cDn6iUynXQ5N8Nxgf6p0f3GBspZ_w0886oDwp5n_ktD6dnB82mGzZg7RqIko4KtzqDDTUxSP8L1AknnDRcmeU-buo6G9bn?key=KYQfERLZnhhk-DQ5svV-Bw" alt=""> <em>Organizers and participants of TBNSS 2024</em></p> <p>The summer school was a particularly enriching experience for me because it was my first summer school. It introduced me to the wonderful world of open science and also to a great community of researchers and friends. The interactions and discussions that ensued provided invaluable insights into neuroscience research and, importantly, about the incorporation of open source tools.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXcGZyOTN2qlNsvpehfBnLuTXruDjyapu3OxPEvt1Bxv22wufK42V5DwoxQ17eDU1_xhO_p36FzkQGGzTRWQoUowrEnOy4RaRyhZqhfiI1tzz3QfbuZLhXkBLr-44DUA4UHAw3Nt6f6wExqpEeKyzQQvJvmd?key=KYQfERLZnhhk-DQ5svV-Bw" alt=""></p> <p><em>Arduino workshop</em> during TBNSS 2024</p> <p>The objective of the summer school was to provide the knowledge and skills to use open-source tools and open-source software to design our own devices and also for data analysis. This aids to surmount the multiple constraints in behavioural neuroscience research such as highly expensive devices and licensed software that may not be affordable for all.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXfWMKA3gLOgHjW9fyDwUKKX5WIJHFjca7NIvcgyH0FRF352nbzRlCefk3JUVR1qW0hsd6rdmji-1sNrHuiIimTinOsy9ipvPN9lZxyn0voUYPDg8AO8dVfBRHT59JXohpr-yTnqZaTbGwHJ_036Ibr3b8S1?key=KYQfERLZnhhk-DQ5svV-Bw" alt=""></p> <p><em>Designing 3D cases and holders during 3D printing workshop</em></p> <p>During the school we learned to use Arduino-based devices and Bonsai code for applications such as modifying the experimental environment and delivering stimuli. We learnt how to 3D print holders or cases for devices. In addition, we also were trained in Deeplabcut, Keypoint-MoSeq, and CEBRA for advanced data analysis. The presentations from invited speakers from various reputed universities and institutions across Europe was the cherry on the cake in our learning experience.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXcYSlANaFKZdLUYCOEioOLwKOn1MXZy-Tth-YD8U_SNJvb6fYyFzvnV2s4306diDOtic2dSiCXIGSJbCf3Zq33Z0DvnF58dz14_fYFLZlPhu3JW8A_yqpZ5JOROHoxrbqvGbRqK0w_9QvkcHNUi_-9FTUOw?key=KYQfERLZnhhk-DQ5svV-Bw" alt=""></p> <p><em>Building mini robots as a part of the Arduino workshop</em></p> <p>We carried out group projects and presented our findings to have a complete hands-on application of what we learnt during the school. My group project consisted of using arduino-controlled devices to assess phototaxis in Drosophila.</p> <p><em>``</em></p> <p><em>Keerthana presenting her project at TBNSS 2024</em></p> <p>The overall learning experience at the school was one of a kind and a maiden one for me. It has initiated me into the world of open science and has opened up a plethora of applications for my own research. The school has successfully managed to bring about participation of early-life researchers from underprivileged/under-represented countries and that is the highlight of this endeavour of TBNSS 2024. On a personal note, I have gained immensely in terms of knowledge enhancement and also made a whole lot of beautiful memories and very special friends at the school. My special thanks to the organizers of TBNSS 2024 for being such wonderful mentors and initiating someone with very little experience with coding into the world of open source software. I am happy that with these connections, I have just begun on a lifelong journey of learning and contributing to open-science. I hope this community continues to grow and I can continue to contribute to it.</p>https://www.open-bio.org/2024/10/11/event-fellowship-2024-3/Fri, 11 Oct 2024 15:45:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/10/11/event-fellowship-2024-3/<h4 id="the-call-for-applications-for-round-3-of-the-obf-event-fellowship-for-2024-is-now-open-the-deadline-for-this-round-is-1-december-2024-you-can-submit-your-application-through-this-google-form-we-have-provided-a-word-template-to-help-you-draft-the-application-locally-before-filling-out-the-form--make-a-copy-of-this-template">The call for applications for <strong>round 3</strong> of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> for 2024 is now open. <strong>The deadline for this round is 1 December 2024.</strong> You can submit your application through <a href="https://forms.gle/D31zSs558aRwj2ig9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">make a copy of this template</a>.</h4> <p>The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events between January and December 2025. <strong><em>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXc0n6JazlFK_6t1b7FvG1YIVXSTUj7mZB43a0hIRIm7_MiawQnnps_llr4FPdP0IVvmzLx7W3BT0qRpDavZgDi86S63lSO7Ax24QTGhWoDJLbXkWBngOnebbwXShIMNpr6Gw7acgsvM35yIb5RZ5lmrVhI?key=VwxjOnrHw844IDJahZBDiQ" alt=""></p> <p><em>Screenshot of our application form information section</em></p> <p><strong>Overview of the second 2024 round of OBF Event Fellowship</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In the second round of 2024 (August 2024), we received numerous applications, and four applicants were selected for funding to support their participation in various events. <strong>Congratulations to the following recipients</strong>:</p> <ol> <li>Jacob González Isa: The 1st Congress by The Spanish Society of Bioinformatics and Computational Biology.</li> <li>Tanakamol Mahawan: Asia &amp; Pacific Bioinformatics Joint Conference 2024.</li> <li>Masturina Binti Md Mansor:  Asia &amp; Pacific Bioinformatics Joint Conference 2024.</li> <li>Keerthana P.: Transatlantic Behavioral Neuroscience Summer School 2024, Mikolajki, Poland.</li> </ol> <p>We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:</p> <p><strong>Urszula Włodkowska</strong> summarised their experience attending the University of Waterloo’s Nengo Summer School with the help from OBF Event Fellowships. You can read about their journey here: <a href="https://www.open-bio.org/2024/07/18/urszula-building-brains/"><strong>Building Brains in Canada</strong></a> <strong>.</strong></p> <p><strong>Zehra Köksal</strong> received the award to present their work at the International Society of Forensic Genetics (ISFG) in Spain and shared <a href="https://www.open-bio.org/2024/09/26/zehra-koksal-isfg-experience/"><strong>their story here</strong></a>.</p> <p><strong>Felipe Castañeda</strong> attended an online EMBL-EBI Cancer Genomics and Transcriptomics 2024 course, with registration fee covered by OBF event fellowship. They reported <a href="https://www.open-bio.org/2024/10/05/with-a-little-help-from-your-friends/"><strong>their experience here</strong></a>.</p> <p>Congratulations to all of our awardees!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and</strong> <a href="https://www.open-bio.org/event-awards/"><strong>apply for the fellowship</strong></a> <strong>before 1 December 2024.</strong></p>https://www.open-bio.org/2024/10/05/with-a-little-help-from-your-friends/Sat, 05 Oct 2024 05:12:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/10/05/with-a-little-help-from-your-friends/<p><em>The</em> <a href="https://www.open-bio.org/travel-awards"><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></a> <em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Felipe de Jesús Castañeda Córdova,</em> an MD/MS student from LIIGH-UNAM (Laboratorio Internacional para la Investigacion sobre el Genoma Humano) Mexico <em>was awarded an OBF Event Fellowship to attend</em> <em>the</em> <a href="https://www.ebi.ac.uk/training/events/cancer-genomics-and-transcriptomics/">EMBL-EBI Cancer Genomics and Transcriptomics 2024</a>.</p> <p>My name is Felipe de Jesús Castañeda Córdova. I am an MD/MS student from Mexico, primarily focusing on the wet lab aspect of lab work at the Cancer Genetics and Bioinformatics Lab. I had limited experience with bioinformatics (I performed some transcriptomic analyses for my master’s project, and I got the bug!), so I decided to apply to the online EMBL-EBI Cancer Genomics and Transcriptomics 2024 course. I was fortunate to be accepted into the program and receive an OBF Event Fellowship, which helped me cover the registration fee.</p> <p>The EMBL-EBI Cancer Genomics and Transcriptomics 2024 course was a week-long intensive course aimed at an international audience. It focused on the theoretical and practical aspects of the most popular bioinformatics analysis tools for cancer research. Despite the time difference between Europe and home, I really enjoyed the entire course. Most of the theoretical classes were inspiring, and the practical portions helped ground our knowledge and resolve most of the questions and doubts that came up as we worked on our scripts. I liked the RNA-seq part of the course, probably because of my previous experience with the subject. Student experience and participation enhanced this section by helping to address many of the questions that typically arise when interpreting GSEA results. During the practical sessions, we had the chance to engage with other students and learn more about their projects and research.</p> <p>I have already started using the skills and insights gained from this course to impact my research. I am reanalyzing my transcriptomic data, considering the new parameters we discussed during the course, and I am excited to apply the new programs and techniques we were introduced to.</p> <p>The knowledge I gained from this experience goes beyond technical skills. It has broadened my perspective and deepened my understanding of the bioinformatics community as a whole. It has made me more aware that regardless of our geographical location, we all encounter similar challenges and obstacles. It has also emphasized the importance of collaboration and continuous learning, which are essential for progress in this rapidly evolving field.</p> <p>I am deeply grateful to the Open Bioinformatics Foundation for providing me with this fellowship and the opportunity to attend the EMBL-EBI Cancer Genomics and Transcriptomics 2024 course. The experience has been immensely rewarding, both professionally and personally. I encourage anyone interested in bioinformatics to consider participating in such events and to take advantage of the opportunities offered by organizations like the OBF.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/10/Felipe_EMBL.jpg" alt="Screenshot of the online participants in the EMBL-EBI Cancer Genomics and Transcriptomics 2024 course"></p>https://www.open-bio.org/2024/09/26/zehra-koksal-isfg-experience/Thu, 26 Sep 2024 06:37:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/09/26/zehra-koksal-isfg-experience/<p><em>The</em> <a href="https://www.open-bio.org/travel-awards"><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></a> <em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Zehra Köksal, a Research assistant at</em> <em>the University Of Copenhagen</em> <em>and Karolinska Institute was awarded an OBF Event Fellowship to attend</em> <em>the <a href="https://isfg2024.com/">30th Congress of the International Society for Forensic Genetics</a></em>.</p> <p>In September 2024, the Open Bioinformatics Foundation enabled me to attend the biennial conference for Forensic Geneticists from the biggest forensic genetics society worldwide – the International Society of Forensic Genetics (ISFG) - that took place in Santiago de Compostela in beautiful Spain.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/09/image-2.png" alt=""></p> <p><em>River in Ribadeo, Ría de Ribadeo o del Eo, separating Galicia and Asturias.</em></p> <p>To appreciate the beauty of Spain prior to the conference, I embarked on a journey along the northern coast of Spain from Cantabria over Asturias and finally to Galicia, where the pilgrimage town Santiago de Compostela is located. My first lesson from this journey was that the north of Spain is not called “Green Spain” for no reason.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/09/image-3.png" alt=""></p> <p><em>Cathedral in Santiago de Compostela.</em></p> <p>Around 1,000 forensic experts attended the ISFG2024 in Santiago de Compostela. One of these experts was me! Attending the ISFG2024 has been extremely valuable for me personally and professionally.</p> <p><strong>#1 Connecting with peers and experts</strong></p> <p>I was able to meet previous colleagues and collaborators spread across the globe. I reconnected with old study mates, celebrated our successes, discussed our career paths, and motivated and inspired each other. I could exchange PhD experiences with peers, meet my mentor and role models, and receive invaluable advice from them.</p> <p><strong>#2 Looking beyond everyday research</strong></p> <p>Our daily work revolves around research and academia. Thus, it was very important to look beyond this by talking to government-funded institutions and commissions to widen my horizon and get different stimulations to gain creativity.</p> <p><strong>#3 Updating on current research in the field</strong></p> <p>The scientific program was extremely stimulating, with great key notes and presentations. I particularly enjoyed the presentations on forensic microbiology and phenotyping, among many other interesting topics covered by experts.</p> <p><strong>#4 My talk</strong></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/09/image.png" alt=""></p> <p><em>Starting my presentation on our software PhyloImpute.</em></p> <p>This leads me to presenting my work in a 10-minute talk in front of 1000 experts. In my talk “PHYLOIMPUTE – Impute missing data on non-recombining DNA using SNP phylogeny” I presented a new software I was working on over the last months for imputing missing SNP data. The main goals of my talk were to convey the need for my tool and its algorithm in a simple and entertaining way with interesting storytelling and visual aids. Further, I wanted to make my tool accessible to people with different degrees of experience and interest in programming. Thus, I provided both a command-line tool (available via <a href="https://github.com/ZehraKoksal/PhyloImpute">https://github.com/ZehraKoksal/PhyloImpute</a>) and a graphical user interface (available via <a href="https://zehrakoksal.com/Y_software.html">https://zehrakoksal.com/Y_software.html</a>). With accessibility being a major goal, I had also made a video tutorial that I uploaded on my new webpage. Since one rarely gets an audience that big, I used this opportunity well and received great interest after my talk. Although nerve-wracking beforehand, presenting my work in front of so many experts was also a very calming and extremely rewarding experience that I will not forget so easily.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/09/image-1.png" alt=""></p> <p><em>Concluding my presentation on our software PhyloImpute.</em></p> <p>Finally, I want to express my deepest gratitude to the Open Bioinformatics Foundation for supporting me on this journey. Particularly as a recent PhD graduate – a time of great changes – attending conferences like these is so important professionally and personally. Feeling supported when celebrating small successes is a big motivator. So, with this, I am encouraging everyone reading this to apply for the fellowship offered by the Open Bioinformatics Foundation!</p>https://www.open-bio.org/2024/09/17/bosc-2024-videos-now-available/Tue, 17 Sep 2024 17:52:12 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/09/17/bosc-2024-videos-now-available/<p>The talk videos from BOSC 2024 are now available on <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZUNv8DStG8LC1I9-MoUgMh">YouTube.</a> They are also linked from the <a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-schedule/#talks">BOSC talk schedule</a> (scroll down to &ldquo;Talks&rdquo;).</p> <p>Stay tuned - our full report on BOSC 2024 will be published soon!</p>https://www.open-bio.org/2024/08/20/meeting-minutes-after-2019/Tue, 20 Aug 2024 17:28:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/08/20/meeting-minutes-after-2019/<p>Starting in July 2019, OBF Board public meeting minutes can be found in <a href="https://github.com/OBF/obf-docs/tree/master/minutes">our GitHub repository</a>.</p>https://www.open-bio.org/events/bosc-2024/bosc-2024-sponsors/Tue, 20 Aug 2024 12:30:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2024/bosc-2024-sponsors/<h1 id="sponsoring-bosc-2024">Sponsoring BOSC 2024</h1> <p>We are thrilled to announce the four sponsors of BOSC 2024! Big thanks to these excellent organizations for supporting open source bioinformatics and enabling us to offer free registration to some qualified participants!</p> <h3 id="platinum-sponsors">Platinum Sponsors:</h3> <p><a href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" alt="seqera"></a></p> <p>Seqera makes complex data analysis accessible at any scale<a href="https://chanzuckerberg.com/science"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="CZI"></a></p> <p><strong>Gold Sponsor:</strong></p> <p><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Data Science"></a></p> <p><strong>Silver Sponsor:</strong></p> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Geraldine-BoF-composite.png" alt="Screenshot from BOSC 2021"></p> <p>Sponsorships from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some conference participants. In 2023, thanks to our <a href="https://www.open-bio.org/events/sponsors-2023/">sponsors&rsquo;</a> generous support, we were able to grant free registration to 15 participants (13 from underrepresented groups) at <a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a>, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you’re interested in sponsoring BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p>Thanks to our 2021 sponsors, we were able to offer free ISMB/ECCB 2021 registration to 20 participants from all over the world! <iframe loading="lazy" src="https://www.google.com/maps/d/embed?mid=1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width="640" height="480"> </iframe> </p> <h2 id="what-is-bosc">What is BOSC?</h2> <p>BOSC is an annual meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. Whether in-person or online, each BOSC ​includes ​talks,​ ​poster​ ​sessions,​ ​birds-of-a-feather gatherings, and ​lots​ ​of​ ​opportunities​ ​for​ ​networking. It is followed by​ ​collaborative​ ​working​ ​sessions​ ​at the CollaborationFest.​ ​These​ ​events​ ​bring​ ​together​ ​software​ ​engineers,​ ​bioinformaticians,​ ​and​ ​researchers​ ​to collaborate​ ​and​ ​extend​ ​open​ ​source​ ​bioinformatics​ ​tools.</p> <p>Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB). In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>. In July 2020, BOSC again joined forces with GCC to form the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>. Held online, BCC2020 attracted over 600 participants from 62 countries. <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> was part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, and took place July 29-30, 2021 (followed by a two-day <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest</a>).</p> <p><a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> was held July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> in person in Madison, Wisconsin, USA, and simultaneously online.</p> <p><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a> took place July 24-25, 2023 as part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> in Lyon, France and online. Like the previous year, we joined forces with Bio-Ontologies for part of a day!</p> <p><a href="https://www.open-bio.org/events/bosc-2024/">BOSC 2024</a>, the 25th annual Bioinformatics Open Source Conference, will take place July 15-16, 2024 as part of <a href="https://www.iscb.org/ismb2024/home">ISMB 2024</a> in Montreal, Canada and online.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/OBF-BoF-2018-25-300x225.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/43248502932_2395bc3cc6_z-300x200.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2017-panel-1.jpg" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Jason-PeterSelby-FotisPsomopoulos-DhrithiDespande.png" alt=""></p> <p>BOSC​ ​participants​ ​come​ ​from​ ​a​ ​wide​ ​variety​ ​of​ ​research​ ​environments​ ​and​ ​backgrounds:</p> <ul> <li> <p>Biological​ ​researchers,​ ​students,​ ​and​ ​post-docs​ ​who​ ​​ ​are​ ​learning​ ​bioinformatics​ ​analysis tools and techniques</p> </li> <li> <p>Power​ ​bioinformatics​ ​users</p> </li> <li> <p>Bioinformatics​ ​tool​ ​and​ ​workflow​ ​developers</p> </li> <li> <p>Bioinformatics​-focused​ ​principal​ ​investigators​ ​and​ ​researchers</p> </li> <li> <p>Sequencing​ ​core​ ​facility​ ​staff</p> </li> <li> <p>Industry​ ​scientists​ ​and​ ​bioinformaticians</p> </li> <li> <p>Data​ ​producers</p> </li> </ul> <h1 id="previous-events">Previous Events</h1> <p>The​ ​OBF​ ​has​ ​organized​ ​BOSC​ ​ <a href="https://www.open-bio.org/events/bosc/about/">every​ ​year​ ​since​ ​2000</a>.​ From 2000 to 2017 and again in 2019,​ ​BOSC​ ​was ​run​ ​as​ ​part​ ​of​ ​the​ ​large​ ​ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference.​ ​The​ ​OBF​ ​CodeFest​s (now renamed CollaborationFest, or CoFest) have ​been​ ​held​ ​every​ ​year​ after BOSC ​since​ ​2010.</p> <p>The table below shows the approximate number of participants in BOSC and the CoFest. Figures​ ​for​ ​the​ ​CoFest​ ​and​ ​BOSC​ ​are​ ​number​ ​of​ ​people​ ​registered​ ​for​ ​at​ ​least​ ​one​ ​day​ ​of​ ​the​ ​meeting.​ ​The​ ​BOSC figures​ ​do​ ​not​ ​include​ ​drop-in​ ​attendees​ ​from​ ​the​ ​parallel​ ​sessions​ ​organized​ ​by​ ​other​ ​groups.​ ​The​ ​figures​ ​for CoFest​ ​do​ ​not​ ​include​ ​remote​ ​participants.</p> <p>YearLocation BOSC Participants (approximate)CoFest Participants 2023BOSC 2023: Lyon, France and virtual200<del>152022BOSC 2022: Madison, WI, USA and virtual200</del>152021BOSC 2021: virtual200<del>252020BCC2020 (BOSC + Galaxy): virtual300</del>1502019Basel, Switzerland109352018 Portland, OR, USA1501002017 Prague, Czech Republic 230652016 Orlando, FL, USA90362015Dublin, Ireland125352014Boston, MA, USA100602013Berlin, Germany100372012Long Beach, CA, USA 100132011 Vienna, Austria 12035</p> <h1 id="sponsorship">Sponsorship</h1> <p>We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to</p> <ul> <li>offer free registration to some BOSC participants</li> <li>support the <a href="https://www.open-bio.org/travel-awards/">OBF&rsquo;s Event Fellowship program</a>, increasing participation from underrepresented groups</li> <li>provide child care at the conference</li> <li>underwrite the cost of conference events such as dinners or refreshments at poster sessions</li> <li>help defray the cost of videography</li> <li>provide space and catering at the CoFest</li> <li>offer honoraria to keynote speakers</li> <li>pay for captioning and translations</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/BOSC2020-party-attendees-e1609719125821.png" alt=""></p> <h2 id="sponsoring-bosc">Sponsoring BOSC</h2> <p>Sponsorships from private companies and organizations help to defray some of our costs and allow us to offer registration fee waivers to some attendees. If you are interested in becoming a BOSC sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <h1 id="benefits-of-sponsorship">Benefits of Sponsorship</h1> <p>We acknowledge our sponsors before, during and after the event in multiple ways:</p> <ul> <li>We list our sponsors on the BOSC website</li> <li>Sponsors are thanked and named in the introduction/closing slides during the meeting</li> <li>We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area</li> <li>The sponsors are thanked in selected emails to our mailing list, tweets and blog posts (with your logo) that go out before, during and after the event</li> <li>The sponsors are listed in our published reports after the meeting, e.g., <a href="https://f1000research.com/articles/7-1309/v1">https://f1000research.com/articles/7-1309/v1</a></li> <li>We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.</li> </ul> <h1 id="sponsors-from-previous-years">Sponsors from previous years</h1> <h2 id="bosc-2023-platinum-sponsor">BOSC 2023 Platinum Sponsor</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a></p> <h3 id="bosc-2023-silver-sponsors">BOSC 2023 Silver Sponsors</h3> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a><a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a><a href="https://www.software.ac.uk/"><img src="https://www.open-bio.org/wp-content/uploads/2023/04/SSI_PRIMARY-LOGO-300x96.png" alt="SSI logo"></a></p> <h2 id="bosc-2022-platinum-sponsors">BOSC 2022 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a></p> <h2 id="bosc-2022-gold-sponsors">BOSC 2022 Gold Sponsors</h2> <p><a href="https://www.broadinstitute.org/data-sciences-platform"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/Broad-DSP-logo-1.png" alt="Broad Institute Data Science Platform"></a><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Office of Data Science Strategy"></a></p> <h3 id="bosc-2022-silver-sponsors">BOSC 2022 Silver Sponsors</h3> <p><a href="https://arvados.org"><img src="https://www.open-bio.org/wp-content/uploads/2022/05/ArvadosCurii.png" alt="Arvados, supported by Curii"></a><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="Gigascience"></a></p> <h2 id="bosc-2021-platinum-sponsors">BOSC 2021 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="https://www.alzheimersdata.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/ADDI_Logo_FullColor_Vert_RGB.png" alt="Alzheimer’s Disease Data Initiative"></a></p> <h2 id="bosc-2021-gold-sponsors">BOSC 2021 Gold Sponsors</h2> <p><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a><a href="https://www.broadinstitute.org/"><img src="https://www.broadinstitute.org/files/news/media-images/logos//BroadInstLogoforDigitalRGB.png" alt="Broad Institute Logo"></a></p> <h2 id="bosc-2021-silver-sponsors">BOSC 2021 Silver Sponsors</h2> <p><a href="https://elifesciences.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/04/image.png" alt=""></a> <a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a> <a href="https://oup.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/OUP_logo_navy.png" alt="Oxford University Press"></a><a href="https://bioteam.net"><img src="https://www.open-bio.org/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png" alt=""></a></p> <p>If you are interested in becoming a sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p>https://www.open-bio.org/2024/08/02/my-amazing-bosc-2024-experience/Fri, 02 Aug 2024 18:00:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/08/02/my-amazing-bosc-2024-experience/<p>By Beatrice Mihalache</p> <p>Examining open source projects has been most useful to me while I am sharpening my coding skills, so I was excited to learn about the Bioinformatics Open Source Conference &ndash; BOSC.  I am a rising senior at UCLA, studying biophysics and data science. I strongly believe in open source, so I submitted the work I’d done with my PI and my grad student collaborator for a poster presentation at BOSC. My research lab at UCLA allocates conference participation funds only for graduate students, therefore I also included a request for fee waiver with my conference submission. I was excited when a few weeks later I received notification that not only I was accepted as a poster presenter, but that I also got free registration to both BOSC and to the entire ISMB (Intelligent Systems for Molecular Biology) conference!</p> <p>Attending BOSC and ISMB was such an incredible experience. On Saturday and Sunday I attended different sub-conferences at ISMB including multiple talks on deep-learning applications to biological problems such as enzyme design and protein function prediction. I was stoked and humbled by how much I learned. The coffee and lunch breaks were a super welcome opportunity to network and talk to other poster presenters about their research.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXcQvVjt6ypqukDzqvX0OGY0301oezGK3Jd2CES6sLWvBwcU2O7kcmFW4Di-SXyfHabCknTOh3ss8h5DDSYN3Z3UBspLGnyX5ZxhxbSXpB5xqFe6X-tP5LhkIQdTtBRHrlomPbApoz475fRiD7_Xv4ROniY?key=SCgC-vPc28I0Qz9ZVx4WgQ" alt=""></p> <p>Palais de Congress, the conference venue, at night. The colorful window architecture is cool.</p> <p>On Monday, BOSC kicked off with Melanie Courtot’s keynote about the necessity for better quality data. I learned more about Findable, Accessible, Interoperable, Reusable (FAIR) code, as this was never explicitly mentioned in any of my computer science classes at school.</p> <p>Tuesday’s talks were also very cool, the most memorable to me being Andrew Su’s keynote, specifically the part where he had us imagine what AI would be like in the future. In a world that is changing at an accelerated pace, this is a difficult exercise, but a valuable one that also gives insight into the skills that will be most valued in future researchers such as creativity and linking interdisciplinary applications together well.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXcu4o3GqEuq0L7cJ68VJS4LZ3nemVE7lqnmmT3ULlesp8njx6BSV0L8M0MYZcpf5EzI9eD9YKnPHx92a25IC8WUTU2Srv0j7WeWMiqddRcpZSFrZ812b9NA7Eb3oV1lol3hY_1EOAxfuGVMn38bWMdt7io?key=SCgC-vPc28I0Qz9ZVx4WgQ" alt=""></p> <p>Me in front of my poster at BOSC, enjoying this most awesome experience</p> <p>One of my favorite conference experiences was going to dinner with some of the conference attendees. Monday night we ate at LOV McGill, an impressively delicious vegan restaurant. It was so valuable to personally connect with people. I sat between Andrew Su, a professor and researcher at Scripps who would be giving the next day’s keynote, and Bhavesh Patel, the founder of the FAIR data innovations hub. It was nice to learn about people’s personal experiences, about how they got to where they are, and also random snippets and stories.</p> <p>I am most grateful to BOSC’s sponsors Seqera, NIH ODSS, the Chan Zuckerberg Initiative, and GigaScience for helping me attend BOSC. This experience has been invaluable. I am inspired and energized by it. I look forward to applying the things I’ve learned to new projects. I will make sure that all my future projects’ code is FAIR.</p> <p><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXe4jDmLLj-B8rDE7LedEpZgcbnuB1MwENZrK-RVFhIx5bZBXxK_OQ_2agVe92yscE1M0cyfuZAj-NvB9z1P0tgbyEalobVkpGF-RS5mVM6ZMDpyuwpCchkP2c9eKr00_DgiOPaPLJ5nOpP-8zJ2V6aKrvo?key=SCgC-vPc28I0Qz9ZVx4WgQ" alt=""></p> <p>The conference was hosted in Montreal, and I had never been there before, so I took this trip as an opportunity to do some sightseeing and exploring, by staying a few extra days after the conference. I was impressed by how well Montreal blends the old architecture with the modern. I climbed the stairs of Mont Royal, ate poutine with some friends I made at the conference, and visited the Museum of Fine Arts and the Archeology and History Museum.</p>https://www.open-bio.org/2024/07/18/urszula-building-brains/Thu, 18 Jul 2024 12:11:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/07/18/urszula-building-brains/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Urszula Włodkowska,</em></strong> <em><strong>a PhD Researcher at</strong></em> <em><strong>the</strong></em> <strong><em>Nencki Institute of Experimental Biology PAS was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the</strong></em> <strong><em><a href="https://www.nengo.ai/summer-school/">University of Waterloo’s Nengo Summer School</a></em></strong>.</p> <p>In June of 2024, I had a great opportunity to attend the University of Waterloo’s Nengo Summer School (also known as Brain Camp). This was only possible thanks to the fellowship I received from the Open Bioinformatics Foundation.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/07/IMG_1711-scaled.jpg" alt=""> <em>Urszula</em> <em>Presenting her project to the group</em>.</p> <p>This summer school was an important event for many reasons. First, I was excited to learn about the Nengo simulation package (<a href="https://www.nengo.ai/)">https://www.nengo.ai/)</a>, which is a powerful platform for designing cognitive and neural systems. Nengo has recently become open source, and for me, using open tools means having not only a better understanding of how they work but also being able to contribute to and influence their growth. This creates a community of users that give back and support each other. The fact that Nengo is newly open source also provided a unique opportunity to talk to the creators about the challenges of transitioning into that mode.</p> <p>The Nengo Summer School also provided an introduction to the Neural Engineering Framework. The NEF has been developed by the Computational Neuroscience Research Group led by Chris Eliasmith at the Waterloo Centre for Theoretical Neuroscience as a tool for understanding neurobiological principles through constructing simulations of neural systems. Learning about it provided a satisfyingly complete view of the subject - connecting tools with theory and reasoning behind how the tools have been constructed.</p> <p>The two weeks I spent in Waterloo were intense. The first week focused on the introduction to the framework and practical tutorials translating theory into code. On top of that, with other participants and TAs we discussed projects that everyone brought with them to work on during the school, looking for common interests and ways to collaborate. During the second week, we worked on our projects and attended tutorials on advanced applications of Nengo. The school ended with project presentations - first, for other participants, and then in an open event at the University of Waterloo.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/07/IMG_1563-scaled.jpg" alt=""> <em>Tutorial at the Waterloo Centre for Theoretical Neuroscience</em></p> <p>My project focused on simulating how a mouse learns to optimally explore the environment while gradually learning the rules governing the behavioral setup. I learned a lot, especially thanks to the help of one of the TAs - Nicole Dumont. I intend to continue working on this project, so the summer school leaves a lasting impression on my research.</p> <p>But my personal gain was not the only reason I wanted to attend this school. As a part of the Nencki Open Lab initiative (<a href="https://nenckiopenlab.org/">https://nenckiopenlab.org/</a>) that connects young neuroscience researchers from underprivileged regions, I always see the events I attend as an opportunity to share the knowledge and connections I’ve made with others. The Nencki Open Lab events touch on two aspects - teaching people how to use open tools and how to approach research as a part of a bigger picture, connecting theory and practice. The Nengo Summer School helped me grow in both of these areas and I hope to bring the concepts and the people I’ve met there to our own summer schools.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/07/IMG_1518-scaled.jpg" alt=""> <em>Group photo of this year’s attendees and teachers</em></p>https://www.open-bio.org/2024/06/28/biopython-1-84-released/Fri, 28 Jun 2024 05:43:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/06/28/biopython-1-84-released/<p>Biopython 1.84 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.84">PyPI</a>.</p> <p>This contains about 5 months worth of updates, so the <a href="https://github.com/biopython/biopython/blob/biopython-184/NEWS.rst">change-log in the news file</a> is longer than usual. There have also been a few <a href="https://github.com/biopython/biopython/blob/biopython-184/DEPRECATED.rst">deprecations</a>, most noteworthy this may be our last release with Python 3.9 support.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Anil Tuncel (first contribution)</li> <li>David Cain</li> <li>Fabio Zanini (first contribution)</li> <li>Joao Rodrigues</li> <li>Judith Bernett (first contribution)</li> <li>Luca Monari (first contribution)</li> <li>Meridia Jane Bryant (first contribution)</li> <li>Manuel Lera-Ramirez</li> <li>Michael M. (first contribution)</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Rudolf Koopmann (first contribution)</li> <li>Will Tyler (first contribution)</li> </ul>https://www.open-bio.org/2024/06/18/event-fellowship-2024-2/Tue, 18 Jun 2024 13:05:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/06/18/event-fellowship-2024-2/<h4 id="the-call-for-applications-for-the-obf-event-fellowship-2024-round-2-is-now-open-the-deadline-for-this-round-is-1-august-2024-applications-should-be-submitted-via-this-google-form-we-have-provided-a-word-template-to-help-you-draft-the-application-locally-before-filling-out-the-form--make-a-copy-of-this-template">The call for applications for the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> 2024, <strong>round 2</strong>, is now open. <strong>The deadline for this round is 1 August 2024.</strong> Applications should be submitted via <a href="https://forms.gle/D31zSs558aRwj2ig9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">make a copy of this template</a>.</h4> <p>The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from September 2024 to March 2025. <strong><em>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><img src="https://lh7-us.googleusercontent.com/docsz/AD_4nXd6eliHUFKvP0PF3_fOqwg3kfEOF0DSw7cX1jeHwa6RSwYv8ljheRNND-COMhpOnZCz2ZEM-8ZmBgcTwnCxsSmSFqy8TuzCw2Zziyriwdp_OSo0-LA8tCnsrZISaZehD29gI36KBfDHvg8iO3VHUKLG94E?key=ci7wLwVjJQAhdiqV6_gubA" alt=""></p> <p><em>Screenshot of our application form information section</em></p> <p><strong>Overview of the first round of OBF Event Fellowship 2024</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. Starting in 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In the first round of 2024 (April 2024), we received numerous applications, and seven applicants were selected for funding to support their participation in various events. <strong>Congratulations to the following recipients</strong>:</p> <ol> <li>Urszula Włodkowska: Nengo Summer School</li> <li>Tolulope Uzoka: Bioinformatics for Immunologists/EMBL-EBI Training</li> <li>Sushma Naithani: BOSC 2024</li> <li>Li Chuin Chong: 23rd European Conference on Computational Biology (ECCB2024)</li> <li>Zehra Köksal: 30th Congress of the International Society for Forensic Genetics</li> <li>Erin (Rin) Krichilsky: International Congress of Entomology (ICE)</li> <li>Felipe Castañeda: Cancer Genomics and Transcriptomics 2024</li> </ol> <p>This fellowship will provide financial support to enable them to attend the aforementioned events.</p> <p>We recently published a blog post from our latest awardee summarising their experience attending an event with help from OBF Event Fellowships:</p> <p>Thea Fennell: <a href="https://www.open-bio.org/2024/03/27/open-data-open-doors/"><strong>Open Data, Open Doors</strong></a></p> <p>Congratulations to all of our awardees!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and apply for the fellowship before 1 August 2024.</strong></p>https://www.open-bio.org/2024/06/14/join-us-for-cofest-2024/Fri, 14 Jun 2024 18:20:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/06/14/join-us-for-cofest-2024/<p>This year will mark the 15th edition of the BOSC-associated CollaborationFest, or CoFest for short. At these events, participants work together on code, documentation, training materials, use cases, and analyses.</p> <p>CoFest 2024 will take place on July 17-18, right after ISMB and BOSC 2024. This will be a hybrid event, hosted at <a href="https://www.linkedin.com/company/uqam/">UQAM | Université du Québec à Montréal</a> and online. Many thanks to Abdoulaye Baniré Diallo , BF Francis Ouellette, and Karen Reynard for finding and donating the use of this venue!</p> <p>Interested in joining us to discuss and contribute to open-source and open-science projects? Registration is free but mandatory. More information, and link to register, is available at <a href="https://www.open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/">/events/bosc-2024/obf-bosc-collaborationfest-2024/</a></p> <div class="box"> <figure><img src="https://www.open-bio.org/wp-content/uploads/2023/08/CoFest2023-lunch-1-216x300.png" width="317"> </figure> </div> https://www.open-bio.org/events/bosc-2024/bosc-2024-panel/Fri, 07 Jun 2024 23:04:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2024/bosc-2024-panel/<h1 id="open-source-aiml-a-game-changer-for-bioinformatics">Open Source AI/ML: A Game Changer for Bioinformatics?</h1> <p>Tired of locked-away algorithms hindering your research? This panel dives into the exciting world of open-source AI/ML for bioinformatics. Join BOSC in a conversation with renowned experts as they explore the potential of open models to revolutionize the field.</p> <p><strong>Uncover the advantages:</strong></p> <ul> <li>Transparency: Gain deeper insights into model training, fostering trust and ethical practices.</li> <li>Collaborative Power: Leverage the collective brilliance of a global community for faster innovation.</li> </ul> <p><strong>But is it all sunshine and rainbows?</strong></p> <ul> <li>Data Limitations: Open models often rely on publicly available data, which might lack diversity and introduce bias.</li> <li>Resource Constraints: Open-source projects can struggle with funding and computational power, impacting performance.</li> </ul> <p><strong>This panel tackles these challenges head-on, offering:</strong></p> <ul> <li>Expert Insights: Learn from leading figures in open-source AI/ML bioinformatics.</li> <li>Q&amp;A: Unleash your burning questions about the future of open models.</li> </ul> <p>Join us for the final session of BOSC 2024. Don&rsquo;t miss this chance to explore the potential of open-source AI/ML to propel your bioinformatics research to new heights!</p> <h2 id="panelists">Panelists</h2> <h3 id="lawrence-hunter">Lawrence Hunter</h3> <div class="splitbox"><div class="left"> <p>Dr. Lawrence Hunter is widely recognized as one of the founders of bioinformatics. He published some of the first papers in biomedical NLP and in machine learning predictions of molecular function; he served as the first President of the International Society for Computational Biology (ISCB); and he created several of the most important conferences in the field, including ISMB, PSB and the Rocky Mountain Conference on Bioinformatics. Dr. Hunter&rsquo;s research interests span a wide range of areas, from cognitive science to rational drug design. He has published more than 200 scientific papers, holds two patents and has been elected a fellow of both the ISCB and the American College of Medical Informatics. Dr. Hunter is a professor at the University of Chicago.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/06/3697B1D6-F058-4C25-8A43-6D13C5025F8E.jpeg" alt="Larry Hunter"></p> </div><div style="clear:both"></div></div> <h3 id="thomas-hervé-mboa-nkoudou">Thomas Hervé Mboa Nkoudou</h3> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/06/Thomas-Mboa-1-1.png" alt="Thomas Mboa"></p> </div><div class="right"> <p>Dr. Thomas Mboa is a social scientist with a focus on Responsible AI, Open Science and knowledge transfer. He is currently Researcher in Residence at the International Centre of Expertise In Montreal on Artificial Intelligence (CEIMIA), where his main mission is to put in place mechanisms to ensure a better representation of Africa in the international ecosystem of Artificial Intelligence. The Mboalab Biotech, a collaborative space founded by Dr. Mboa, hosts community-focused technology projects including the ML-enhanced Open Diseases Screener App, which can diagnose diseases such as malaria, typhoid fever and many other tropical diseases. To learn more about Dr. Mboa&rsquo;s work, visit <a href="https://orcid.org/0000-0001-9678-7765">https://orcid.org/0000-0001-9678-7765</a>.</p> </div><div style="clear:both"></div></div> <h3 id="mélanie-courtot">Mélanie Courtot</h3> <div class="splitbox"><div class="left"> <p>Dr Mélanie Courtot is the Director of Genome Informatics at the Ontario Institute for Cancer Research in Toronto, and an Assistant Professor in the Department of Medical Biophysics at University of Toronto. Dr Courtot&rsquo;s focus is translational informatics - designing intelligent systems to gain new insights and build a globally shared knowledge ecosystem to advance science and improve health for all. Dr Courtot co-leads the Clinical and Phenotypic workstream and Data Use and Cohort representation groups for the Global Alliance for Genomics and Health (GA4GH) as well as cohort harmonization efforts for the International HundredK+ Cohorts Consortium.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/06/Melane_Courtot_square-1.png" alt="Mélanie Courtot"></p> </div><div style="clear:both"></div></div> <h3 id="andrew-su">Andrew Su</h3> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/03/Andrew_Su_smll.jpg" alt="Andrew Su"></p> </div><div class="right"> <p>Andrew Su, Ph.D., is the Elden and Verna Strahm Professor at the Scripps Research Institute in the Department of Integrative Structural and Computational Biology (ISCB). Dr. Su&rsquo;s lab focuses on building and applying bioinformatics infrastructure for biomedical discovery. Dr. Su has had a long-standing interest in leveraging crowdsourcing to organize and integrate knowledge though projects like the Gene Wiki and Wikidata. He has also worked extensively on creating biomedical APIs and enabling API interoperability through the BioThings project, and on constructing and mining knowledge graphs for drug repurposing.</p> </div><div style="clear:both"></div></div> <h3 id="moderator-monica-munoz-torres">MODERATOR: Monica Munoz-Torres</h3> <div class="splitbox"><div class="left"> <p>Dr. Munoz-Torres is an Associate Professor at the University of Colorado Anschutz Medical Campus. She leads the Standards Team and is the Co-chair of the Steering Committee for the NIH-funded program Bridge to Artificial Intelligence (Bridge2AI) Program. She is also the Program Director for the Phenomics First Resource, an NHGRI Center of Excellence in Genomic Science, and for the Monarch Initiative. Dr. Munoz-Torres&rsquo;s expertise, education, and enthusiasm span genomics, biocuration, knowledge representation, and data harmonization – and the development of software tools and standards to advance these fields.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Monica_Munoz-Torres-2.jpeg" alt="Monica Munoz-Torres"></p> </div><div style="clear:both"></div></div> https://www.open-bio.org/events/bosc-2024/bosc-2024-schedule/Fri, 19 Apr 2024 00:09:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2024/bosc-2024-schedule/<h2 id="bosc-2024-keynote-speakers-and-panelists"><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes/">BOSC 2024 keynote speakers and panelists</a></h2> <div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/wp-content/uploads/2025/01/Melanie-Courtot-square.jpeg" alt="Mélanie Courtot" style="width:85%" /> <p><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes">KEYNOTE: Mélanie Courtot: The Data Shows We Need Better Data</a></p> </div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2024/03/Andrew_Su_smll.jpg" alt="Andrew Su" style="width:85%" /> <p><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes">KEYNOTE: Andrew Su: Open Data, Knowledge Graphs, and Large Language Models</a></p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/wp-content/uploads/2024/06/3697B1D6-F058-4C25-8A43-6D13C5025F8E.jpeg" alt="Larry Hunter" style="width:65%" /> </div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2024/06/Thomas-Mboa-1-1.png" alt="Thomas Mboa" style="width:65%" /> </div><div style="clear:both"></div></div> <center> <p><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-panel/">Panel: Open Source AI/ML: A Game Changer for Bioinformatics?</a></p> </center> <br/> <h2 id="bosc-2024-schedule-at-a-glance">BOSC 2024 Schedule at a Glance</h2> <p>(Scroll down more to see the full schedule of talks!)</p> <div style="position: relative; padding-top: 90%;"><iframe style="position: absolute; top: 0; left: 0; width:95%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vRwKVweZ3gqJ0JS0EHXQO1AiDOlRrwn58W-oAz2ELM_9ATuCG-VZAWcTHQGQD8l5PThebpmSq9VzgLj/pubhtml?gid=0&amp;single=true&amp;widget=true&amp;headers=false" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h2 id="talks---bosc-2024">Talks - BOSC 2024</h2> <div style="position: relative; padding-top: 90%;"><iframe style="position: absolute; top: 0; left: 0; width: 150%; height: 99%;" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vRwKVweZ3gqJ0JS0EHXQO1AiDOlRrwn58W-oAz2ELM_9ATuCG-VZAWcTHQGQD8l5PThebpmSq9VzgLj/pubhtml?gid=1729310258&#038;single=true" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h2 id="posters---bosc-2024">Posters - BOSC 2024</h2> <div style="position: relative; padding-top: 85%;"><iframe style="position: absolute; top: 0; left: 0; width: 120%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vRwKVweZ3gqJ0JS0EHXQO1AiDOlRrwn58W-oAz2ELM_9ATuCG-VZAWcTHQGQD8l5PThebpmSq9VzgLj/pubhtml?gid=1094351563&#038;single=true" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <br/> <h5 id="bosc-2023-schedule">(<a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/">BOSC 2023 schedule</a>)</h5>https://www.open-bio.org/2024/04/12/bosc-2024-review-committee/Fri, 12 Apr 2024 16:09:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/04/12/bosc-2024-review-committee/<p>BOSC is an entirely volunteer-run event. We have an organizing committee of 8 people (see /events/bosc-2024/), and we are assisted by a larger review committee. The review committee is responsible for reading all the submitted abstracts and assessing them for quality and appropriateness to BOSC. You can <a href="https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md">read more about our review process here</a>.</p> <p>Our tentative review committee for 2024 is listed below. If you have any concerns about anyone on the list, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> (that mailing list is private to the organizing committee and is not accessible to the larger review committee) or private-message any of the organizing committee members by email or in <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">Slack</a>.</p> <p>Review Committee (tentative): Arpita Joshi, Aziz Khan, Bastian Greshake Tzovaras, bhavesh patel, Christopher Fields, Emmanuel Adamolekun, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, jenea adams, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov, Monica Munoz-Torres, Nehemiah Ongeso, rachel torchet, Seth Carbon, Suruchi Ahuja, Surya Saha, Swapnil Sawant, Tazro Ohta, Titus Brown, Tyrone Chen</p>https://www.open-bio.org/2024/03/27/open-data-open-doors/Wed, 27 Mar 2024 05:34:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/03/27/open-data-open-doors/<h2 id="a-phd-students-perspective-on-attending-the-17th-annual-international-biocuration-conference-in-faridabad-india"><em>A PhD student’s perspective on attending the 17th Annual International Biocuration Conference in Faridabad, India</em></h2> <p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Thea Fennell,</em></strong> <em><strong>a PhD Researcher at</strong></em> <em><strong>the MRC Laboratory of Molecular Biology</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the <a href="https://ibdc.rcb.res.in/biocuration2024/">17th Annual International Biocuration Conference</a></strong></em>.</p> <p>“The best use for your data will be thought of by someone else” — Rufus Pollock encapsulates this concept in all its power and humility. It is at the core of open science and biocuration. Almost by definition, FAIR data is non-proprietary, yet the work done to generate, curate, and share it is invaluable. Recent proceedings at the 17th Annual International Biocuration Conference (AIBC), hosted at the Indian Biological Data Centre (IBDC) in Faridabad, were a testament to this duality.</p> <p><img src="https://lh7-eu.googleusercontent.com/_znLEYPPI90LQLRYscPodWVcLZDXh6t_OCeBEnELQU6_p61csENu_6xSVs2E4Ks2W7HBueK0CxZav8D9ZDxK3iOaycb97x3L4hoZCXciKcVsBN_l1I2leBlfm8zi4PNgc198vLevVRfQRVSFz5tkS34" alt=""><em>The Indian Biological Data Centre, Faridabad, just an hour’s drive from New Delhi.</em></p> <p>Opening the conference, Professor Saurabh Raghuvanshi emphasised the altruistic nature of the field and its principles: integrity, accessibility, and usability. He went on to highlight the milestones reached thanks to this public-minded approach to biodata within India: development of the ZyCoV-D vaccine, widespread HPV vaccine distribution, and establishment of the world’s only Crop Phenome Database. These positive achievements prove what open bioinformatics can do – when there is sufficient political will.</p> <p>This necessary symbiosis between institutional support and open science principles can also be observed at the international level. In the first conference session, covering the International Sequence Database Collaboration (INSDC), Dr Guy Cochrane highlighted how international data sharing has facilitated breakthroughs worldwide: from global virome discoveries to COVID vaccines to – of course – AlphaFold. This initial session also revealed how data standards depend upon institutional policy at multiple levels.</p> <p>Professor Masanori Arita touched not only on how academic publishing companies have begun to mandate data submission to the INSDC – connecting primary researchers to data sharing by default – but also on growing links to industry data, such as through liaison with the Japanese and Korean Patent Offices. Meanwhile, the constituent members of the INSDC – the DNA Data Bank of Japan (DDBNJ), the European Bioinformatics Institute (EBI), and the National Centre for Biotechnology Information (NCBI) – are themselves governmental institutions with a corresponding role to play in shaping data policy.</p> <p><img src="https://lh7-eu.googleusercontent.com/l2YgrK-ZgfJv4eOFrXkFLt5poDKaUhSSbF2lARwpWhObuATTECFb-Zd8krqk5rv1doNkbtJEfY18r5YwcQGbqXvMfe-UfYgQEynojiLhCYD-E-t0D92THeT5kE0DRgl07Iq9NTogtZJeTaAarxRicNI" alt=""><em>The 17th AIBC was ceremonially inaugurated by Minister of State, Dr Jitendra Singh.</em></p> <p>International collaboration remained a key theme throughout the proceedings in the context of various global concerns, from food security to epidemiological modelling. These collaborations are evidently not without their challenges, as evident from the conference’s session on global biodata. Decentralised collaboration may be an asset in linking efforts more directly to the coalface of primary research. However, it can also lead to conflict regarding scientific or political priorities. These competing interests are writ large in the competing policies on FAIR data – from the Convention on Biology Diversity (CBD) to the World Health Organisation (WHO) to country-specific guidelines.</p> <p>Data accessibility appeared to be an area of particular contention. Professor Arita initiated the discussion, delineating how FAIR principles can conflict with guidelines on indigenous data governance – the CARE principles – reflecting an ambiguity in negotiating accessibility for sensitive data over which specific individuals or groups may reasonably claim authority. This thread was taken up again by Dr Ilene Mizrachi, whose US-based work at NCBI is subject to fewer legal restrictions regarding data ownership, and then again by Dr Harpreet Singh, whose work with the Indian Council of Medical Research necessitates policy compromise in the form of “responsible data sharing”.</p> <p>Despite these difficult and necessary conversations, the overall feeling of the conference was one of optimism. Perhaps, as the speakers took to the stage in the newly built IBDC, they thought of the public good – vaccines, plant breeding, drug development – already enabled by biocuration and the wider world of open bioinformatics. Perhaps, too, they were bolstered by the profession’s reputation for handling complexity, facing challenges not only with intellectual rigour but with informed compassion; what Dr Sarah Davies terms “care-ful work”. Indeed, Dr Davies’ talk – on her ethnographic study of biocurators – provided vital context for the conference (and profession).</p> <p>Outlining the discipline, Dr Davies described biocuration as “being precise and exact […] to support the people in our community”, which aligned well with the technical scholarship and ethical concern showcased throughout the conference. However, she also observed economic precarity among curators, exacerbated by epistemic exclusion and “fauxtomation”. In the words of one of her study’s subjects, many database users see biocurators as “some kind of gnome, that fills the database at night”, diminishing or erasing their scientific contribution and labour without necessarily intending to do so.</p> <p><img src="https://lh7-eu.googleusercontent.com/EG3OHnh0frI3Rjazh-WeHYql4qDCUDrBSNdGajgVUPetTzZ5RqeMKfCkUtkY5HQIbVI1LHwAIOPZztNy3Sdp9bwOaJWP4R7lk87hNSf1H0A-liI0lISS2dOOUR3jcmY7cychyCExHIW25d7dDJnmzHU" alt=""><em>Delegates, speakers, and organisers came together from all around the world.</em></p> <p>Whilst Dr Davies’ talk was the only one to take biocuration itself as the object of study, her findings were consistent with many of the themes that emerged at this year’s AIBC. Economic sustainability, in particular, was a recurring focus – with environmental and social dimensions acknowledged but shelved in the face of even more pressing matters. It transpires that biocuration is precarious not only in terms of individual curators “living on those short-term contracts”, as demonstrated by Dr Davies but also at the institutional level. Dr Lynn Schriml, Professor Arita, Dr Frederic Bastian, and Dr Cochrane focused on the latter scale of economic insecurity and how best to ameliorate it. Dr Schriml, specifically, stressed the importance of database longevity – along with reliability and availability/access – as a pillar of effective biodata sharing and re-use.</p> <p>Altogether, this proved an enlightening exchange for me as an early-career scientist, illuminating the peaks and pitfalls of the funding landscape. It shed light, too, on the transient availability of institutional funding and support. This can, in turn, cause the casualisation of curational labour, contributing to institutions undervaluing biocurators’ expertise and employment. No wonder, then, that so many of the pioneering collaborations covered in this conference began either as solidifications of informal researcher networks – e.g. the Global Biodata Coalition – or under the aegis of more specialised funding bodies – e.g. Bgee, as a Swiss initiative “of national importance”.</p> <p><img src="https://lh7-eu.googleusercontent.com/maMIjdWhKrojzbHOj0h_SSMFh240sjvXErvRHGIdcF2fg2SadC8Az-A-6JGv3p8iWSbv7b1Wv1ReBQNRCKv47cDe_5YLzSYHQwnA-YHfk-ru9bReSecWRMVtYyQDkScSsBeKaCP1ApYhrXIKSot1dZ0" alt=""><em>I was honoured to present my work on synthetic cell types to a global audience.</em></p> <p>As a young researcher – with all the idealism and enthusiasm that implies – I am inclined to hope that biocuration will receive the recognition due to it in time. Certainly, I see no reason why a career dedicated to enabling ethical, open bioinformatics should be any less deserving of professional recognition – let alone a living wage – than any industry researcher or governmental policymaker. That said, shifting the culture of science (not to mention society!) will hardly happen overnight. I am also aware that the issues of ethical conundra and economic precarity are widespread in academia. However, biocuration as a discipline is especially unsung, offering fewer research grants and individual awards than other biological fields. Nor is it a coincidence that most curators were and are women – invisible women, doing invisible work.</p> <p>Fittingly enough, for a female-dominated field, International Women’s Day fell during the conference itself. Whilst AIBC’s speaker lists have yet to achieve gender parity, the hosts at IBDC nevertheless took the opportunity to give women their flowers, literally. I can truthfully say I was touched by the gesture (and the beautiful bouquet of roses and baby’s breath). As discussed though, professional accreditation is far more crucial to effect change. It is a first step towards ensuring economic security for databases and their curators and cultivating mutual respect between curators and the communities they serve.</p> <p><img src="https://lh7-eu.googleusercontent.com/NdBCjW4ejX8KCO7bF9dbOAaOuZApi37XYcsclebb-eEGW4goRCvmjXcs105bp5Z9tHJLBsUq9LFanYkgY6snCRLcoZyQ83jFvmqTJsLisAf-9H99-K9RDGV7I8DYohNv7tIpTmpgeCgqkUuaBrhXaZI" alt=""><em>Thank you to the IBDC, the ISB, and the OBF for making this award possible!</em></p> <p>I am immeasurably grateful to this year’s organisers for awarding “Best Flash Talk” for my presentation on the application of biocuration standards for innovation in direct cell reprogramming. My thanks must also go to the Open Bioinformatics Foundation – without being awarded an OBF fellowship, I could never have afforded to present my doctoral work at AIBC. So, in the best tradition of open bioinformatics – epitomised in every speaker and delegate I had the pleasure to meet – I shall do my best to pay it forward. After all, to paraphrase Dr Pollock, the best use for my success is to open doors for someone else. And isn’t that what open science is all about?</p>https://www.open-bio.org/2024/03/26/gemma-turon-iscbacademy-talk-video/Tue, 26 Mar 2024 03:44:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/03/26/gemma-turon-iscbacademy-talk-video/<p>Gemma Turon, PhD spoke at an ISCBacademy webinar on March 5, 2024. Her talk was entitled “Ersilia, open source AI/ML for (antimicrobial) drug discovery”. The talk video is now available on YouTube: <a href="https://www.youtube.com/watch?v=xcEkCuJpZbw">https://www.youtube.com/watch?v=xcEkCuJpZbw</a>. Dr. Turon&rsquo;s bio and talk abstract can be found in <a href="https://www.open-bio.org/2024/02/08/iscbacademy-gemma-turon/">this blog post</a>.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share; fullscreen" loading="eager" referrerpolicy="strict-origin-when-cross-origin" src="https://www.youtube.com/embed/xcEkCuJpZbw?autoplay=0&amp;controls=1&amp;end=0&amp;loop=0&amp;mute=0&amp;start=0" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" title="YouTube video"></iframe> </div> https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes/Wed, 13 Mar 2024 04:29:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes/<img src="https://www.open-bio.org/wp-content/uploads/2024/03/Melanie-Courtot-1-1.png" alt ="Mélanie Courtot" style="width:50%"/> <h3 id="mélanie-courtot-ontario-institute-for-cancer-research">Mélanie Courtot (Ontario Institute for Cancer Research)</h3> <h4 id="the-data-shows-we-need-better-data"><em>The Data Shows We Need Better Data</em></h4> <p>Big data, AI, LLMs… do they live up to the hype? In a bright and hopeful future, AI accelerates progress, revolutionizes healthcare, alerts us to health risks, and creates fresh career paths. Yet, in a bleaker outlook, it obliterates jobs, fosters rampant misinformation and increases inequity.</p> <p>At the root of AI is the data it relies on. In this talk we will discuss how to steer the course by improving the data AI leverages. We will explore the vast ecosystem formed by data, projects and infrastructure. We will travel along different axes to think about the data we are generating and using every day. We will consider data governance - where does it come from, who owns it, and how can we access it? We will investigate open data - how can we leverage health care knowledge for research? Finally, we will share a few thoughts about data quality and data sharing to increase reproducibility and reuse.</p> <p><em>Dr Mélanie Courtot is the Director of Genome Informatics at the Ontario Institute for Cancer Research in Toronto, and an Assistant Professor in the Department of Medical Biophysics at University of Toronto. Dr Courtot is passionate about translational informatics - building intelligent systems to gain new insights and impact human health. Her lab aims to build a globally shared knowledge ecosystem to advance science and improve health for all. Her team develops the <a href="https://www.overture.bio/">Overture</a> open source software suite, which supports many active large-scale cancer genomics projects including ICGC and ICGC-ARGO, VirusSeq, and the upcoming Pan-Canadian Genome Library. It also drives the African Pathogen Data Sharing and Archive Platform.</em></p> <p><em>Dr Courtot obtained her PhD in Bioinformatics from the University of British Columbia in 2014, followed by a postdoctoral fellowship in Public Health. Dr Courtot co-leads the Clinical and Phenotypic workstream and Data Use and Cohort representation groups for the Global Alliance for Genomics and Health (GA4GH) as well as cohort harmonization efforts for the International HundredK+ Cohorts Consortium. She is an advisory board member for the Public Health Alliance for Genomic Epidemiology coalition, European Open Science Cloud for Cancer project and the eLwazi open data science platform.</em></p> <br/> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/03/Andrew_Su_smll.jpg" alt="Andrew Su"></p> <h3 id="andrew-su-scripps-research-institute">Andrew Su (Scripps Research Institute)</h3> <h4 id="open-data-knowledge-graphs-and-large-language-models"><em>Open Data, Knowledge Graphs, and Large Language Models</em></h4> <p>Bioinformatics is the science of collecting, storing, analyzing, and disseminating biological data and information. As in most domains of data science, bioinformaticians have long focused on structured data – information that is represented using ontologies and controlled vocabularies in well-defined data formats and often stored in databases with predefined schemas. This focus on structured data over the last 30 years has been the most efficient way to convert information into testable hypotheses and new scientific insights.</p> <p>Recent developments in artificial intelligence, particularly the advent of large language models (LLMs), have started to challenge this traditional focus on structured data. By utilizing massive training sets of unstructured text, LLMs have shown exceptional capabilities not only in tasks like question answering and text generation but also in summarization, translation, and code generation. In this presentation, we will examine how LLMs are changing and will continue to change the practice of bioinformatics, particularly at the interface between structured and unstructured data.</p> <p><em>Andrew Su, Ph.D., is the Elden and Verna Strahm Professor at the Scripps Research Institute in the Department of Integrative Structural and Computational Biology (ISCB). Dr. Su earned his PhD in chemistry at Scripps Research in 2002, and was the Associate Director of Bioinformatics at The Genomics Institute of the Novartis Research Foundation (GNF) before returning to Scripps Research as a faculty member in 2011.</em></p> <p><em>The <a href="https://sulab.org/">Su lab</a> focuses on building and applying bioinformatics infrastructure for biomedical discovery. Dr. Su has had a long-standing interest in leveraging crowdsourcing to organize and integrate knowledge though projects like the Gene Wiki and Wikidata. In partnership with Chunlei Wu’s lab, he has also worked extensively on creating biomedical APIs and enabling API interoperability through the BioThings project. Most recently, his lab has a particular emphasis on constructing and mining knowledge graphs for drug repurposing. In all this work, the Su lab has embraced the principles of open science, open data, and open source software.</em></p> <div class="well"> <h3 id="bosc-keynote-speaker-selection-process">BOSC keynote speaker selection process</h3> <p>BOSC usually includes two or three keynote talks given by prominent individuals or emerging leaders who are accomplished in areas relevant to the bioinformatics open source community and who represent a range of backgrounds and ideas. Please see our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker rubric</a> for more information about our keynote speaker selection process and criteria.</p> </div>https://www.open-bio.org/2024/02/23/event-fellowship-2024-1/Fri, 23 Feb 2024 17:37:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/02/23/event-fellowship-2024-1/<p>The call for applications for the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> 2024, round 1, is now open. <strong>The deadline for this round is 1 April 2024.</strong> Applications should be submitted via <a href="https://forms.gle/D31zSs558aRwj2ig9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">make a copy of this template</a>.</p> <p>The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from May 2024 to December 2024. <strong><em>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><em><img src="https://lh7-us.googleusercontent.com/juVq-_8Rna4dP1xunoHPIy85G6x5Jl1WDcxL1VHJBi76K7NsZhNKPsJGk3DEeriGQsuUsCKlvw9IUe3dMdXPmKtwXd2VbOYkK8XQwG6cLqmPDDEoE2iwl9Vs9hAF8vjOp4CUT4xvWqxbQCPv3Bp6Gns" alt=""></em></p> <p><em>Screenshot of our application form information section</em></p> <p><strong>Overview of the last round of OBF Event Fellowship 2023</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. Starting in 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In 2023 round 3 (December 2023), we received numerous applications, of which one applicant was awarded a fellowship for the event they were participating in. Congratulations to Thea Fennell. This fellowship will support their participation in the 17th Annual International Biocuration Conference to present their work on “Developing an open-source atlas charting functional module distribution across cell types in a range of mammalian species”.</p> <p>We recently published blog posts from two of our latest awardees summarising their experiences attending events with help from OBF Event Fellowships:</p> <ul> <li>Raquel Garcia: <a href="https://www.open-bio.org/2023/12/17/journey-at-nf-core-hackathon-and-nextflow-summit-2023/">My Journey at the nf-core Hackathon and Nextflow Summit 2023: Coding and Community</a></li> <li>Yvonne Walburga: <a href="https://www.open-bio.org/2023/12/13/yvonne-walburga-journeys-across-oceans/">Journeys across oceans</a></li> </ul> <p>Congratulations to all of our awardees!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and apply for the fellowship before 1 April 2024.</strong></p>https://www.open-bio.org/2024/02/18/early-poster-acceptance-2024/Sun, 18 Feb 2024 23:20:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/02/18/early-poster-acceptance-2024/<p>Abstract submission for BOSC 2024 is now open! Since some people can’t get conference travel approval from their institution until they get confirmation that their abstract has been accepted for a presentation, we started offering <strong>Early Poster Acceptance</strong> last year, and we are continuing the experiment this year. If you <a href="https://www.open-bio.org/events/bosc-2024/submit/">submit your abstract</a> by March 21, 2024, we will notify you by March 29 whether it has been accepted or not for (at least) a poster.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/02/pears-with-posters1.jpg" alt=""></p> <p>When you submit your abstract, you can choose to apply for a poster, or to try for a talk. If you choose talk, then after the Early Poster Acceptance round your abstract will stay in the pool for the regular review round and you will find out on May 13 whether your abstract was chosen for a talk &ndash; but you will still get early notification on March 29 that you got at least a poster slot!</p> <p>After you submit an abstract in our Early Poster Acceptance round, you are free to update it in the EasyChair submission portal until the regular deadline on April 19! So, you don&rsquo;t lose anything by submitting early and securing your poster acceptance.</p> <p>Key dates March 21: Early Poster Acceptance submission deadline March 29: Notification of poster acceptance April 19: Regular submission deadline May 13: Notification of talk (or poster) acceptance</p> <h3 id="faq">FAQ</h3> <p>Q: How do I submit my abstract for the Early Poster Acceptance round? A: The same way all abstracts are submitted to BOSC: via the ISMB EasyChair submission portal. Please see <a href="https://www.open-bio.org/events/bosc-2024/submit/">/events/bosc-2024/submit/</a> for instructions and submission link.</p> <p>Q: Can I submit in the Early Poster Acceptance round if I want to be considered for a talk? A: Yes, though you won’t get early notification about whether your abstract was chosen for a talk. All abstracts submitted early will be reviewed for possible talk acceptance in the regular review round, and you will be informed on May 13 whether you got a talk.</p> <p>Q: Will I get a full review of my submission in the Early Poster Acceptance round? A: No, you will just get “accepted for poster” or “declined for poster”. However, your abstract will get a full review in the regular round, and the reviews will be sent to you on May 13.</p> <p>Q: What are the criteria for poster acceptance in the Early Poster Acceptance round? A: Please see <a href="https://www.open-bio.org/events/bosc-2024/submit/">/events/bosc-2024/submit/</a> for the criteria, but note that early submissions will receive a streamlined review in the Early Poster Acceptance round. They will go through a full review in the regular round.</p> <p>Q: What are the possible outcomes in this Early Poster Acceptance round? A: 1. Accepted for poster (to be considered for talk in the regular round, if you requested a talk) 2. Declined (not suitable for presentation at BOSC) 3. Deferred (we can’t decide; you will need to wait for a full review in the regular round). (We do not expect many submissions to fall into category #3.)</p> <p>Q: Can I submit updates to my abstract? A: Yes! After you submit an abstract (whether in our Early Poster Acceptance round or the regular round) to update it in the EasyChair submission portal until the regular deadline on April 19!</p> <p>Q: Can I present a talk AND a poster at BOSC? A: In the past you could, but ISMB has instituted a new rule for 2024: a presenting author may present NO MORE THAN ONE talk or poster. If you want to present your work as both a talk and a poster, you have to do a separate poster submission with a different author. Note that this is unaffected by early submission.</p> <p>Q: Are other COSIs also doing an Early Poster Acceptance round? A: Probably not, but we don’t know; you’d have to check with them. (But it was BOSC’s idea first.:-)</p>https://www.open-bio.org/events/sponsors-2023/Thu, 15 Feb 2024 16:34:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/sponsors-2023/<h1 id="sponsors-of-bosc-2023">Sponsors of BOSC 2023</h1> <h2 id="bosc-2023-platinum-sponsor">BOSC 2023 Platinum Sponsor</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="CZI"></a></p> <h2 id="bosc-2023-silver-sponsors">BOSC 2023 Silver Sponsors</h2> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a><a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a><a href="https://www.software.ac.uk/"><img src="https://www.open-bio.org/wp-content/uploads/2023/04/SSI_PRIMARY-LOGO-300x96.png" alt="SSI logo"></a></p> <h4 id="if-youre-interested-in-sponsoring-bosc-2024-please-contact-us-at-">If you’re interested in sponsoring BOSC 2024, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</h4> <hr> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Geraldine-BoF-composite.png" alt="Screenshot from BOSC 2021"></p> <p>Sponsorships from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some conference participants. In 2022, thanks to our sponsors&rsquo; generous support, we were able to grant free registration to 19 participants at <a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a>, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you’re interested in sponsoring BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p>Thanks to our 2021 sponsors, we were able to offer free ISMB/ECCB 2021 registration to 20 participants from all over the world! <iframe loading="lazy" src="https://www.google.com/maps/d/embed?mid=1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width="640" height="480"> </iframe> </p> <h2 id="what-is-bosc">What is BOSC?</h2> <p>BOSC is an annual meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. Whether in-person or online, each BOSC ​includes ​talks,​ ​poster​ ​sessions,​ ​birds-of-a-feather gatherings, and ​lots​ ​of​ ​opportunities​ ​for​ ​networking. It is followed by​ ​collaborative​ ​working​ ​sessions​ ​at the CollaborationFest.​ ​These​ ​events​ ​bring​ ​together​ ​software​ ​engineers,​ ​bioinformaticians,​ ​and​ ​researchers​ ​to collaborate​ ​and​ ​extend​ ​open​ ​source​ ​bioinformatics​ ​tools.</p> <p>Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB). In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>. In July 2020, BOSC again joined forces with GCC to form the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>. Held online, BCC2020 attracted over 600 participants from 62 countries. <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> was part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, and took place July 29-30, 2021 (followed by a two-day <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest</a>).</p> <p><a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> was held July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> in person in Madison, Wisconsin, USA, and simultaneously online.</p> <p><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a>, the 24th annual Bioinformatics Open Source Conference, will take place July 24-25 as part of ISMB/ECCB 2023 in Lyon, France and online. Like last year, we will join forces with Bio-Ontologies for part of a day!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/OBF-BoF-2018-25-300x225.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/43248502932_2395bc3cc6_z-300x200.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2017-panel-1.jpg" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Jason-PeterSelby-FotisPsomopoulos-DhrithiDespande.png" alt=""></p> <p>BOSC​ ​participants​ ​come​ ​from​ ​a​ ​wide​ ​variety​ ​of​ ​research​ ​environments​ ​and​ ​backgrounds:</p> <ul> <li> <p>Biological​ ​researchers,​ ​students,​ ​and​ ​post-docs​ ​who​ ​​ ​are​ ​learning​ ​bioinformatics​ ​analysis tools and techniques</p> </li> <li> <p>Power​ ​bioinformatics​ ​users</p> </li> <li> <p>Bioinformatics​ ​tool​ ​and​ ​workflow​ ​developers</p> </li> <li> <p>Bioinformatics​-focused​ ​principal​ ​investigators​ ​and​ ​researchers</p> </li> <li> <p>Sequencing​ ​core​ ​facility​ ​staff</p> </li> <li> <p>Industry​ ​scientists​ ​and​ ​bioinformaticians</p> </li> <li> <p>Data​ ​producers</p> </li> </ul> <h1 id="previous-events">Previous Events</h1> <p>The​ ​OBF​ ​has​ ​organized​ ​BOSC​ ​ <a href="https://www.open-bio.org/events/bosc/about/">every​ ​year​ ​since​ ​2000</a>.​ From 2000 to 2017 and again in 2019,​ ​BOSC​ ​was ​run​ ​as​ ​part​ ​of​ ​the​ ​large​ ​ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference.​ ​The​ ​OBF​ ​CodeFest​s (now renamed CollaborationFest, or CoFest) have ​been​ ​held​ ​every​ ​year​ after BOSC ​since​ ​2010.</p> <p>The table below shows the approximate number of participants in BOSC and the CoFest. Figures​ ​for​ ​the​ ​CoFest​ ​and​ ​BOSC​ ​are​ ​number​ ​of​ ​people​ ​registered​ ​for​ ​at​ ​least​ ​one​ ​day​ ​of​ ​the​ ​meeting.​ ​The​ ​BOSC figures​ ​do​ ​not​ ​include​ ​drop-in​ ​attendees​ ​from​ ​the​ ​parallel​ ​sessions​ ​organized​ ​by​ ​other​ ​groups.​ ​The​ ​figures​ ​for CoFest​ ​do​ ​not​ ​include​ ​remote​ ​participants.</p> <p>YearLocation BOSC ParticipantsCoFest Participants 2022BOSC 2022: Madison, WI, USA and virtual<del>200</del>152021BOSC 2021: virtual<del>200</del>252020BCC2020 (BOSC + Galaxy): virtual<del>300</del>1502019Basel, Switzerland109352018 Portland, OR, USA1501002017 Prague, Czech Republic 230652016 Orlando, FL, USA90362015Dublin, Ireland125352014Boston, MA, USA100602013Berlin, Germany100372012Long Beach, CA, USA 100132011 Vienna, Austria 12035</p> <h1 id="sponsorship">Sponsorship</h1> <p>We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to</p> <ul> <li>offer free registration to some BOSC participants</li> <li>support the <a href="https://www.open-bio.org/travel-awards/">OBF&rsquo;s Event Fellowship program</a>, increasing participation from underrepresented groups</li> <li>provide child care at the conference</li> <li>underwrite the cost of conference events such as dinners or refreshments at poster sessions</li> <li>help defray the cost of videography</li> <li>provide space and catering at the CoFest</li> <li>offer honoraria to keynote speakers</li> <li>pay for captioning and translations</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/BOSC2020-party-attendees-e1609719125821.png" alt=""></p> <h2 id="sponsoring-bosc">Sponsoring BOSC</h2> <p>Sponsorships from private companies and organizations help to defray some of our costs and allow us to offer registration fee waivers to some attendees. If you are interested in becoming a BOSC sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <h1 id="benefits-of-sponsorship">Benefits of Sponsorship</h1> <p>We acknowledge our sponsors before, during and after the event in multiple ways:</p> <ul> <li>We list our sponsors on the BOSC website</li> <li>Sponsors are thanked and named in the introduction/closing slides during the meeting</li> <li>We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area</li> <li>The sponsors are thanked in selected emails to our mailing list, tweets and blog posts (with your logo) that go out before, during and after the event</li> <li>The sponsors are listed in our published reports after the meeting, e.g., <a href="https://f1000research.com/articles/7-1309/v1">https://f1000research.com/articles/7-1309/v1</a></li> <li>We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.</li> </ul> <h1 id="sponsors-from-previous-years">Sponsors from previous years</h1> <h2 id="bosc-2022-platinum-sponsors">BOSC 2022 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a></p> <h2 id="bosc-2022-gold-sponsors">BOSC 2022 Gold Sponsors</h2> <p><a href="https://www.broadinstitute.org/data-sciences-platform"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/Broad-DSP-logo-1.png" alt="Broad Institute Data Science Platform"></a><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Office of Data Science Strategy"></a></p> <h3 id="bosc-2022-silver-sponsors">BOSC 2022 Silver Sponsors</h3> <p><a href="https://arvados.org"><img src="https://www.open-bio.org/wp-content/uploads/2022/05/ArvadosCurii.png" alt="Arvados, supported by Curii"></a><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="Gigascience"></a></p> <h2 id="bosc-2021-platinum-sponsors">BOSC 2021 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="https://www.alzheimersdata.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/ADDI_Logo_FullColor_Vert_RGB.png" alt="Alzheimer’s Disease Data Initiative"></a></p> <h2 id="bosc-2021-gold-sponsors">BOSC 2021 Gold Sponsors</h2> <p><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a><a href="https://www.broadinstitute.org/"><img src="https://www.broadinstitute.org/files/news/media-images/logos//BroadInstLogoforDigitalRGB.png" alt="Broad Institute Logo"></a></p> <h2 id="bosc-2021-silver-sponsors">BOSC 2021 Silver Sponsors</h2> <p><a href="https://elifesciences.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/04/image.png" alt=""></a> <a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a> <a href="https://oup.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/OUP_logo_navy.png" alt="Oxford University Press"></a><a href="https://bioteam.net"><img src="https://www.open-bio.org/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png" alt=""></a></p> <p>If you are interested in becoming a sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p>https://www.open-bio.org/2024/02/08/iscbacademy-gemma-turon/Thu, 08 Feb 2024 17:32:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/02/08/iscbacademy-gemma-turon/<h3 id="gemma-turon-phd-ceo-and-co-founder-at-ersilia-open-source-initiative-will-present-on-march-5">Gemma Turon, PhD (CEO and co-founder at Ersilia Open Source Initiative) will present on March 5</h3> <p>BOSC and the OBF will host an <a href="https://www.iscb.org/iscbacademy">ISCBacademy webinar</a> on <strong>March 5, 2024, at 8am PST (16:00 UTC).</strong> Gemma Turon (see bio below) will speak about &ldquo;Ersilia, open source AI/ML for (antimicrobial) drug discovery&rdquo;.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/02/Gemma-Turon-1.png" alt=""></p> <h4 id="abstract">Abstract</h4> <p>The <a href="https://www.ersilia.io/">Ersilia Open-Source Initiative</a> is a non-profit organisation whose mission is to equip laboratories, clinics and universities in lower and middle income countries (LMICs) with artificial intelligence (AI) tools for infectious disease research. The goal of our mission is to strengthen the research capacity in those countries where these diseases are predominant, supporting the in-country drug discovery pipelines for neglected and infectious diseases. Since its foundation in 2020, we have collaborated with several institutions in the Global South as well as international consortiums. In this introductory talk we will present our computational approach and infrastructure, including the Ersilia Model Hub, a unified platform offering ready- to-use AI models to researchers worldwide, and how we have used it across multiple projects, offering a perspective on how AI/ML can transform drug discovery and contribute towards a more egalitarian world of biomedical research.</p> <h4 id="about-the-speaker">About the speaker</h4> <p>Trained as a molecular biologist, Gemma Turon completed a PhD in colorectal cancer and stem cells at IRB Barcelona in 2019, before taking a one-year break to focus on working and volunteering in the third sector. This shifted her scientific interest to global health and neglected diseases, and the existing barriers to tackle some of the most urgent health issues in developing countries. With Ersilia, she aims to explore new ways of community building and engagement in the scientific arena, at the intersection between academia, biotech start-ups and NPOs.</p> <h4 id="iscbacademy">ISCBacademy</h4> <p><a href="https://www.iscb.org/iscbacademy">ISCBacademy</a> is a series of free webinars sponsored by the International Society for Computational Biology. They are open to all, including those who are not ISCB members. ISCB members can access the webinars via the ISCB Nucleus platform: <a href="https://iscb.junolive.co/">https://iscb.junolive.co/</a>. Non-members need to register for Nucleus: <a href="https://iscb.swoogo.com/ISCBnucleus-registration">https://iscb.swoogo.com/ISCBnucleus-registration</a></p>https://www.open-bio.org/events/bosc-2025/submit/Wed, 24 Jan 2024 16:09:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2025/submit/<h1 id="bosc-2025-abstract-submission">BOSC 2025 Abstract Submission</h1> <p><div class="splitbox"><div class="left"> BOSC 2025, the 26th annual Bioinformatics Open Source Conference, will take place July 21-22, 2025 in Liverpool, UK (as part of <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a>).</p> <p>SUBMISSION IS NOW CLOSED. The full lineup of talks for 2025 is available on our <a href="https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/">Schedule page</a>.</p> <p>Please see below for submission instructions.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/11/Festus-Nyastimi-poster-BOSC2022.png" alt="Poster from BOSC 2022"></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/08/speakers-in-Standards-and-frameworks-for-open-science-session-1.jpeg" alt="Photo of some speakers at BOSC 2024"></p> </div><div style="clear:both"></div></div> <br/> <div class='well'> <h3 id="key-dates">Key Dates</h3> <ul> <li>April 17, 2025: Abstract submission deadline (talks and posters) - no extensions</li> <li>May 13: Talk and/or poster acceptance notifications</li> <li>May 15: Late poster submission deadline</li> <li>July 20-24, 2025: <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a> (Liverpool, UK, and online)</li> <li><strong>July 21-22, 2025:</strong> <strong>BOSC 2025</strong> (part of ISMB/ECCB 2025)</li> <li>July 23-24: ISMB CollaborationFest</li> </ul> </div> <h1 id="submission-guidelines">Submission guidelines</h1> <div class="splitbox"><div class="left"> <h3 id="what-to-submit">What to submit</h3> <ul> <li>A 250-word short abstract (text only) is required for ALL submissions (talk and/or poster).</li> <li>If you want to be considered for a talk, you also MUST attach a 1-2 page &ldquo;long abstract&rdquo; as a PDF. Figures welcome as long as the total length is 2 pages or less.</li> <li>In your long abstract, please describe how your work fits into the open source / open science ecosystem. We like to see examples of biological applications of your work, and a summary of the current and/or projected community aspects of your project.</li> </ul> <div class="well"> <p>Watch a video of <a href="https://youtu.be/DwJRrh1Tpew">BOSC organizing committee member Jason Williams discussing how to write a great BOSC abstract</a>!</p> <p><a target="_new" href="https://youtu.be/DwJRrh1Tpew"><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Screen-Shot-2022-01-19-at-3.59.31-PM.png" style="width:60%" alt="Jason Williams" /></a></p> </div> </div><div class="right"> <h3 id="requirements">Requirements</h3> <p>To be accepted, abstracts submitted to BOSC must be:</p> <ul> <li><strong>Relevant</strong>: Your abstract must describe how your work relates to some aspect of open source software, open science or open data applied to biology or biomedical science.</li> <li><strong>Available</strong>: Your code / data / materials must be available <strong>at the time of review</strong> at the URL you list.</li> <li><strong>Open Content</strong>: Work discussed in BOSC presentations must be open source / open content, with a recognized license (which must be included in the repository). For abstracts about non-software products (e.g., educational materials), these should also be freely available with an appropriate open license (see below).</li> <li><strong>Updated</strong>: If you presented this work at a previous BOSC in any form, your abstract must describe progress since the last BOSC presentation.</li> </ul> </div><div style="clear:both"></div></div> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/08/Panel-only-1.jpeg" alt="Panel at BOSC 2024"></p> <h3 id="additional-criteria">Additional criteria</h3> <p>In addition to the requirements listed above, we consider the following when selecting abstracts for short or long talks.</p> <ul> <li><strong>Community impact</strong>: Please describe how your work fits into the open source bioinformatics / open science ecosystem. A summary of the current and/or projected community aspect of your project is very helpful.</li> <li><strong>Novelty</strong>: Innovative approaches are interesting to hear about, but it’s fine to build on existing technology! If you can compare your approach with existing approaches, that’s a plus.</li> <li><strong>Examples</strong>: We like abstracts with examples of how your approach works (e.g. a figure showing the output of a visualization tool, an example of software input/output, or benchmarks on relevant data).</li> <li><strong>Runnable</strong>: Although we are happy to consider abstracts that describe early-phase projects, our reviewers are likely to look at your code and try to run it. Reviewers like projects that they are able to download and run, and that are well-documented and easy to use.</li> </ul> <h3 id="how-to-submit">How to Submit</h3> <ul> <li>Submissions are via the ISMB EasyChair. If you don&rsquo;t already have an EasyChair account, you will need to create one. <ul> <li>After signing in, click &ldquo;make a new submission&rdquo;</li> <li>You will see &ldquo;Please select the track relevant for your submission.&rdquo; Select BOSC (5th line down).</li> <li>Later in the submission process, you will be able to specify one or two other COSIs/tracks that your abstract might also fit into.</li> </ul> </li> <li>A 250-word short abstract is required for ALL submissions (talk and/or poster). (Confusingly, the submission form refers to this as simply &ldquo;Abstract&rdquo;.)</li> <li>If you want to be considered for a talk, you also MUST submit a 1-2 page &ldquo;long abstract&rdquo; as a PDF. (Yes, we did suggest to ISMB that calling both of these things &ldquo;abstracts&rdquo; was confusing.)</li> <li>If you submit for a talk but your abstract is not chosen for a talk, it will automatically be considered for a poster.</li> <li>New ISMB rule this year: a presenting author may present NO MORE THAN ONE talk or poster. If you want your work to be presented as both a talk and a poster, a different presenting author needs to submit for a poster.</li> <li>Abstract template for formatting your PDF (optional): <a href="https://www.open-bio.org/wp-content/uploads/2022/04/bosc2022-abstract-template.docx">bosc-abstract-template</a> (MS Word)</li> <li>You don&rsquo;t need to register before you submit your abstract, but to present your talk or poster you will need to register for ISMB.</li> </ul> <h2 id="bosc-open-content-requirement">BOSC Open Content Requirement</h2> <p>The <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a>, which coordinates BOSC, is dedicated to promoting the practice and philosophy of Open Source Software Development and Open Science within the biological research community.</p> <p>For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate. Similarly, abstracts with a focus on data, analysis methods, and/or documentation must make these available in a manner consistent with Open Science standards, utilizing appropriate licensing and approaches that promote open sharing, reuse, and redistribution.</p> <p>See the following websites for further information and examples of recognized Open Source Licenses and Public Domain Dedications:</p> <ul> <li><a href="https://choosealicense.com/">ChooseALicense</a>, with options for source code and non-source code licensing</li> <li><a href="http://www.opensource.org/licenses/">Open Source Initiative (OSI) Approved Licenses</a></li> <li><a href="http://www.opensource.org/docs/definition.php">Definition of the Open Source Philosophy</a></li> <li><a href="https://creativecommons.org/share-your-work/public-domain/freeworks/">Creative Commons licenses that support free “cultural works”</a> : <a href="https://creativecommons.org/share-your-work/public-domain/cc0">CC0</a>, <a href="https://creativecommons.org/licenses/by/3.0/">CC-BY</a>, <a href="https://creativecommons.org/licenses/by-sa/3.0/">CC-BY-SA</a></li> <li><a href="https://creativecommons.org/share-your-work/public-domain/">Public Domain Dedications</a> and <a href="https://en.wikipedia.org/wiki/Public-domain-equivalent_license">Public-domain-equivalent licenses</a>: <a href="https://creativecommons.org/share-your-work/public-domain/cc0">CC0</a>, <a href="https://unlicense.org/">Unlicense</a></li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Paul-Pavlidis-asks-Andrew-Su-a-question.jpg" alt="At BOSC 2024, Paul Pavlidis asks Andrew Su a question"></p> <h2 id="ismb-rules">ISMB rules</h2> <p><strong>In-person presentation</strong>: &ldquo;For a variety of reasons, ISCB strongly prefers that scientific research accepted for oral presentation be presented in-person at the conference venue. ISCB will grant remote presentation options for reasons associated with maternity/paternity leave, care for a family member, personal/medical disability, sickness, financial hardship, or potential visa problems.&rdquo;</p> <p><strong>Talk OR poster</strong>: The same abstract can&rsquo;t be presented as both a talk and a poster.</p> <h3 id="presentation-formats">Presentation formats</h3> <p>Talks chosen from submitted abstracts are generally either &ldquo;long&rdquo; (around 15-20 minutes + 3 minutes for question) or short/&ldquo;lightning&rdquo; (5 minutes).</p> <p>In the late round, abstracts will be considered for posters and, if space permits, for &ldquo;Late-Breaking Lightning Talks&rdquo;. The LBLTs are grouped together in a single session, rather than being slotted into the themed sessions (which are already set in the first round). Abstracts submitted in the late round are not eligible for long talks.</p> <h3 id="bosc-review-process">BOSC review process</h3> <p>Abstracts submitted to BOSC are reviewed by at least three reviewers. Our review process and rubric can be found <a href="https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md">here</a>.</p> <div class="well"> <h3 id="requesting-registration-fee-assistance">Requesting registration fee assistance</h3> <div class="splitbox"><div class="left"> <p>We realize that the cost of ISMB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests &ndash; the abstract reviewers will not.) Last year, thanks to help from our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors</a>, we were able to grant free registration to 15 participants.</p> <p></div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2019/02/farah-presentation.jpg" alt="Farah Khan and her poster"></p> </div><div style="clear:both"></div></div> </div>https://www.open-bio.org/events/bosc-2026/submit/Wed, 24 Jan 2024 16:09:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2026/submit/<h1 id="bosc-2026-abstract-submission">BOSC 2026 Abstract Submission</h1> <p><div class="splitbox"><div class="left"> <strong>BOSC 2026</strong>, the 27th annual Bioinformatics Open Source Conference, will take place <strong>July 14-15</strong> as part of <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a> in Washington DC. We hope you will join us in person or online!</p> <p><strong>Abstract submission is open!</strong> See below for instructions.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/08/speakers-in-Standards-and-frameworks-for-open-science-session-1.jpeg" alt="Photo of some speakers at BOSC 2024"></p> </div><div style="clear:both"></div></div> <br/> <div class='well'> <h3 id="key-dates">Key Dates</h3> <div class="splitbox"><div class="left"> <ul> <li>April 1, 2026: <a href="https://www.open-bio.org/event-awards/">OBF Event Award application deadline</a></li> <li><strong>April 9: Abstract submission deadline (talks and posters)</strong>. Submission is via ISMB&rsquo;s EasyChair.</li> <li>May 5: Talk/poster acceptance notifications</li> <li>May 7: Late poster submission deadline</li> <li>July 12-16: <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a> (Washington, DC and online)</li> <li><strong>July 14-15:</strong> <strong>BOSC 2026</strong> (part of ISMB 2026)</li> </ul> <p></div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2024/08/Larry-and-Melanie-in-BOSC-audience-1.jpeg" alt="Larry Hunter and Melanie Courtot at BOSC 2024"> </div><div style="clear:both"></div></div> </p> </div> <h1 id="submission-guidelines">Submission guidelines</h1> <div class="splitbox"><div class="left"> <h3 id="what-to-submit-overview">What to submit: Overview</h3> <ul> <li>A 250-word short abstract (text only) is required for ALL submissions (talk and/or poster).</li> <li>If you want to be considered for a talk, you also MUST attach a 1-2 page &ldquo;long abstract&rdquo; as a PDF. Figures are welcome as long as the total length is 2 pages or less.</li> <li>In your long abstract, please describe how your work fits into the open source / open science ecosystem. We like to see examples of biological applications of your work, and a summary of the current and/or projected community aspects of your project.</li> <li>Your abstract should not contain your title/position or any personal information (e.g., affiliation). These details will be collected through the EasyChair submission system.</li> </ul> </div><div class="right"> <h3 id="requirements">Requirements</h3> <p>To be accepted, abstracts submitted to BOSC must be:</p> <ul> <li><strong>Relevant</strong>: Your abstract must describe how your work relates to some aspect of open source software, open science or open data applied to biology or biomedical science.</li> <li><strong>Available</strong>: Your code / data / materials must be available <strong>at the time of review</strong> at the URL you list.</li> <li><strong>Open Content</strong>: Work discussed in BOSC presentations must be open source / open content, with a recognized license (which should also be included in the repository). If your abstract concerns non-software products (e.g., educational materials), these should also be freely available with an appropriate open license (see below).</li> <li><strong>Updated</strong>: If you presented this work at a previous BOSC in any form, your abstract must describe progress since the last BOSC presentation.</li> <li><strong>Human-written</strong>: AI/LLMs must not be used to write sections your abstract&ndash;please see the &ldquo;AI Use Policy&rdquo; section below.</li> </ul> </div><div style="clear:both"></div></div> <h3 id="additional-criteria">Additional criteria</h3> <p>In addition to the requirements listed above, we consider the following when selecting abstracts for short or long talks.</p> <ul> <li><strong>Community impact</strong>: Please describe how your work fits into the open source bioinformatics / open science ecosystem. A summary of the current and/or projected community aspect of your project is very helpful.</li> <li><strong>Novelty</strong>: Innovative approaches are interesting to hear about, but it’s fine to build on existing technology! If you can compare your approach with existing approaches, that’s a plus.</li> <li><strong>Examples</strong>: We like abstracts with examples of how your approach works (e.g. a figure showing the output of a visualization tool, an example of software input/output, or benchmarks on relevant data).</li> <li><strong>Usable</strong>: Although we are happy to consider abstracts that describe early-phase projects, our reviewers are likely to look at your code and try to run it. Reviewers like projects that they are able to download and run, and that are well-documented and easy to use.</li> </ul> <h3 id="how-to-submit">How to Submit</h3> <ul> <li>Submissions are via the ISMB EasyChair. If you don&rsquo;t already have an EasyChair account, you will need to create one. <ul> <li>After signing in, click &ldquo;make a new submission&rdquo;</li> <li>You will see &ldquo;Please select the track relevant for your submission.&rdquo; Select BOSC (5th line down).</li> <li>Later in the submission process, you will be able to specify one or two other COSIs/tracks that your abstract might also fit into.</li> </ul> </li> <li>A 250-word short abstract is required for ALL submissions (talk and/or poster). (Confusingly, the submission form refers to this as simply &ldquo;Abstract&rdquo;.)</li> <li>If you want to be considered for a talk, you also MUST submit a 1-2 page &ldquo;long abstract&rdquo; as a PDF. (Yes, we did suggest to ISMB that calling both of these things &ldquo;abstracts&rdquo; was confusing.)</li> <li>If you submit for a talk but your abstract is not chosen for a talk, it will automatically be considered for a poster.</li> <li>You don&rsquo;t need to register before you submit your abstract, but to present your talk or poster you will need to register for ISMB.</li> </ul> <center> <a href="https://easychair.org/conferences/?conf=ismb2026" class="btn btn-lg btn-primary">Submit Abstract</a> </center> <h2 id="bosc-open-content-requirement">BOSC open content requirement</h2> <p>The <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a>, which coordinates BOSC, is dedicated to promoting the practice and philosophy of Open Source Software Development and Open Science within the biological research community.</p> <p>For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate. Similarly, abstracts with a focus on data, analysis methods, and/or documentation must make these available in a manner consistent with Open Science standards, utilizing appropriate licensing and approaches that promote open sharing, reuse, and redistribution.</p> <p>See the following websites for further information and examples of recognized Open Source Licenses and Public Domain Dedications:</p> <ul> <li><a href="https://choosealicense.com/">ChooseALicense</a>, with options for source code and non-source code licensing</li> <li><a href="http://www.opensource.org/licenses/">Open Source Initiative (OSI) Approved Licenses</a></li> <li><a href="http://www.opensource.org/docs/definition.php">Definition of the Open Source Philosophy</a></li> <li><a href="https://creativecommons.org/share-your-work/public-domain/freeworks/">Creative Commons licenses that support free “cultural works”</a> : <a href="https://creativecommons.org/share-your-work/public-domain/cc0">CC0</a>, <a href="https://creativecommons.org/licenses/by/3.0/">CC-BY</a>, <a href="https://creativecommons.org/licenses/by-sa/3.0/">CC-BY-SA</a></li> <li><a href="https://creativecommons.org/share-your-work/public-domain/">Public Domain Dedications</a> and <a href="https://en.wikipedia.org/wiki/Public-domain-equivalent_license">Public-domain-equivalent licenses</a>: <a href="https://creativecommons.org/share-your-work/public-domain/cc0">CC0</a>, <a href="https://unlicense.org/">Unlicense</a></li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Paul-Pavlidis-asks-Andrew-Su-a-question.jpg" alt="At BOSC 2024, Paul Pavlidis asks Andrew Su a question"></p> <h2 id="ai-use-policy">AI use policy</h2> <p>BOSC follows the <a href="https://www.iscb.org/about-iscb/policy-statements-bylaws-and-legal-documents/acceptable-use-of-large-language-models-policy">ISCB policy on acceptable use of large language models (LLMs)</a>. Key points:</p> <ul> <li>Abstracts and papers <strong>must be written by humans</strong>. LLMs must not be used to draft or write sections of your submission.</li> <li>Acceptable uses of LLMs include spell/grammar checking, language translation assistance, and code development support — but the submitting authors remain responsible for all content.</li> <li>If you used AI tools as part of the research described in your submission, please describe that usage in the submission form.</li> </ul> <h2 id="ismb-rules">ISMB rules</h2> <p><strong>In-person presentation</strong>: &ldquo;ISCB strongly prefers that scientific research accepted for oral presentation be presented in-person at the conference venue. ISCB will grant remote presentation options for reasons associated with maternity/paternity leave, care for a family member, personal/medical disability, sickness, financial hardship, or potential visa problems.&rdquo;</p> <p><strong>Talk OR poster</strong>: ISMB does not allow a presenting author to present both a talk and a poster on the same topic. If you want your work to be presented as both a talk and a poster, a different presenting author needs to submit for each.</p> <h3 id="presentation-formats">Presentation formats</h3> <p>At BOSC, talks chosen from submitted abstracts are generally either &ldquo;long&rdquo; (typically 16 minutes plus 4 minutes for questions) or short/&ldquo;lightning&rdquo; (5 minutes, scheduled in groups of three lightning talks followed by 5 minutes for questions for all three). Abstracts submitted in the Late Poster round are not eligible for talks.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/08/BOSC-org-committee-Montreal-1.jpeg" alt="BOSC 2024 organizing committee"></p> <h3 id="bosc-review-process">BOSC review process</h3> <p>Talk abstracts submitted to BOSC are typically reviewed by three reviewers; poster abstracts by two. Our review process and rubric can be found <a href="https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md">here</a>.</p> <div class="well"> <h3 id="requesting-registration-fee-assistance">Requesting registration fee assistance</h3> <div class="splitbox"><div class="left"> <p>We realize that the cost of ISMB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests &ndash; the abstract reviewers will not.) Last year, thanks to help from our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors</a>, we were able to grant free registration to 15 participants.</p> <p></div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2019/02/farah-presentation.jpg" alt="Farah Khan and her poster"></p> </div><div style="clear:both"></div></div> </div> <center> <a href="https://easychair.org/conferences/?conf=ismb2026" class="btn btn-lg btn-primary">Submit Abstract</a> </center>https://www.open-bio.org/2024/01/19/community-comment-bosc-2024-keynotes/Fri, 19 Jan 2024 06:48:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/01/19/community-comment-bosc-2024-keynotes/<p><img src="https://www.open-bio.org/wp-content/uploads/2024/01/pears-commenting-300x300.jpg" alt=""></p> <p>We <a href="https://www.open-bio.org/2024/01/10/nominate-a-keynote-speaker-for-bosc/">asked our community to nominate potential BOSC keynote speakers</a>, and we were pleased with the great suggestions! In the next phase of our process, we’re giving you a chance to let us know if there is anything that makes any of the nominated individuals NOT appropriate as BOSC keynote speakers.</p> <p>Our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker process and rubric</a> gives examples of some possible reasons for exclusion. If you have concerns about any of the people on our list, please let us know (with as much specificity as you feel comfortable providing) via <a href="https://docs.google.com/forms/d/e/1FAIpQLSe3hUXZ5BQv2-I7DpL-SdEovAVh6Bq9wWgs93FMx5LylAC_Eg/viewform">this anonymous form</a> no later than Thursday 2024-01-25.</p> <p>And the nominees are…</p> <ul> <li>Andrew I. Su</li> <li>Anne Carpenter</li> <li>Chris Evelo</li> <li>Chris Mungall</li> <li>Emma Hodcroft</li> <li>Gary Bader</li> <li>Gemma Turon</li> <li>Heng Li</li> <li>Inioluwa Deborah Raji</li> <li>Laura Ación</li> <li>Melanie Courtot</li> <li>Noah Fahlgren</li> <li>Ziad Obermeyer</li> </ul> <p>After the community comment period closes, the BOSC organizing committee will draw on this list to extend invitations to potential keynote speakers. Since we cannot know in advance which speakers might accept the invitation, we may have to go beyond the list of those nominated. In that case, we would not rerun this process, but community members will always be encouraged to inform the Organizing Committee if they believe any speaker does not meet our standards.</p> <p><a href="https://docs.google.com/forms/d/e/1FAIpQLSe3hUXZ5BQv2-I7DpL-SdEovAVh6Bq9wWgs93FMx5LylAC_Eg/viewform">Submit anonymous feedback</a></p>https://www.open-bio.org/2024/01/10/nominate-a-keynote-speaker-for-bosc/Wed, 10 Jan 2024 21:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/01/10/nominate-a-keynote-speaker-for-bosc/<p>We are seeking a diverse list of potential BOSC keynote speakers. We invite you, our community, to nominate people you think would be appropriate (and at least somewhat likely to accept the invitation – for example, it is extremely unlikely that we would get a &lsquo;yes&rsquo; from a recent Nobel Laureate). Please submit your nominations <a href="https://docs.google.com/forms/d/e/1FAIpQLSe6Dx_WJidS6j7UMOuFurm-OZ7N2op_d6RxGZg_K283jIhd0Q/viewform">here</a> (as many as you like; you can fill out the form more than once to submit additional suggestions) by the end of the day on Wednesday 2024-01-17.</p> <p>Keynote talks are a highlight at BOSC. BOSC typically bookends keynotes at the beginning and end of the conference. These invited speakers are prominent individuals or emerging leaders who are accomplished in their fields, and whose work is likely to be of interest to the bioinformatics open source community. Before 2023, the process of selecting appropriate keynote speakers was done by the BOSC Organizing Committee. Last year, we realized that making the process more consistent, fair and transparent would better align with our values of openness and inclusivity; we therefore developed an <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">open process and rubric for choosing keynote speakers.</a> This process worked well, so we will use it again in 2024.</p> <p><a href="https://docs.google.com/forms/d/e/1FAIpQLSe6Dx_WJidS6j7UMOuFurm-OZ7N2op_d6RxGZg_K283jIhd0Q/viewform">Nominate a keynote speaker!</a></p>https://www.open-bio.org/2024/01/10/biopython-1-83-released/Wed, 10 Jan 2024 13:46:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2024/01/10/biopython-1-83-released/<p>Dear Biopythoneers,</p> <p>Our first release of 2024 is now out, sooner than planned as this is purely to revert the removal of the <code>.strand</code>, <code>.ref</code>, and <code>.ref_db</code> attributes of the <code>SeqFeature</code> which was done in Biopython 1.82 without a deprecation period. They are again aliases for <code>.location.strand</code> etc, but now trigger deprecation warnings. See our <a href="https://biopython.org/wiki/Deprecation_policy">deprecation policy</a>. We apologize for any inconvenience, and thank you to those reporting this.</p> <p>This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.9 v7.3.13. Python 3.8 is approaching end of life, our support for it is now deprecated.</p> <p>Biopython 1.83 source releases are available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.83">PyPI</a>, which also has pre-compiled wheels for the major platforms. We would expect the release to be on conda-forge shortly too.</p> <p>Happy New Year!</p>https://www.open-bio.org/2023/12/22/biopython-1-82-released/Fri, 22 Dec 2023 15:41:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/12/22/biopython-1-82-released/<p>Biopython 1.82 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.82">PyPI</a>.</p> <p>Our second release of 2023 is now out, albeit way later than we&rsquo;d all intended.</p> <p>This contains about 10 months worth of updates, so the NEWS file information is denser than usual: <a href="https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst">https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst</a></p> <p>Also, there have been more deprecations and removals of deprecated code than typical - see the DEPRECATED file too: <a href="https://github.com/biopython/biopython/blob/biopython-182/DEPRECATED.rst">https://github.com/biopython/biopython/blob/biopython-182/DEPRECATED.rst</a></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alex Crocker (first contribution)</li> <li>Antonio Trande (first contribution)</li> <li>Arpan Sahoo (first contribution)</li> <li>Benedict Carling (first contribution)</li> <li>Cam McMenamie (first contribution)</li> <li>Ernesto Rodriguez (first contribution)</li> <li>Jacob Byerly (first contribution)</li> <li>João Rodrigues</li> <li>Joe Greener</li> <li>Manuel Lera Ramirez</li> <li>Michael R. Crusoe</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Ricardas Ralys (first contribution)</li> <li>Rob Miller</li> <li>Thomas Holder</li> <li>Tom Eulenfeld (first contribution)</li> <li>Vladislav Kuznetsov (first contribution)</li> <li>Wibowo Arindrarto</li> <li>Yiming Qu (first contribution)</li> </ul> <p>Thank you all, and also those unnamed who have helped indirectly, though bug reports or otherwise.</p>https://www.open-bio.org/2023/12/17/journey-at-nf-core-hackathon-and-nextflow-summit-2023/Sun, 17 Dec 2023 16:00:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/12/17/journey-at-nf-core-hackathon-and-nextflow-summit-2023/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Raquel Manzano Garcia,</em></strong> <em><strong>a PhD researcher at</strong></em> <em><strong>the University of Cambridge</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the</strong></em> <strong><em><a href="https://summit.nextflow.io/barcelona/">Nextflow Summit 2023</a> .</em></strong></p> <p>This October, I had the incredible opportunity to attend the <a href="https://summit.nextflow.io/barcelona/">Nextflow Summit 2023</a> in Barcelona, thanks to the support of a generous travel grant from the Open Bioinformatics Foundation (OBF) and my supervisor Prof. Carlos Caldas. The eent wasn&rsquo;t just a conference; it was a confluence of ideas, coding, and camaraderie, set against the vibrant backdrop of one of Spain&rsquo;s most iconic cities.</p> <p>One of the most memorable aspects for me was the transition from digital interactions to real, meaningful connections. Meeting individuals I had previously only connected with online, such as my nf-core mentor, Maxime Garcia, was an incredible experience. The chance to collaborate in person, beyond the confines of a shared screen, was both enriching and inspiring. It brought a fresh and exciting dimension to our ongoing work.</p> <p>The hackathon wasn&rsquo;t just about coding; it was about building connections. I found myself surrounded by beautiful minds. The experience of learning new tricks and tips in such a collaborative setting has prompted me to reflect on my career trajectory, reaffirming my desire to thrive in similar environments. I am immensely thankful for the individuals I encountered – their patience, kindness, and enjoyable approach to addressing every question, discussion or concern were truly remarkable. Among them were professionals from my own area, with whom I&rsquo;ve not only reconnected since the event but also started making plans for potential collaborations.</p> <p>Additionally, I got the opportunity to meet Geraldine Van der Auwera, someone whose work I&rsquo;ve followed and admired for quite some time.   Her work has always amazed me, and meeting her in person was another highlight. This experience was enriched when I was invited to do an interview for the Nextflow podcast channel, an unexpected but thrilling event as it was a first for both of us.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share; fullscreen" loading="eager" referrerpolicy="strict-origin-when-cross-origin" src="https://www.youtube.com/embed/cDZWNIB3MIY?autoplay=0&amp;controls=1&amp;end=0&amp;loop=0&amp;mute=0&amp;start=0" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" title="YouTube video"></iframe> </div> <p>I also had the chance to present my work at the Nextflow Summit in a talk. The interaction with the audience during my presentation reinforced the sense of collaboration and community, making it clear that my coding efforts were part of a larger, shared journey.  It&rsquo;s these moments of exchange and learning that represent the spirit of the Nextflow Summit.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/12/Combined_34-1024x460.png" alt=""><em>Left: hackathon buzz; right: me presenting my talk at the Nextflow summit</em></p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share; fullscreen" loading="eager" referrerpolicy="strict-origin-when-cross-origin" src="https://www.youtube.com/embed/PzGOvqSI5n0?autoplay=0&amp;controls=1&amp;end=0&amp;loop=0&amp;mute=0&amp;start=0" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" title="YouTube video"></iframe> </div> <p>Raquel&rsquo;s presentation at the Nextflow Summit.</p> <p>But it wasn&rsquo;t all work! The summit ensured our schedules were packed with fascinating talks and social events. Making paella, going for runs, and attending a fancy party at the Barcelona port with Seqera&rsquo;s new sponsored team were just a few highlights. These experiences were fun and engaging, truly enjoyable events. Plus Barcelona, with its incredible beauty, was the perfect host. A walk – and a run – along the beach was a nostalgic reminder of my coastal hometown (Cadiz, Spain), bringing a piece of my heart into this global gathering.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/12/Combined_3-1-1024x807.png" alt=""><em>Top: Morning run along the beach; bottom left Shoko dinner party; bottom right: Social event in La Patente - cooking traditional paella.</em></p> <p>In conclusion, the nf-core Hackathon and Nextflow Summit 2023 were more than just gatherings; they were vibrant showcases of innovation, collaboration, and diverse cultures. With the support of the OBF travel grant and my supervisor, I&rsquo;ve come back not only re-energized about my work but also enriched with valuable new professional connections.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/12/Figure6.png" alt=""></p> <p><em>Participants at the nf-core hackathon</em></p>https://www.open-bio.org/2023/12/13/yvonne-walburga-journeys-across-oceans/Wed, 13 Dec 2023 13:59:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/12/13/yvonne-walburga-journeys-across-oceans/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Dr Yvonne Joko Walburga,</em></strong> <em><strong>a Post-doc at</strong></em> <em><strong>the University of Cambridge</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the</strong></em> <em><strong><a href="https://aorticconference.org/">African Organisation for Research and Training in Cancer (AORTIC) Cancer Conference</a></strong></em>.</p> <p>I initially applied for the OBF Travel Fellowship to attend the African Organisation for Research and Training in Cancer (AORTIC) Genomics Conference, and was accepted, but the timing was too tight. Happily, the board agreed to defer my funding to the next AORTIC Conference in November 2023 instead. So, I could make it for the AORTIC conference in Dakar, Senegal from November 2nd – 6th 2023 with support from the OBF Travel Fellowship and the African Cancer Registry Network.</p> <p>And what a conference it was!</p> <p>This was the third in-person AORTIC conference I have had the opportunity to present at. At this AORTIC conference, I was invited to give two oral presentations on work we had done during my PhD with the African Cancer Registry Network ( <a href="https://www.afcrn.org">https://www.afcrn.org</a>), at the University of Oxford, under the supervision of Prof. Max Parkin and Dr Paul McGale.</p> <p>It was an opportunity to give back and report on the work carried out by the registrars, who meticulously collect data on cancer incidence across sub-Saharan Africa. The AFCRN works with cancer registrars across the continent to harmonise the data collection, building capacity for robust data collection and analysis, and on how to use the CanReg5 software. CanReg5 is a freely accessible open-source tool that is used to input, store, quality check and analyse cancer registration data. ( <a href="http://www.iacr.com.fr/index.php?option=com_content&amp;view=article&amp;id=9:canreg5&amp;catid=68&amp;Itemid=445">http://www.iacr.com.fr/index.php?option=com_content&amp;view=article&amp;id=9:canreg5&amp;catid=68&amp;Itemid=445</a>). This generated data is used by national cancer control programs and by the International Agency for Research on Cancer (IARC) for the GLOBOCAN data reports <a href="https://gco.iarc.fr/today/home">https://gco.iarc.fr/today/home</a>.</p> <p>The first day of the conference (November 2nd, 2023) gave me the opportunity to join the satellite meeting of the Network for Oncology Research in Africa (NORA) consortium and to listen to and contribute to ideas on how we could collaborate and build partnerships for cancer surveillance and genomics research in sub-Saharan Africa.</p> <p>Following the NORA session, the organisers of the NORA consortium carved out time at the end of the session to visit the Island of Gorée. In typing Gorée, my English word editor quickly underlines it; curious as to what suggestions it would give me, I let my mouse hover.. it suggested <em>“Gore”</em> which means <em>“Blood, Stab, Violence”</em>. The Gorée Island is unspeakably beautiful; however, within its beauty, along its shores and especially at the “Door of No Return” – <em>“Porte du Voyage sans Retour”</em>, we must grapple with our shared history – that of slavery and its consequences – and also of a history stripped with <em>Gore</em> – <em>blood, stabs and violence</em>. As a post-doctoral researcher in cancer epidemiology who is now exploring population-level cancer genomics – I constantly think about the consequences of our shared ancestry with African- Americans, the immigrants from the Caribbean to the United Kingdom, and the Africans living on our beautiful African continent. However, there is such under-representation of this vast continent with very diverse populations, and in the era of personalised medicine and personalised risk reduction, we would widen health inequities if we do not improve access to progress in genomics to under-represented populations.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/12/Figure1.png" alt=""></p> <p>Figure 1: The &ldquo;Door of No Return&rdquo;/ &ldquo;Porte du Voyage Sans Retour&rdquo;, Gorée, Senegal</p> <p>My first oral abstract presentation on November 4th, 2023, was on “Cancer Survival in sub-Saharan Africa”. In this work, we described the population-level cancer survival outcomes of more than 10,000 sub-Saharan African patients with 18 different cancer types. This work was done with data from the African Cancer Registry Network, and in collaboration with the International Agency for Research on Cancer (IARC) and Vital Strategies. We highlighted the disparities in access to care and diagnostics for patients with cancers in sub-Saharan Africa and the resultant disastrous health outcomes. This work would not have been possible without working alongside the cancer registrars to improve the quality and representation of population-level cancer survival data, via the use of the open source CanReg5 software developed by IARC.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/12/Figure2.png" alt=""></p> <p>Figure 2: Oral presentation at the African Organisation for Research and Training in Cancer Meeting, Dakar 2023</p> <p>My second oral presentation was part of the African Cancer Registry’s Network session on “Cancer Surveillance in sub-Saharan Africa” on November 5th, 2023. In this session, I gave a talk on the “Incidence trends, stage and survival from breast cancer in sub-Saharan Africa”, the subject of my doctoral thesis. Studying trends in cancer incidence requires the availability of good quality data spanning several years. This was possible for 12 sub-Saharan African countries, largely thanks to the work of the AFCRN, on improving data coverage for cancer surveillance in Sub-Saharan Africa.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/12/Figure3.png" alt=""></p> <p>Figure 3: Presenters at the session on &ldquo;Cancer Surveillance in sub-Saharan Africa&rdquo;, hosted by the African Cancer Registry Network (AFCRN) at the African Organisation for Research on Cancer Conference (AORTIC), Dakar, Senegal.</p> <p>From left to right: Myself (Dr.Yvonne Joko Walburga), Dr. Mazvita Sengayi (Head of Department, National Cancer Registry South Africa), Prof. Cesaltina Lorenzoni (Pathologist, Head of the National Cancer Control Program at the Mozambican Ministry of Health and President-Elect – African Organisation for Research and Training in Cancer), Ms Biying Liu (Administrator of the AFCRN), Ms Lydia Businge (Rwanda Cancer Registry), Prof Max Parkin (Coordinator of the African Cancer Registry Network) and Dr. Muluken Gizaw (Assistant Professor, Addis Ababa University)</p> <p>I also had the opportunity to present an abstract titled “Systematic Review of Breast Cancer Risk Factors in sub-Saharan Africa” during the poster sessions. This enabled me to meet with, and discuss with researchers across the continent on how we could build collaborations to ensure more robust studies are conducted on the burden of risk factors pertinent to our context and to explore unique gene-environmental interactions.</p> <p>This AORTIC conference was my first post PhD, and during which I strongly felt that, the onus is on us to drive the change we want to see in terms of research, mentoring and collaboration. We are of the generation who <em>can</em> return to <em>the land</em> they could never return to. We must answer the questions that are pertinent to our continent, and we must leverage the power of our networks, our teams, and leap-frogs in technology to generate the data necessary to answer our health challenges. However, I know it is not an easy task; in a continent with a history of exploitation, how do we ensure that sharing our data brings the greatest good for all involved? Yet, as a continent, in spite of its history, we are known for our generosity, for being our brother’s keeper, and for the concept of <em>“Ubuntu”</em>. Thus, I strongly believe that together, we would find ways of tapping into what unites us, to carry out and share the benefits of our research on the African continent with those who need it most, and to help close the gaps of equity in access to quality healthcare.</p> <p>Finally, reflecting on this journey I made to Senegal, and on all the journeys we make across all types of boundaries and oceans, we must remember, we are never really alone, we are carried by the love and support of our families, by the encouragement of our mentors and advisers, and by the courage of those who went before us.</p>https://www.open-bio.org/2023/12/04/obf-public-board-meeting-2023-12-19/Mon, 04 Dec 2023 05:40:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/12/04/obf-public-board-meeting-2023-12-19/<h5 id="all-are-invited-to-join-us-via-zoom-at-the-obfs-upcoming-public-board-meeting">All are invited to join us (via Zoom) at the OBF&rsquo;s upcoming public Board meeting.</h5> <h2 id="date-time-and-how-to-join">Date, Time, and How to Join</h2> <ul> <li>Date and time: 2023-12-19, 16:00 UTC (8am PT / 11am ET / 4pm UK)</li> </ul> <h2 id="agenda">Agenda</h2> <h3 id="approve-october-2022-public-board-meeting-minutes">Approve <a href="https://github.com/OBF/obf-docs/pull/106">October 2022 Public Board Meeting minutes</a></h3> <h3 id="review-and-approve-minor-changes-to-bylaws">Review and approve minor changes to <a href="https://github.com/OBF/obf-docs/pull/102">bylaws</a></h3> <ul> <li>Remove one instance of gendered language, replacing &ldquo;her&rdquo; with &ldquo;their&rdquo;</li> <li>Change title of &ldquo;Secretary&rdquo; of Board to &ldquo;Vice President&rdquo; (with duties unchanged)</li> </ul> <h3 id="elections-to-the-board">Elections to the Board</h3> <ul> <li>Three Board members are up for re-election: Peter Cock (President), Heather Wiencko (Treasurer), and Hilmar Lapp (Member at Large)</li> <li>This will be an electronic ballot of the current board members</li> </ul> <h4 id="after-the-meeting-the-meeting-minutes-will-be-made-available-in-the-obf-docs-github-repository-as-a-pull-request">After the meeting, the meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs/tree/master/minutes">obf-docs GitHub repository</a> as a pull request.</h4>https://www.open-bio.org/2023/11/20/leaving-x/Mon, 20 Nov 2023 19:38:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/11/20/leaving-x/<p>As of November 21, 2023, the Open Bioinformatics Foundation and BOSC will no longer post on Twitter/X. Although in the past it was a useful social medium, it is no longer compatible with our values, as expressed in the <a href="https://github.com/OBF/obf-docs/blob/master/code-of-conduct/CODE_OF_CONDUCT.md">OBF Code of Conduct</a>:</p> <div class="well"> <p>We are committed to creating a friendly and respectful place for learning, sharing and contributing. All participants in our events and communications are expected to show respect and courtesy to others.</p> </div> <p>Currently, we are not planning to delete our X/Twitter accounts (@OBF_NEWS and @OBF_BOSC); we will leave them as archives.</p> <p>Even before recent events prompted our final departure, we were already transitioning off of X in favor of other social media. You can find us at:</p> <ul> <li>LinkedIn: <ul> <li>BOSC: <a href="https://www.linkedin.com/groups/14344023/">https://www.linkedin.com/groups/14344023/</a></li> <li>OBF: <a href="https://www.linkedin.com/groups/9539620/">https://www.linkedin.com/groups/9539620/</a></li> </ul> </li> <li>Mastodon: <ul> <li>BOSC: <a href="https://genomic.social/@BOSC">https://genomic.social/@BOSC</a></li> <li>OBF: <a href="https://genomic.social/@OpenBio">https://genomic.social/@OpenBio</a></li> </ul> </li> <li>Blue Sky: <ul> <li>BOSC: <a href="https://bsky.app/profile/bosc.bsky.social">https://bsky.app/profile/bosc.bsky.social</a></li> <li>OBF: <a href="https://bsky.app/profile/openbio.bsky.social">https://bsky.app/profile/openbio.bsky.social</a></li> </ul> </li> <li>Slack: <ul> <li><a href="https://obf-bosc.slack.com/join/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew#/shared-invite/email">BOSC</a></li> <li><a href="https://open-bio.slack.com/join/shared_invite/zt-1pnswao9y-8igcckVxBXhQHCMweHt_NA#/shared-invite/email">OBF</a></li> </ul> </li> <li>YouTube: <a href="http://youtube.com/c/OBFBOSC">http://youtube.com/c/OBFBOSC</a></li> <li>Blog: <a href="https://www.open-bio.org/blog/">https://open-bio.org/blog/</a></li> </ul> <p>We encourage our community to join us on these platforms that foster respectful and constructive dialogue.</p>https://www.open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/Thu, 09 Nov 2023 17:43:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/<p>In conjunction with our annual meeting, <a href="https://www.open-bio.org/events/bosc/">BOSC</a>, the <a href="https://www.open-bio.org/">OBF</a> runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you.</p> <p>The 2024 BOSC CoFest, which will follow ISMB 2024, will take place July 17-18, and will be hybrid (in person in Montréal + online).</p> <p>We encourage you to register for ISMB, but the CoFest itself is free. Three easy steps to sign up:</p> <ul> <li>add yourself to this <a href="https://docs.google.com/spreadsheets/d/1FWH-SUPNVUi70-oVuqoaYZq4Klt03WWAFCGe1eHZJZM/edit?usp=sharing">spreadsheet</a> to help us gauge interest, coordinate topic groups and logistics</li> <li>add your project ideas in this <a href="https://docs.google.com/document/d/1-tvrtBBcJJ8EhiIXQhjo4B3x796cSb9OG_6ynPVM_zM/edit?usp=sharing">document</a> if you have something in mind,</li> <li>join the #cofest channel in the <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">BOSC Slack</a>!</li> </ul> <p>Please register in advance to help us set up everything!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/codefest-big-group-on-steps.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h3 id="date">Date</h3> <p>Wednesday July 17 to Thursday July 18.</p> <h3 id="location">Location</h3> <p>We will be hosted by the <a href="https://uqam.ca/">UQAM</a>, on the “east” campus in downtown Montreal, in the Room A-M640 of the <a href="https://plancampus.uqam.ca/pavillon-a">Hubert-Aquin building</a>, located at <a href="https://g.co/kgs/59yiicF">400 rue Sainte-Catherine Est, Montréal, QC H2L 2C5</a>.</p> <h3 id="public-transport">Public transport</h3> <p><a href="https://maps.app.goo.gl/pdgwcnKUxqX2sKru6">Berri-UQAM metro station</a></p> <h3 id="sponsors">Sponsors</h3> <div class="splitbox"><div class="left"> <p><a href="https://diallolab.com"><img src="https://www.open-bio.org/wp-content/uploads/2024/06/Logo_BioInfo.jpg" alt=""> <br> Diallo Lab</a></p> </div><div class="right"> <p>[<img src="https://www.open-bio.org/wp-content/uploads/2024/06/UQAM.png" alt=""> <a href="https://uqam.ca/">Université du Québec à Montréal</a></p> </div><div style="clear:both"></div></div> <h3 id="history">History</h3> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/CoFest2023-lunch-1.png" alt="Lunch at the 2023 BOSC CoFest"></p> </div><div class="right"> <p>CoFest 2024 will be the 15th annual pre- or post-BOSC collaboration fest. Previous fun and successful events were <a href="https://www.open-bio.org/wiki/Codefest_2010">Codefest 2010</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> in Vienna, <a href="https://www.open-bio.org/wiki/Codefest_2012">Codefest 2012</a> in Los Angeles, <a href="https://www.open-bio.org/wiki/Codefest_2013">Codefest 2013</a> in Berlin, <a href="https://www.open-bio.org/wiki/Codefest_2014">Codefest 2014</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2015">Codefest 2015</a> in Dublin, <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a> in Orlando, <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> in Prague, <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC Collaboration Fest 2018</a> in Portland, <a href="https://www.open-bio.org/events/bosc/bosc-2019-collaborationfest">Collaboration Fest 2019</a> in Basel, and the last two worldwide virtual editions <a href="https://www.open-bio.org/events/bosc-2020/bosc-2020-collaborationfest/">BOSC 2020 CollaborationFest</a>/ <a href="https://bcc2020.github.io/cofest/">BCC2020 CollaborationFest</a> (online) and <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">Collaboration Fest 2021</a> (online). The <a href="https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/">2022 CollaborationFest</a> was hybrid (virtual + in person). The <a href="https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest/">2023 CollaborationFest</a> was in Lyon (+ remote attendees).</p> </div><div style="clear:both"></div></div> <h3 id="code-of-conduct">Code of Conduct</h3> <p>This event is under the <a href="https://www.open-bio.org/code-of-conduct/">OBF Code of Conduct</a>.</p>https://www.open-bio.org/events/bosc-2024/Sun, 29 Oct 2023 00:29:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2024/<p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/BOSC2023-crowded-room-Karsten-holding-mic-1-1-1024x307.png" alt=""></p> <p><strong>BOSC 2024</strong>, the 25th annual Bioinformatics Open Source Conference, took place place July 15-16, 2024, as part of <a href="https://www.iscb.org/ismb2024/">ISMB 2024</a>, in Montréal, Canada and online. BOSC covers open source bioinformatics and open science. The theme for 2024 was Open Approaches to AI/ML; it was reflected in a <a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-panel">panel discussion</a> and a talk session.</p> <p>Videos of the talks from BOSC 2024 are available on our <a href="https://www.youtube.com/@OBFBOSC/">YouTube channel</a>. Our report about BOSC 2024 is <a href="https://f1000research.com/articles/13-1100">published in F1000Research</a>.</p> <p><strong><a href="https://www.open-bio.org/events/bosc-2025/">BOSC 2025</a></strong> will take place July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025).</p> <h3 id="bosc-2024-keynotes"><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes/">BOSC 2024 Keynotes:</a></h3> <img src="https://www.open-bio.org/wp-content/uploads/2024/03/Melanie-Courtot-1-1.png" alt ="Mélanie Courtot" style="width:50%"/> <p><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes/"><strong>Mélanie Courtot: The Data Shows We Need Better Data</strong></a></p> <img src="https://www.open-bio.org/wp-content/uploads/2024/03/Andrew_Su_smll.jpg" alt ="Andrew Su" style="width:50%"/> <p><a href="https://www.open-bio.org/events/bosc-2024/bosc-2024-keynotes/"><strong>Andrew Su: Open Data, Knowledge Graphs, and Large Language Models</strong></a></p> <h3 id="2024-key-dates">2024 Key Dates</h3> <ul> <li>March 21, 2024: <a href="https://www.open-bio.org/2023/03/09/bosc-early-poster-acceptance/">Early Poster Acceptance</a> submission deadline</li> <li>April 19, 2024: Regular abstract submission deadline (talks and posters)</li> <li>May 20, 2024: Late poster submission deadline</li> <li>July 12-16, 2024: <a href="https://www.iscb.org/ismb2024/">ISMB 2024</a> (Montréal, Canada and online)</li> <li><strong>July 15-16, 2024:</strong> <strong>BOSC 2024</strong> (part of ISMB)</li> <li>July 17-18, 2024: Post-BOSC <a href="https://www.open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/">CollaborationFest</a></li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Sara-El-Gebali_Scott-Edmunds_Deepak-Unni-1-1024x768.jpeg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Nomi-Deepak-Vasundra-1-1024x782.jpeg" alt=""></p> <h3 id="topics">Topics</h3> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Data Access and Visualization</li> <li>Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach and Training</li> <li>AI/ML: open approaches</li> </ul> <h3 id="registration-and-financial-assistance">Registration and Financial Assistance</h3> <p>To participate in BOSC 2024, you will need to <a href="https://www.iscb.org/ismb2024/register">register for ISMB 2024</a>. Those who submit abstracts to BOSC can request a fee waiver on the submission form. You can also apply for an <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation Event Award</a> (deadlines in April, August, and November).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image4-1024x610.jpg" alt="Panelists Verena Ras, Sara El-Gebali, Bastian Greshake Tzovaras, and Monica Munoz-Torres"></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Ferdous-Nasri-1-1-1.png" alt=""></p> <h2 id="sponsorships">Sponsorships</h2> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from companies and non-profit organizations help to defray some of our costs and support our diversity/inclusion efforts. Thanks to our sponsors, we were able to grant free registration to 15 participants at BOSC 2023, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you&rsquo;re interested in sponsoring BOSC 2024, please see our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors page</a>!</p> <p><strong>Platinum Sponsors:</strong></p> <p><a href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" alt="seqera"></a></p> <p><a href="https://chanzuckerberg.com/science"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="CZI"></a></p> <p><strong>Gold Sponsor:</strong></p> <p><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Data Science"></a></p> <p><strong>Silver Sponsor:</strong></p> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a></p> <h2 id="bosc-2024-organizing-committee">BOSC 2024 Organizing Committee</h2> <p><strong>Chair: Nomi L. Harris</strong> (Lawrence Berkeley National Laboratory)</p> <ul> <li>Karsten Hokamp (Trinity College Dublin)</li> <li>Jason Williams (Cold Spring Harbor Laboratory)</li> <li>Jessica Maia (BD)</li> <li>Chris Fields (University of Illinois, Champaign-Urbana)</li> <li>Deepak Unni (SIB, Swiss Institute of Bioinformatics)</li> <li>Swapnil Sawant (Phoenix Bioinformatics)</li> <li>Monica Munoz-Torres (Univ. of Colorado Anschutz Medical Campus)</li> <li>Hervé Ménager (Institut Pasteur)</li> </ul> <h3 id="2024-review-committee">2024 Review Committee</h3> <p>Emmanuel Adamolekun, Jenea Adams, Suruchi Ahuja, C.Titus Brown, Seth Carbon, J. Harry Caufield, Tyrone Chen, Christopher Fields, Bastian Greshake Tzovaras, Karsten Hokamp, Arpita Joshi, Aziz Khan, Kartik Khosa, Hilmar Lapp, Hervé Ménager, Nehemiah Mosioma, Monica Munoz-Torres, Tazro Ohta, Konstantin Okonechnikov, Bhavesh Patel, Surya Saha, Swapnil Sawant, Ian Simpson, Rachel Torchet, Deepak Unni</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/05/bosc-2024-org-committee.png" alt="BOSC 2024 Organizing Committee"></p> <h2 id="about-bosc">About BOSC</h2> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <p>BOSC is usually preceded or followed by what we now call <a href="https://www.open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/">CollaborationFest</a> ( <a href="https://www.open-bio.org/events/bosc-2024/obf-bosc-collaborationfest-2024/">CoFest</a> for short), a two-day community development session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. All are welcome to attend CoFest, whether or not you attend BOSC!</p> <p><a href="https://www.open-bio.org/events/bosc/about/">More about BOSC&hellip;</a></p> <h2 id="code-of-conduct">Code of Conduct</h2> <p>As part of ISMB 2024, BOSC 2024 is covered by the <a href="https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct">ISCB Code of Ethics and Professional Conduct</a>.</p>https://www.open-bio.org/2023/10/19/event-fellowship-2023-3/Thu, 19 Oct 2023 00:27:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/10/19/event-fellowship-2023-3/<h3 id="the-call-for-applications-for-the-obf-event-fellowship-2023-round-3-is-now-open-the-deadline-for-this-round-is-1-december-2023-applications-should-be-submitted-via-this-google-form-we-have-provided-a-word-template-to-help-you-draft-the-application-locally-before-filling-out-the-form--make-a-copy-of-this-template">The call for applications for the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> 2023, round 3, is now open. <strong>The deadline for this round is 1 December 2023.</strong> Applications should be submitted via <a href="https://forms.gle/BK2wQbmEgmX2iLbH7">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/1-9NUd5_gv2PnuGR7Rl9vN7Kl3vV5gUFO-GyIC1LK0wI/edit?usp=sharing">make a copy of this template</a>.</h3> <p>The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from January 2024 to August 2024. <strong><em>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><img src="https://lh7-us.googleusercontent.com/ILTxVO48ccZ6TAE7eLiXeNhg5_iWnuNbH9eD-h4QVwSrIQGmp-EmR1Dtz7AcJsmSgy5DI_bLprp3nSEVZ2_piDpjANSDUfiEdGRe_zonQglJObJOp16onaiZ84mf2G77E3dudzoyB3GpNd5GFWjwFJ4" alt=""></p> <p><em>Screenshot of our application form information section</em></p> <p><strong>Overview of round two of OBF Event Fellowship 2023</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 7th year. Starting in 2023, we open three calls for applications with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In 2023 round 2 (August 2023), we received numerous applications, of which one applicant was awarded this fellowship for the event they were participating in. Congratulations to <strong>Raquel Manzano Garcia.</strong> This fellowship will support her participation in the Nextflow summit, where she will be presenting her work on “Development of an Integrated DNA and RNA Variant Calling Pipeline”.</p> <p>We recently published blog posts from three of our recent awardees summarising their experiences attending conferences with help from OBF Event Fellowships:</p> <ul> <li>Nehemiah Ongeso: <a href="https://www.open-bio.org/2023/08/07/nehemia-conference-experience-at-smbe23/">Embracing Science and Culture: My Memorable Conference Experience at SMBE23 in Ferrara, Italy</a></li> <li>Daniela Senra: <a href="https://www.open-bio.org/2023/08/02/daniela-senra-experience-human-cell-atlas-2023/">My Experience at the Human Cell Atlas General Meeting 2023</a></li> <li> Michell Salcan <a href="https://www.open-bio.org/2023/09/16/my-wonderful-experience-at-lanet-2023/">My Wonderful Experience at LANET 2023 in Cusco, Peru</a></li> </ul> <p>Congratulations to all of our awardees!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and apply for the fellowship before 1 December 2023</strong>.</p>https://www.open-bio.org/2023/09/29/bosc-collaborationfest-2023-report/Fri, 29 Sep 2023 22:08:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/09/29/bosc-collaborationfest-2023-report/<p><img src="https://www.open-bio.org/wp-content/uploads/2023/10/CoFest2023_welcome.jpg" alt=""></p> <p><strong>CollaborationFest</strong>, CoFest for short, is a collaborative work event that has been held each of the past 13 years as a satellite event of BOSC. At these free events, held right before or after BOSC, participants  gather in small groups to exchange ideas and work together on projects including but not limited to hacking. Participants were encouraged to submit their project ideas in advance to facilitate collaboration.</p> <p><a href="https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/"><strong>CoFest 2023</strong></a> took place during the two days just before <a href="https://www.open-bio.org/2023/08/14/bosc-2023-report/">BOSC</a>, which was part of ISMB/ECCB 2023 in Lyon and online. It was the first in-person edition after several online-only CoFests, due to Covid pandemics. It was hosted by Jérémy Just at the nearby <a href="https://www.ens-lyon.fr/en/"><em>École Normale Supérieure de Lyon</em></a>, which provided space and infrastructure, with funding from <a href="https://www.ixxi.fr/?set_language=en"><em>Complex Systems Institute</em></a> for lunches and coffee breaks. Free virtual machines were made available by the <a href="https://www.france-bioinformatique.fr/en/home/"><em>French Institute for Bioinformatics</em></a> and the <a href="https://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil"><em>Pôle scientifique de modélisation numérique</em></a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/09/project_list-1024x1024.jpg" alt="">List of the projects submitted in advance by the participants for BOSC CoFest 2023.</p> <p>CoFest brought together 29 in-person participants as well as numerous online participants, experts in fields as diverse as plant biology and personalized medicine.</p> <p>We were pleased to have many local and first-time attendees participate in this edition of CoFest.</p> <p>A 360° webcam, kindly lent by <a href="https://elixir-europe.org/">Elixir</a> for the CoFest, allowed remote attendees to see the whole meeting room during work sessions.</p> <p>As in previous years, CoFest participants engaged in a wide variety of projects focused on topics such as the documentation of existing software, the review and discussion of novel technologies, the improvement of existing tools, and several FAIR-related projects.</p> <p>In total, the participants worked on ten different projects, with tangible accomplishments for several subtasks of these projects. In addition, cross-project discussions facilitated progress on many projects, exchanging perspectives and pointers between participants. The synergies and discussions between the various groups were remarkable.</p> <blockquote> <p><strong>We would like to thank the entire <a href="https://www.open-bio.org/">OBF community</a> for maintaining the positive atmosphere that makes such events a reproducible success!</strong></p> </blockquote> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/09/CoFest_lunch_collage-1024x575.jpg" alt="">A few pictures of lunches during BOSC CoFest 2023, in the ENS gardens.</p> <h1 id="some-advances-made-during-cofest-2023">Some advances made during CoFest 2023</h1> <p>(Many thanks to Hervé Ménager for keeping track of the projects during the CoFest, and for his warm encouragement during all the preparation for the event!)</p> <h2 id="new-features-added-to-icn3d-protein-viewer">New features added to iCn3D protein viewer</h2> <h3 id="proposal">Proposal</h3> <p><a href="https://doi.org/10.1093/bioinformatics/btz502">iCn3D</a> is a web-based 3D structure viewer synchronizing 1D, 2D, and 3D view, <em>e.g.</em> <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=1TUP&amp;showanno=1&amp;show2d=1">https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=1TUP&amp;showanno=1&amp;show2d=1</a>. The 1D sequence view shows all kinds of annotations ( <em>e.g.</em> domains, SNPs, etc) in tracks. This project will show the start and end positions of exons in the sequence, and show the sequence of isoforms of the protein and their exons. Thus users can clearly see the exon skipping and potentially relate the exon skipping to the protein functions.</p> <h3 id="what-was-done">What was done</h3> <p>During the CoFest, the <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/">iCn3D viewer</a> got a new feature to show isoforms and exons as tracks with the button &ldquo;Add Track&rdquo; in the &ldquo;Sequences &amp; Annotations&rdquo; window via the menu &ldquo;Analysis &gt; Sequences &amp; Annotations&rdquo;. One example is at <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?pA3pPu7LxdiuZDVX7">https://structure.ncbi.nlm.nih.gov/icn3d/share.html?pA3pPu7LxdiuZDVX7</a>:</p> <p><img src="https://lh6.googleusercontent.com/dA1--0Lbv64qwvLSA5dgZmrns9Wbm8yZqRrLWEIiRUiJqn0QgEcKZXXNnY_ScF2taDziqInDVv2u0eHgZuUs5ElMOb8STzZePrJbY0shxpo-a1EFfiAMQbGOOAtyWo_KIN9Ov7ZXGhQBGt5icf2wBFQ" alt=""></p> <p>Users can also predict structures from sequences using ESMFold directly in iCn3D via the menu &ldquo;File &gt; Predict by Seq. &gt; ESMFold&rdquo;. Other features of iCn3D are listed in its GitHub page: <a href="https://github.com/ncbi/icn3d">https://github.com/ncbi/icn3d</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/09/9780596002992_internet_w290.jpg" alt="">The BLAST book from 2003 (cover).</p> <h2 id="updating-the-blast-book">Updating the BLAST book</h2> <h3 id="proposal-1">Proposal</h3> <p>The <a href="https://www.oreilly.com/library/view/blast/0596002998/">BLAST book</a>, by Ian Korf, was published in 2003. It provides a lot of &ldquo;recipes&rdquo; for Blast searches in different contexts. Since then, however, the syntax of most tools from the Blast suite has changed, with the introduction of Blast+ in 2009. The wrapper currently distributed with Blast+ to convert the old syntax (blastall) has quite limited features. My idea is to update the command examples in the book to the new syntax, explain new options, and identify places that need more in-depth updating.</p> <p>The main author, <a href="http://korflab.ucdavis.edu/Bios/bio_ian.html">Ian Korf</a>, had been contacted in advance: he&rsquo;s not against a new book about Blast, but he doesn&rsquo;t want to be involved. Two hard copies of Korf’s book will be available during CoFest.</p> <h3 id="what-was-done-1">What was done</h3> <ul> <li>Scoping discussion on Slack (when should we contact the original publisher?),</li> <li>Side-by-side option table ( <em>old</em> vs <em>new</em> options),</li> <li>Practical testing of old examples from the book using the new syntax.</li> </ul> <h3 id="future-work">Future work</h3> <ul> <li>Write down the updated examples as a <a href="https://github.com/jejust/blast_book_plus">web page</a>,</li> <li>Contact O’Reilly, the publisher of the book, and see if they are interested in a new edition. In any case, the updated examples will be available to the community on a webpage (GitHub or better).</li> </ul> <p><a href="https://biopython.org/"><img src="https://www.open-bio.org/wp-content/uploads/2023/09/biopython_logo_s.png" alt=""></a></p> <h2 id="progress-on-various-biopython-projects">Progress on various Biopython projects</h2> <h3 id="proposal-2">Proposal</h3> <p>Peter Cock will be attending remotely, but as one of the regular Biopython contributors will try to match any newcomers with suitable projects/issues. He hopes to work on migrating the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Tutorial documentation</a> from LaTeX to RST to simplify and automate it for each release (see <a href="https://github.com/biopython/biopython/pull/4371">PR 4371</a>). See the #cofest-biopython channel on <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">BOSC Slack</a>.</p> <h3 id="what-was-done-2">What was done</h3> <ul> <li>Progress on LaTeX to RST/Sphinx conversion of <a href="https://github.com/biopython/biopython/tree/master/Doc">Tutorial</a> (tables, citations).</li> <li>Improvements to a script dealing with big FASTQ files: speed up reads extraction (6x faster).</li> </ul> <h3 id="future-work-1">Future work</h3> <ul> <li>Try to get the converted Tutorial to build without errors.</li> </ul> <h3 id="question-to-cofest-group">Question to CoFest group</h3> <p>What file format would you prefer for the Tutorial (HTML, PDF, eBook&hellip;)?</p> <h2 id="multik-parallelization-using-future">MultiK parallelization using <strong><code>Future</code></strong></h2> <h3 id="proposal-3">Proposal</h3> <p><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02445-5">MultiK</a> is a R package built upon <a href="https://satijalab.org/seurat/">Seurat</a> that objectively selects multiple insightful numbers of clusters ( <em>K</em>) in a single-cell RNA-seq dataset.</p> <p>However the main function of the package is very expensive both in computing and in time since it is not parallelized.</p> <p>The idea would be to attempt to parallelize it using the <a href="https://future.futureverse.org/">Future</a> package (which is already used by Seurat) in order to speed up scRNA-Seq workflows making use of it.</p> <h3 id="what-was-done-3">What was done</h3> <ul> <li>The first main loop (out of two) was parallelized: <ul> <li>works when used locally &amp; remotely on a small dataset,</li> <li>10x performance for the whole function.</li> </ul> </li> </ul> <h3 id="future-work-2">Future work</h3> <ul> <li>MultiK crashes when processing the whole dataset remotely (“ <code>Error: Detected a non-exportable reference ('externalptr') used in the future expression</code>”): we plan to investigate further on that,</li> <li>Parallelize the second main loop of MultiK.</li> </ul> <h2 id="make-installation-of-bionano-tools-easier">Make installation of Bionano tools easier</h2> <h3 id="proposal-4">Proposal</h3> <p><a href="https://bionano.com/">Bionano</a> is a technology to create optical maps from HMW DNA. One major problem is the lack of tools options for analysis since there are only tools provided by <em>Bionano Genomics</em> : Bionano Access (server and GUI) and Bionano Solve (analysis software).</p> <p>The <a href="https://bionano.com/wp-content/uploads/2023/04/CG-30182_Bionano-Solve-Installation-Guide.pdf">installation of Bionano Solve</a> is clumsy : it uses a docker image to install dependencies. My idea is to retrieve all the dependencies used from the docker image to create a bioconda recipe in order to easily install and maintain Bionano Solve software dependencies.</p> <h3 id="what-was-done-4">What was done</h3> <ul> <li>Installation of currently available Bionano docker image,</li> <li>Inspection of Bionano tools installation script.</li> </ul> <h3 id="future-work-3">Future work</h3> <ul> <li>Detailed list of dependencies, starting from Python / R packages and software present in the docker image,</li> <li>(Bio)Conda recipe documentation exploration.</li> </ul> <h2 id="applications-of-open-source-llms-in-bioinformatics">Applications of open source LLMs in bioinformatics</h2> <h3 id="proposal-5">Proposal</h3> <p>This group aims to explore the applications and promotion of open source large language models (LLMs) in the field of bioinformatics. LLMs have gained popularity, and the community seeks models that offer accessibility and transparency. Strategies for collaboration and community engagement, including the use of shared repositories and benchmarking frameworks, will be discussed. Ethical considerations such as data privacy, bias, and interpretability will also be explored.</p> <p><strong>Sharing resources and ideas:</strong></p> <p><a href="https://docs.google.com/document/d/1fxA3JCtPkScm7vXSFQqPJtgP6OEZgAwN7-o_pKtoH5c/edit?usp=sharing">https://docs.google.com/document/d/1fxA3JCtPkScm7vXSFQqPJtgP6OEZgAwN7-o_pKtoH5c/edit?usp=sharing</a></p> <h3 id="what-was-done-5">What was done</h3> <ul> <li>Shared documentation to collect ideas and useful links: <ul> <li>Tips for choosing/testing open source LLMs,</li> <li>Some ideas for applications and benchmarking of the models.</li> </ul> </li> </ul> <h3 id="future-work-4">Future work</h3> <ul> <li>Summarize the document and merge it into the paper being prepared by the LLM group from <a href="https://2023.biohackathon.org/">BioHackathon Japan</a> that will be submitted to <a href="http://preview.biohackrxiv.org/">BioHackrXiv</a> : <ul> <li><a href="https://biohackrxiv.org/discover?q=BioHackJP%202023">BioHackJP 2023</a>.</li> </ul> </li> </ul> <h2 id="fair-biomedical-research-software-fair-biors">FAIR Biomedical Research Software (FAIR-BioRS)</h2> <h3 id="proposal-6">Proposal</h3> <p>Most would agree that making biomedical research software (code, scripts, desktop software, Jupyter Notebooks, etc.) reusable is essential to prevent duplicate effort, enable building on top of existing work, and ultimately increase the pace of discoveries and innovations for improving human health. The question then is, how do we make biomedical research software reusable? The Findable, Accessible, Interoperable, and Reusable principles for Research Software (or <a href="https://doi.org/10.1038/s41597-022-01710-x">FAIR4RS principles</a>) published in 2022 provide high-level instructions to achieve that. It is the result of a large-scale effort and is backed by a large community of research software developers. However, just like the original FAIR principles, the FAIR4RS principles remain aspirational and do not provide clear actionable instructions. To address this, we have established the FAIR Biomedical Research Software (FAIR-BioRS) guidelines, that provide clear, actionable step-by-step instructions for making biomedical research software reusable in line with the FAIR4RS principles. Our idea here is to discuss the current version (v2.0.0) of the FAIR-BioRS guidelines, identify if/how they can be improved, brainstorm on how they can be maintained going forward, etc. so as a community we can start adhering consistently with the FAIR4RS principles to make our software reusable and also provide clear guidelines to do so especially for the next generation of biomedical software developers.</p> <h3 id="what-was-done-6">What was done</h3> <ul> <li>Worked with some attendees to explore how the <a href="https://github.com/FAIR-BioRS/Code">guidelines</a> would apply to their project,</li> <li>Scope discussion, and at least one pull request merged,</li> <li>Notes from discussion available at <a href="https://etherpad.osuosl.org/p/Cofest2023-fair-BioRS">https://etherpad.osuosl.org/p/Cofest2023-fair-BioRS</a>,</li> <li>Discussion to wrap up on the paper and plan for future outreach/communication effort.</li> </ul> <p><strong>That’s the second CoFest edition this project is worked on (already in 2022), and its outcome is now published in a peer-reviewed paper:</strong></p> <p><em>Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool</em>. Bhavesh Patel, Sanjay Soundarajan, Hervé Ménager and Zicheng Hu, <em>Scientific Data</em> <strong>10</strong>:557 (2023). <a href="https://doi.org/10.1038/s41597-023-02463-x">doi:10.1038/s41597-023-02463-x</a></p> <h3 id="future-work-5">Future work</h3> <ul> <li>Outreach/communication effort.</li> </ul> <h3 id="question-to-cofest-group-1">Question to CoFest group</h3> <ul> <li>Would you use the guidelines to make your research software reusable? If not, why, how can they be improved?</li> </ul> <p><a href="https://www.commonwl.org/"><img src="https://www.open-bio.org/wp-content/uploads/2023/09/CWL-Logo-HD-2-1024x654.png" alt=""></a></p> <h2 id="next-release-of-common-workflow-language">Next release of Common Workflow Language</h2> <h3 id="proposal-7">Proposal</h3> <p>108 proposed clarifications to the <a href="https://www.commonwl.org/"><em>Common Workflow Language</em></a> <em>v1.2 standards</em> need summarizing before release v1.2.1.</p> <h3 id="what-was-done-7">What was done</h3> <ul> <li>All done!</li> </ul> <p><strong>See:</strong></p> <ul> <li><a href="https://deploy-preview-262--cwl-v1-2-dev.netlify.app/commandlinetool#Introduction_to_the_CWL_Command_Line_Tool_draft_standard_v1.2.1">Introduction to the CWL Command Line Tool draft standard v1.2.1</a>,</li> <li><a href="https://deploy-preview-262--cwl-v1-2-dev.netlify.app/workflow#Changelog_for_v1.2.1">Changelog_for_v1.2.1</a>.</li> </ul> <h3 id="future-work-6">Future work</h3> <ul> <li>Get these changes reviewed &amp; merged.</li> </ul> <h3 id="questions-to-cofest-group">Questions to CoFest group</h3> <ul> <li><a href="https://github.com/common-workflow-language/cwl-v1.2/pull/262/files">Reviews</a> are very welcome! (Especially by those with CWL experience)</li> </ul> <h2 id="sparql-wr-ro-crate-queries">SPARQL WR RO-Crate queries</h2> <h3 id="what-was-done-8">What was done</h3> <ul> <li>Made <a href="https://github.com/RenskeW/runcrate-analysis/tree/main/test-prov">SPARQL queries</a> to answer provenance questions from <code>ro-crate-manifest.json</code>.</li> </ul> <h3 id="future-work-7">Future work</h3> <ul> <li>Add more queries to the list.</li> </ul> <h3 id="question-to-cofest-group-2">Question to CoFest group</h3> <ul> <li>How to use SPARQL queries as unit tests?</li> </ul> <h2 id="wfexs-backend-changes-to-support-envvars-and-get-conformant-to-workflow-run-ro-crate-02">WfExS-backend changes to support <strong><code>envvars</code></strong> and get conformant to Workflow Run RO-Crate 0.2</h2> <h3 id="what-was-done-9">What was done</h3> <ul> <li>Added support to describe environment variables needed by a workflow execution.</li> <li>Integrated used environment variables as inputs in Workflow Run RO-Crate, using FormalParameter. There is no standard way to signal which FormalParameters are a traditional workflow parameter and which are environment variables (besides the id).</li> <li><em>(partially implemented)</em> Output files and directories are not using an nih URI any more.</li> <li><em>(work in progress)</em> Better representation of CWL workflow dependencies, so the usage of an external ontology does not appear as a &ldquo;hard&rdquo; dependency itself.</li> </ul> <h1 id="our-sponsors">Our sponsors</h1> <p>We are grateful to all the sponsors who allowed us to host the BOSC CoFest 2023 in Lyon in excellent conditions and made it so successful:</p> <p><a href="https://www.ixxi.fr/"><img src="https://www.open-bio.org/wp-content/uploads/2023/09/IXXI_Logo.png" alt=""></a><a href="https://www.ixxi.fr/">Complex Systems Institute Rhône-Alpes</a><a href="http://www.ens-lyon.fr/"><img src="https://www.open-bio.org/wp-content/uploads/2023/06/ens_logo.png" alt=""></a><a href="http://www.ens-lyon.fr">École normale supérieure de Lyon</a><a href="http://www.ens-lyon.fr/RDP/"><img src="https://www.open-bio.org/wp-content/uploads/2023/06/ens_rdp_logo.jpeg" alt=""></a><a href="http://www.ens-lyon.fr/RDP/">Laboratoire Reproduction et développement des plantes</a><a href="https://www.france-bioinformatique.fr/en/"><img src="https://www.open-bio.org/wp-content/uploads/2023/09/IFB-HAUT-COULEUR-GRAND.png" alt=""></a><a href="https://www.france-bioinformatique.fr/en/">French Institute for Bioinformatics</a></p> <p>We would also like to apologize to all our colleagues who would have liked to attend but had holiday date constraints this summer. Keep updated for next editions!</p> <h2 id="our-suppliers">Our suppliers</h2> <p>All the catering was purchased from local providers and carried by bike. They will probably not deliver abroad, but if you pass by Lyon and feel hungry, you can for sure trust them:</p> <ul> <li>Main caterer for lunches: <a href="https://www.cyril-nitard.com/">Cyril Nitard</a>,</li> <li>Baker: boulangerie <a href="https://www.leprogres.fr/economie/2022/07/15/la-boulangerie-patisserie-ondo-vernin-une-affaire-de-famille">Ondo-Vernin</a>,</li> <li>Cheese-seller: fromagerie <a href="https://www.fromagerielestroisjean.com/">Les Trois Jean</a>,</li> <li>Fruits and fruit juices: <a href="https://www.cerise-et-potiron.fr/store/monplaisir/">Cerise et Potiron Monplaisir</a> (have a look <a href="https://www.instagram.com/sebgana/">at some creations</a>).</li> </ul> <p>We did our best to minimize waste, by using reusable containers for lunches and coffee breaks (including drink bottles, glasses, cups, plates, silverware…).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/09/CoFest_baker_delivery-576x1024.jpg" alt="">Coffee break</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/09/CoFest_lunch_table-768x1024.jpg" alt="">Happy participants at lunch</p>https://www.open-bio.org/2023/09/18/iscbacademy-webinar-oct-3/Mon, 18 Sep 2023 05:31:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/09/18/iscbacademy-webinar-oct-3/<h3 id="sierra-moxon-to-speak-about-linkml-an-open-data-modeling-framework-grounded-with-ontologies">Sierra Moxon to speak about &ldquo;LinkML: an open data modeling framework, grounded with ontologies&rdquo;</h3> <p><strong>[If you missed the webinar, the video is <a href="https://www.youtube.com/watch?v=nyNp09WYLzw">here</a> and the slides are <a href="https://docs.google.com/presentation/d/1elqZxqtQeVzRUiBlmxnyzPhcE4OgOoKoPCaKH_z2d3g/edit">here</a>.]</strong></p> <p><a href="https://www.iscb.org/iscbacademy">ISCBacademy</a> is a series of free webinars sponsored by the International Society for Computational Biology. They are open to all, including those who are not ISCB members. ISCB members can access the webinars via the ISCB Nucleus platform: <a href="https://iscb.junolive.co/">https://iscb.junolive.co/</a>. Non-members need to register for Nucleus: <a href="https://iscb.swoogo.com/ISCBnucleus-registration">https://iscb.swoogo.com/ISCBnucleus-registration</a></p> <p>BOSC and Bio-Ontologies are pleased to co-host an ISCBacademy talk on <strong>October 3, 2023, at 8am Pacific Daylight Time (15:00 UTC).</strong> Sierra Moxon (see bio below) will speak about &ldquo;LinkML: an open data modeling framework, grounded with ontologies&rdquo;.</p> <h4 id="abstract">Abstract</h4> <p>The Linked data Modeling Language (LinkML, <a href="https://linkml.io">https://linkml.io</a>) is an open, extensible modeling framework that allows computers and people to work cooperatively to document, validate, and distribute data that is reusable and interoperable. It provides a flexible yet expressive standard for describing many kinds of data models from value sets and flat, checklist-style standards to complex normalized data structures that use polymorphism and inheritance. LinkML enables even non-developers to create data models. It is designed to allow software engineers and subject matter experts to communicate effectively in the same language, while also providing the semantic underpinnings to make data easier to validate, understand and reuse computationally. LinkML has an active and growing user community, and has seen uptake by projects including cancer data harmonization, environmental genomics, microbiome data, knowledge graph integration, ontology mappings and language profiles.</p> <p>In this talk, which expands on the short talk I gave at BOSC 2023, I will describe the LinkML framework and give examples demonstrating how to use it for biological data modeling, ontology-supported validation, conversion, and serialization. I will discuss how LinkML was used to create the Biolink Model, a unifying data model that brings together heterogeneous datasets to answer novel biomedical questions. I’ll also introduce the role the Biolink Model plays in the NCATS Biomedical Data Translator project.</p> <h4 id="about-the-speaker">About the speaker</h4> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Sierra-at-podium-1.png" alt=""></p> <p><strong>Sierra Moxon</strong> is a software developer in the Biosystems Data Science group at the Lawrence Berkeley National Laboratory. Sierra’s work focuses on designing and developing reusable software to harmonize diverse scientific research data into findable, accessible, interoperable and reproducible (FAIR) formats, with applications ranging from biomedicine to the environment.</p> <p>Sierra leads the Data Modeling Committee for the NCATS Biomedical Data Translator project, which aims to accelerate the path from biomedical research to clinical trials. She is a lead developer of the LinkML data modeling framework and the LinkML-based knowledge graph standard called Biolink Model, which forms a core part of the Translator infrastructure. Additionally, she is the Data Harmonization Lead for the Alliance of Genome Resources project, and she writes software used by the Gene Ontology, one of the most widely used ontologies in biology.</p>https://www.open-bio.org/2023/09/16/my-wonderful-experience-at-lanet-2023/Sat, 16 Sep 2023 08:28:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/09/16/my-wonderful-experience-at-lanet-2023/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Michell Salcan,</em></strong> <em><strong>an undergraduate at</strong></em> <em><strong>the Universidad Regional Amazonica Ikiami</strong></em>, <strong><em>was awarded an OBF Event Fellowship to atten</em></strong> d <em><strong><a href="https://lanet2023.uandina.edu.pe/">The 3rd Latin American Conference on Complex Networks in Cusco, Peru</a>.</strong></em></p> <p>The week of August 21 to 25 has been one of the most beautiful and satisfying experiences of my personal life and the beginning of my professional life because I had the opportunity to attend and present my undergraduate thesis at the LANET 2023 event.</p> <p><img src="https://lh3.googleusercontent.com/_T4h8wGxMFii5jyDBlMghnCoazlM2CArzhsjU-ka0q8M4ZSiCXTvk_lSQ5yard-SS8EtrGP88Td3_lk_L2xv2we5k23730NNRy3gz4VTN7EbPpFZc73CSlzkkRmC4ht-t3igGqsRfuNGkbHPUZ2Uy_A" alt=""></p> <p><strong>Photo of Qoricancha Temple,</strong> <strong>one of the most representative archeological places of the Inca Empire.</strong></p> <p>During the event, there were introductory talks, talks on research lines of network science or complex networks applied to different fields of science, and cultural and tourist activities organised by Andean University of Cusco. Throughout the days, networks were reviewed to understand social, dynamic, technological, biological, neuroscience, and epidemiological aspects like opinion states, modelling crime, Kuramoto Oscillators, synchronisation of neuron models, and metapopulation models to explain the spread of diseases.</p> <p>The main talk that captivated me was entitled “Identification of areas for the release of Wolbachia for dengue control using a metapopulation model,” which is mainly based on the biological control of the vectors that transmit the dengue virus. This talk particularly resonated with me because my work, &ldquo;Bipartite network modelling and analysis to understand the dynamics of dengue incidence in Ecuador during the 2014-2021 period&rdquo;, is based on identifying the main areas for the chemical control of these vectors.</p> <p>Speakers discussed the limitations of their research, with the lack of open data being the main problem in many of them. Since access to certain types of data is not free, or in some other cases, the data ceased to be accessible a few years ago, it is no longer possible to update the research. Many speakers, including me, promoted open source and open data approaches. As I have mentioned many times, open source allows collaborations between scientists, promoting the accessibility, modification, distribution, and expansion of software in various lines of study.</p> <p><img src="https://lh3.googleusercontent.com/hdFsCrHyj4gy6ZyDnecifJ56fuwxN-74U6uO8GdjWmV0r2J-6sh6KcivqW3bMdSdLJAEdYE7pXnt_W5YuK4pU_SyVTsmrqPdC1DNeoPPcfGZjzGG9qc_zlQaQ1YXA9cC7RhqjF4OolD62Ri-g5Y1DKs" alt=""></p> <p><strong>Photo of Shirley giving her talk about the dengue epidemiological network.</strong></p> <p>On the day of my talk, I was nervous at first since it was my first time at this type of event, and I felt scared. Then friends that I had made during that week told me, “You will do super well, you are wonderful and talented,” and “Just enjoy the adrenaline.” After that, I understood that I was not the only one and that probably many experts like them always felt nervous before giving a presentation, and that beyond the nerves, perhaps it was simply the emotion.</p> <p>In my presentation, I was able to relax more and was able to explain my research. At the end, there were congratulatory comments which made me feel proud. But there were also constructive comments that motivated me more to continue in my line of research and to perfect my disease diffusion model. Also, it allowed me to engage in conversation with an invited speaker whose research was also based on the spread of dengue, and she offered to review my work, which made me very happy.</p> <p>I understood then that this event allows you to get to know other places and cultures, make friends, and establish collaborations. For that, I sincerely thank the Open Bioinformatics Foundation for their support. Without it, my participation in LANET would not have been possible.</p> <p><img src="https://lh4.googleusercontent.com/3kFDlR12eacFsYp66cDzbRCh61Zm8g1siEyZF-OiIIoeyu3s3SYqmEuZb7T6jgVyzRMGhLIG2DyKPGTWf8Tjkt42_HTFLbi7-y0NBhiyWtr4KwVhRbYi8LtLG_CwaPBRtkhOtTCpQU6wao2doK9pY2M" alt=""></p> <p><strong>Photo of Shirley with other LANET participants from Mexico, Guatemala, Colombia, and Peru.</strong></p>https://www.open-bio.org/obf-dei/Sat, 19 Aug 2023 17:48:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/obf-dei/<p>Diversity, inclusion and accessibility (also known as Diversity, Equity and Inclusion, DEI) are a major part of OBF and <a href="https://www.open-bio.org/?obf-events=bosc-2023">BOSC&rsquo;s</a> mission and core values.</p> <p>Below are some of the ways we have worked to promote DEI at OBF, BOSC, ISMB (the host conference for BOSC) and in the broader open bioinformatics community.</p> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/Ruth-Nanjala-cropped-OBF-event-fellowship-winner-260x300.jpg" alt="a person standing next to their conference poster"></p> </div><div class="right"> <p>The Open Bioinformatics Foundation, <strong>funds the <a href="https://www.open-bio.org/event-awards/">OBF event fellowships</a>, which aim to increase diversity at events (including, but not limited to, BOSC) that promote open science as a research practice</strong>. These fellowships fund participants whose attendance will contribute to increase the diversity of such events (e.g. underrepresented demographic groups, ethnic origins, career stages, and disabilities).</p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <p><strong>Authors who submit their work to BOSC can request ISMB registration fee support</strong> on the submission form (these requests are not seen by reviewers). This initiative is funded by <a href="https://www.open-bio.org/events/sponsors/">sponsorships</a>.</p> <p>Since we introduced this option three years ago, we&rsquo;ve been able to offer free registration to dozens of people, most of whom are from groups underrepresented at ISMB/BOSC:</p> <ul> <li>In 2022, 19 people (of whom 18 were from groups that are underrepresented in our community) were granted free registration thanks to a combination of these registration fee waivers and OBF event fellowships.</li> <li>In 2023, 15 people (13 from underrepresented groups) were given free registration to ISMB/BOSC.</li> <li>In 2024, 14 people (13 from underrepresented groups) received free registration.</li> </ul> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Nomi-Deepak-Vasundra-1-1024x782.jpeg" alt="three people standing in a conference room"></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/12/Farica-Zhuang-and-Matthew-Gazzara-1-284x300.jpeg" alt="a person standing at a podium presenting"></p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/BOSC2023-crowded-room-Jason-standing-1-1024x372.png" alt="A crowded conference room"></p> </div><div class="right"> <p>To help everyone feel welcome at BOSC, we <strong>introduced a code of conduct in 2015</strong>, and successfully lobbied our host conference ISMB to adopt one as well. OBF adopted a <a href="https://github.com/OBF/obf-docs/tree/master/code-of-conduct">code of conduct</a> in 2022.</p> </div><div style="clear:both"></div></div> <p><div class="splitbox"><div class="left"> We strive to <strong>choose keynote speakers who represent a diversity of backgrounds and ideas</strong>. To make our selection process fair and transparent, we developed an <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker rubric</a> and an opportunity for <a href="https://www.open-bio.org/2023/02/02/nominate-keynote-speaker-for-bosc-2023/">community members to nominate potential keynote speakers and comment on nominees</a>.</p> <p>Our 2023 keynote speakers both discussed topics related to inclusion and equity. The first <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/">BOSC 2023 keynote</a> was delivered by Sara El-Gebali, who spoke inspiringly about “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration,” with case studies showing <strong>how open collaboration can strengthen inclusive scientific communities and vice-versa</strong>. </div><div class="right"> </p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image7-768x1024.jpg" alt="BOSC 2023 keynote speaker Sara El-Gebali"></p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Joseph-Yracheta-300x296.png" alt="BOSC 2023 keynote speaker Joseph Yracheta"></p> <p></div><div class="right"> The <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/">2023 keynote by Joseph Yracheta</a>, an Amerindigenous scientist, examined thorny questions about the current open data environment and how it impacts American Indian / Native American communities. Joe, the founder of the <a href="https://nativebio.org/">Native BioData Consortium</a>, <strong>discussed our ethical responsibilities as people who work on open source tools and open bioinformatics research to ensure that indigenous data is ethically sourced and used</strong>.</p> </div><div style="clear:both"></div></div> <p><div class="splitbox"><div class="left"> In recognition that not everyone is privileged enough to gift their time, we started <strong>offering honoraria to keynote speakers</strong> in 2021.</p> <p>The <strong>first talk at BOSC (and, to our knowledge, at ISMB) to be delivered in a language other than English</strong> was given in 2021 by <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-keynotes/">keynote speaker Thomas Hervé Mboa Nkoudou of Cameroon</a>. </div><div class="right"> </p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/04/Thomas-Mboa-300x200.jpg" alt="BOSC 2021 keynote speaker Thomas Hervé Mboa Nkoudou"></p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/BOSC2023-org-committee-square-300x293.jpeg" alt="BOSC 2023 organizing committee"></p> <p></div><div class="right"> Although there is not a formal rubric for choosing <a href="https://www.open-bio.org/events/bosc-2023/#org-committee">BOSC organizing committee</a> members, <strong>diverse representation is a factor in choosing an array of people who will help BOSC appeal to and be accessible to the widest range of participants</strong>. The 9 people on the 2023 organizing committee included 4 women, 2 Black people, 2 South Asian people, and one Latin American. BOSC also has a large and diverse review committee, and we <strong>strive to provide fair and constructive feedback to authors</strong>. Our <a href="https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md.">review process and rubric</a> have been published openly since 2020.</p> </div><div style="clear:both"></div></div> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image5-1024x629.png" alt="BOSC 2023 participants"></p> <div class="splitbox"><div class="left"> <p>Some recent BOSCs have included <strong>DEI-focused sessions</strong> such as <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule">&ldquo;Inclusion &amp; Open Science&rdquo;</a> in 2022, and BOSC&rsquo;s landscape of open science includes citizen science, in which the research subjects themselves (for example, those with a disability) participate in the research. <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/">BOSC 2023</a> included a talk entitled &ldquo;AutSPACEs: a co-created and open source citizen science project to improve environments for sensory processing in autistic people&rdquo;.</p> <p>In a 2023 ISCBacademy webinar organized by BOSC, Long COVID sufferer and advocate Hannah Wei presented <a href="https://www.open-bio.org/2023/03/07/iscbacademy-webinar-on-patient-led-research/">Lessons from the Patient-Led Research Collaborative</a>.</p> <p></div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2023/03/Moni-moderating-questions-for-Hannah-Wei-1-266x300.png" alt="Webinar speaker Hannah Wei with moderator Monica Munoz-Torres"></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/2023-panel-1-1-1024x392.png" alt="BOSC 2023 panelists"></p> </div><div style="clear:both"></div></div> <p><div class="splitbox"><div class="left"> <strong>Panel discussions have included topics relating to inclusion and diversity in open science</strong>. BOSC 2015&rsquo;s panel topic was <a href="https://www.open-bio.org/wiki/BOSC_2015_Panel">Open Source, Open Door: increasing diversity in the bioinformatics open source community</a>. BOSC 2022 included a panel on <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/">Building and Sustaining Inclusive Open Science Communities</a>. At BOSC 2023, the panel on <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/">Open and Ethical Data Sharing</a> centered on the idea that we individually, and our scientific societies, can be advocates for better practices in ethical data sharing.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/11/panel-with-Nomi-1-1024x626.jpeg" alt="Panel on Building and Sustaining Inclusive Open Science Communities: Jason Williams (moderator); panelists Jenea Adams, Monica Munoz-Torres, Rachel Torchet, and Gary Williams; BOSC Chair Nomi Harris"></p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/07/Jenea-Adams-1-1.png" alt="Jenea Adams, one of the BOSC 2022 panelists"></p> </div><div class="right"> <p>Inclusion offers mutual advantages: when we give a wider range of people a voice, they benefit from being included and we in turn benefit from their contributions. 2022 panelist <a href="https://www.open-bio.org/2023/07/10/spotlight-on-diversity-jenea-adams/">Jenea Adams shared her thoughts in a blog post</a>, commenting, “BOSC not only showcased the remarkable strides made in computational biology but also emphasized the power of collaboration and inclusivity. Through my participation in the panel on Building and Sustaining Inclusive Open Science Communities, <strong>I witnessed the true potential of harnessing diverse perspectives to drive innovation and create a sustainable foundation for open science</strong>.”</p> </div><div style="clear:both"></div></div> <div class="splitbox"><div class="left"> <p>Our 2020 event (<a href="https://www.open-bio.org/2020/08/13/lessons-learned/">BCC2020</a>, which paired BOSC with the Galaxy Community Conference) was groundbreaking for DEI due to being online and presented twice a day for accessibility around the globe, and all videos professionally captioned. Participants at this event hailed from 61 countries, many of which had never been represented before at BOSC.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/BOSC2020-party-attendees1-1024x576.jpg" alt="a grid of faces on a conference call"></p> </div><div style="clear:both"></div></div> <p><div class="splitbox"><div class="left"> As far as we are aware, BOSC 2022 was the first BOSC, possibly even the first ISMB, to include a service dog, demonstrating tangible progress in our efforts to make BOSC more inclusive and accessible.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Scott-Andrew-Shade-1-212x300.jpeg" alt="two people standing on a hallway talking to each other, with a service dog laying on the floor"></p> </div><div style="clear:both"></div></div> <p><strong>Further reading:</strong> Our annual BOSC reports, published in the open access journal F1000Research, include sections on DEI (see e.g. <a href="https://f1000research.com/articles/11-1034/v1">https://f1000research.com/articles/11-1034/v1</a> for 2022, or <a href="https://f1000research.com/articles/9-1160/v1">https://f1000research.com/articles/9-1160/v1</a> for 2021).</p>https://www.open-bio.org/2023/08/14/bosc-2023-report/Mon, 14 Aug 2023 20:24:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/08/14/bosc-2023-report/<p>The 24th annual Bioinformatics Open Source Conference, <a href="https://open-bio.org/events/bosc-2023">BOSC 2023</a>, took place as part of ISMB/ECCB 2023 in Lyon, France, and online. ISMB/ECCB attracted a near-record number of attendees, with over 2100 in person and  about 900 more online.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image8-1024x410.jpg" alt="Most of the BOSC 2023 Organizing Committee">Most of the BOSC organizing committee (missing: Jessica Maia and Chris Fields)<img src="https://www.open-bio.org/wp-content/uploads/2023/08/BOSC-full-room-wide-1.png" alt="Full room at BOSC 2023">A full room at BOSC 2023</p> <p>The opening session of BOSC kicked off with a welcome from chair Nomi Harris. An overview of BOSC’s parent organization, the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a>, was presented by OBF Board member Bastian Greshake Tzovaras.</p> <p>Hervé Ménager presented the projects undertaken at the pre-BOSC <a href="https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/">CollaborationFest</a>, a collaborative work event (including but not limited to hacking) hosted by Jérémy Just and the nearby <a href="http://www.ens-lyon.fr/">École Normale Supérieure de Lyon</a>, with 29 in-person participants, plus more online. In-person participants enjoyed the lavish lunches organized by and underwritten by CoFest sponsors <a href="https://www.ixxi.fr/">Complex Systems Institute</a>, <a href="http://www.ens-lyon.fr/">ÉNS de Lyon</a>, and <a href="http://www.ens-lyon.fr/RDP/">Laboratoire Reproduction et Développement des Plantes</a> (with additional support from <a href="https://www.france-bioinformatique.fr/en/home/">French Institute of Bioinformatics</a> and <a href="http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil">PSMN</a> to provide free virtual machines to attendees).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/CoFest2023-lunch-1-736x1024.png" alt="Lunch at CoFest 2023">Lunch at CoFest 2023</p> <p>The first <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/">BOSC keynote</a> was delivered by Sara El-Gebali, who spoke inspiringly about “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration,” with case studies showing how open collaboration can strengthen inclusive scientific communities and vice-versa. For example, 95.5% of genomic research participants in GWAS are people of European heritage; this has led to the development of drugs that don’t work for most of the people in the world. Sara made many points that resonated with the BOSC audience, such as the need to revamp research reward systems to take into account open science practices, not just one-dimensional publication metrics.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image7-768x1024.jpg" alt="BOSC 2023 keynote speaker Sara El-Gebali"><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image6-1024x579.png" alt="">BOSC 2023 keynote speakers Sara El-Gebali and Joseph Yracheta</p> <p>The second day of BOSC started with a thought-provoking <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/">keynote by Joseph Yracheta</a> (presented virtually due to a last-minute family emergency) entitled “The Dissonance between Scientific Altruism &amp; Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution”, which examined thorny questions about the current open data environment and how it impacts American Indian / Native American communities. Joe, the founder of the <a href="https://nativebio.org/">Native BioData Consortium</a>, discussed our ethical responsibilities as people who work on open source tools and open bioinformatics research to ensure that indigenous data is ethically sourced and used.</p> <p>Beyond keynotes, BOSC had seven <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/">themed sessions</a> with talks chosen from submitted abstracts, including Translational bioinformatics; Workflows; Data analysis and visualization; and a new BOSC session on AI/ML. The FAIR and Open Data session set the stage for the closing panel, while a session on Open Science reflected the breadth of BOSC topics, including talks relating to open infrastructures and ecosystems, citizen science, training, outreach, and reproducibility. A well-attended joint session brought together BOSC and the Bio-Ontologies COSI for talks relating to standards (including, of course, ontologies) and frameworks for open science. 49 posters were presented at an overflowing poster session. The complete BOSC schedule is available at <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/">/events/bosc-2023/bosc-2023-schedule/</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image5-1024x629.png" alt="BOSC 2023 participants">BOSC 2023 participants</p> <p>BOSC 2023 closed with a <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/">panel on Open and Ethical Data Sharing</a> that expanded upon some of the points made by the two keynote speakers, including the observation that there’s no published ethical code for bioinformaticians, and the idea that we individually, and our scientific societies, can be advocates for better practices in ethical data sharing. Along with moderator Monica Munoz-Torres, the panel featured our two keynote speakers (Sara El-Gebali and Joseph Yracheta) along with Verena Ras of the University of Cape Town and Bastian Greshake Tzovaras, who’s a leader in organizing citizen science projects.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image4-1024x610.jpg" alt="Panelists Verena Ras, Sara El-Gebali, Bastian Greshake Tzovaras, and Monica Munoz-Torres">Panelists Verena Ras, Sara El-Gebali, Bastian Greshake Tzovaras, and Monica Munoz-Torres</p> <p>Two well-attended evening events got BOSC participants mingling: a dinner at a casual food court, and a jam-packed party hosted by our sponsor GigaScience (see their ISMB/BOSC writeup at <a href="http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/">http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/</a>).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image2-1-768x1024.jpg" alt="Julie McMurry and her dog at the GigaScience party">Julie McMurry and her dog at the GigaScience party</p> <p>Speaking of sponsors, we are grateful to our <a href="https://www.open-bio.org/events/sponsors/">BOSC 2023 sponsors</a>: Platinum Sponsor <a href="https://chanzuckerberg.com/">Chan-Zuckerberg Initiative</a>, and Silver Sponsors <a href="https://academic.oup.com/gigascience">GigaScience</a>, <a href="https://geneviatechnologies.com/">Genevia</a>, and <a href="https://www.software.ac.uk/">Software Sustainability Institute</a>. With their help, we were able to offer free registration to 15 BOSC participants, 13 of whom are from groups that are underrepresented in our communities.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/image1-1-1024x602.jpg" alt="BOSC 2023 Chair Nomi Harris thanking Platinum Sponsor, the Chan Zuckerberg Initiative">BOSC 2023 Chair Nomi Harris thanking Platinum Sponsor, the Chan-Zuckerberg Initiative</p> <p>We hope to see you (in person in Montréal, Canada, or online) at BOSC 2024, which will be part of ISMB 2024 from July 12-16, 2024!</p>https://www.open-bio.org/2023/08/07/nehemia-conference-experience-at-smbe23/Mon, 07 Aug 2023 19:23:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/08/07/nehemia-conference-experience-at-smbe23/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Nehemiah Ongeso,</em></strong> <em><strong>an MSc graduate at</strong></em> <em><strong>the University of Nairobi</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the <a href="https://www.smbe2023.org/">SMBE23 conference</a>.</strong></em></p> <p>Attending a prestigious conference can be a turning point in any scientist&rsquo;s career; for me, it was no exception. The Society of Molecular Biology and Evolution (SMBE) conference, hosted in Ferrara, Italy, was an unparalleled experience that combined cutting-edge scientific research with a unique cultural immersion. As a recipient of a travel grant from the Open Bioinformatics Foundation, I participated in the extraordinary <a href="https://www.smbe2023.org/">SMBE23 conference</a>, which broadened my horizons and inspired me to pursue even greater heights in my postgraduate research.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Image1-702x1024.jpg" alt=""></p> <h5 id="the-unconventional-conference"><strong>The Unconventional Conference</strong></h5> <p>The SMBE23 conference was unlike any other I had attended before. Breaking away from the traditional hotel-based format, the conference was diffused across Ferrara. The diffused nature of the conference allowed attendees, including myself, to interact with the local community, experience their culture, language, religion, history, cuisine, and even engage with local authorities. The city of Ferrara became an integral part of the conference experience, fostering a unique atmosphere that encouraged both intellectual exchange and personal growth.</p> <h5 id="presenting-my-postgraduate-work"><strong>Presenting my Postgraduate Work</strong></h5> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Image2-768x1024.jpg" alt=""></p> <p>One of the highlights of my journey was the opportunity to present my postgraduate work titled &quot; <a href="http://dx.doi.org/10.6084/m9.figshare.23867637"><strong><em>Co-expression network analysis of genes mediating Meloidogyne incognita parasitism in tomato-plant nematode interactions</em></strong>.</a>&quot;  Sharing my research findings with a diverse audience of scientists and graduate fellows was exciting and nerve-wracking. To my delight, my work garnered attention from numerous researchers interested in advancing their studies in systems biology. The constructive feedback and stimulating discussions further motivated me to explore new avenues and refine my research objectives.</p> <h5 id="symposium-on-regulatory-evolution-and-the-emergence-of-diversity"><strong>Symposium on Regulatory Evolution and the Emergence of Diversity</strong></h5> <p>During the conference, I actively participated in a symposium titled &ldquo;Regulatory Evolution and the Emergence of Diversity.&rdquo; The symposium proved to be an eye-opening experience as I learned valuable skills in effectively communicating scientific breakthroughs, including new concepts, methodologies, models, and potential areas for collaboration. Engaging with like-minded individuals from diverse backgrounds sparked my enthusiasm for interdisciplinary research, and I left the symposium with a fresh perspective on my work.</p> <h5 id="open-science-and-networking-for-global-advancement"><strong>Open Science and Networking for Global Advancement</strong></h5> <p>On the last conference day, I participated in the SMBE-IDEA symposium, which provided a platform where the SMBE society and affiliate research groups committed to advancing science in the global south while eliminating the detrimental effects of &ldquo;helicopter science.&rdquo; I actively contributed to and championed for SMBE to adopt open science practices. By advocating for accessible data, reproducibility, and collaboration, I aimed to advance science in the global south while ensuring equitable opportunities for researchers from all regions. The conveners of the symposium passed a resolution to sensitize donors and collaborators to always listen to the needs of researchers from the global south.</p> <p>Through the symposium session, I was privileged to connect with researchers who shared similar passions for promoting diversity, inclusivity, and equity in the scientific community. The interactions opened doors to future collaborations and partnerships, potentially broadening the impact of my research and fostering international connections.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/Image3.jpg" alt=""></p> <h5 id="humanizing-science"><strong>Humanizing Science</strong></h5> <p>An intriguing observation during the conference was witnessing senior scientists actively participating in poster presentations. It was heartening to see that their dedication to science extended beyond their academic achievements, and they remained humble and open to sharing their knowledge and insights with their peers. Additionally, some senior scientists were accompanied by their non-scientist spouses, which humanized the experience and emphasized the importance of maintaining a balanced and fulfilling personal life alongside a successful scientific career.</p> <h5 id="acknowledgement"><strong>Acknowledgement</strong></h5> <p>I sincerely thank the Open Bioinformatics Foundation for their generous travel grant, which made this life-changing experience possible. Additionally, my heartfelt thanks go to the organizers of SMBE23 for orchestrating an exceptional conference that transcended the boundaries of traditional academic events. As I return to my research station, I carry with me the valuable lessons learned and the lasting memories of a conference that will forever hold a special place in my heart. The memories and knowledge gained will undoubtedly shape my future endeavours as a scientist and global citizen.</p>https://www.open-bio.org/2023/08/02/daniela-senra-experience-human-cell-atlas-2023/Wed, 02 Aug 2023 04:36:21 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/08/02/daniela-senra-experience-human-cell-atlas-2023/<p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Daniela Senra,</em></strong> <em><strong>a PhD researcher at Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the <a href="https://events.humancellatlas.org/2023gm">Human Cell Atlas General Meeting 2023</a>.</strong></em></p> <p>In July, I had the incredible opportunity to attend and present a lightning talk at the Human Cell Atlas General Meeting 2023, that took place in the city of Toronto, Canada, from July 10th to July 12th, 2023.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/photo1-1024x576.png" alt="">Photo of Daniela giving her talk and sharing about the open-source tool ORIGINS2.</p> <h2 id="discovering-new-insights-at-the-meeting"><strong>Discovering New Insights at the Meeting</strong></h2> <p>The three-day event was packed with activities, including keynote speeches, breakout sessions, lightning talks, and poster sessions covering various topics.</p> <p>On the first day, I was particularly captivated by talks that resonated with my research interests. Notably, the presentation on <em>&lsquo;What makes a stem cell a stem cell and how does it go bad&rsquo;</em> held great relevance to my PhD thesis, focusing on stem cells and cancer stem cells. Additionally, a breakout session on <em>&lsquo;Increasing accessibility/building great scientific communities&rsquo;</em> struck a chord with me as someone from Argentina—a developing country—where access to public data and open-source pipelines is crucial for contributing to the scientific community. Later, I had the privilege of sharing my own research in a talk titled <em>‘Stem cell determination from scRNA-seq data using a protein network-based approach</em>.’ My work, an open-source R package developed in collaboration with my advisors Luis Diambra and Nara Guisoni, originally aimed to quantify pluripotency from scRNA-seq data but evolved into a computational technique to quantify any biological process using protein-protein interaction networks. The application that motivated this work was the identification of stem cells, serving as a starting point for performing trajectory inference. For those interested in our work, the publications can be accessed using the links: <a href="https://www.sciencedirect.com/science/article/pii/S2215016123001796">https://www.sciencedirect.com/science/article/pii/S2215016123001796</a> and <a href="https://www.sciencedirect.com/science/article/pii/S2215016122001583">https://www.sciencedirect.com/science/article/pii/S2215016122001583</a>.</p> <p>The second day&rsquo;s focus on machine learning was especially appealing to me, given my frequent use of unsupervised learning techniques in my research. I also found the section on spatial methods intriguing, considering their potential relevance to my future work. The third and final day concentrated on biological function, directly related to my presentation, making it an interesting topic.</p> <h2 id="open-source-as-a-central-topic"><strong>Open source as a central topic</strong></h2> <p>In my lightning talk, I was able to promote my open source project, as many participants also highlighted. Throughout the conference, the importance of open source became a transversal theme. Undoubtedly, open source plays a pivotal role in science, accessibility and transparency allows scientists to freely access, modify and distribute software tools and solutions. This democratization of knowledge not only enhances the quality of research but also enables scientists from developing countries to actively participate in shaping the future of science and technology.</p> <h2 id="empowering-personal-and-professional-development"><strong>Empowering Personal and Professional Development</strong></h2> <p>Having attended virtual HCA events during the pandemic, the opportunity to participate in person at the General Meeting was unique for me. It was my first time participating in an international event, and I was very excited. Yet, two months before the event, I was unsure if I could afford to attend, as the travel costs seemed impossible. Securing funding for such activities can be a daunting challenge for scientists in developing countries. However, my hopes were restored when I received an email from the Open Bioinformatics Foundation informing me that I had been awarded the OBF Event Fellowship. This news enabled my participation, which was especially meaningful as I am on the brink of completing my PhD and exploring new opportunities for my future endeavors.</p> <p>The experience was undeniably one of the highlights of my ongoing PhD journey. I had the privilege of connecting with fellow researchers who shared similar interests—an opportunity that is limited in Argentina, given the still-developing nature of this area of research. The networking opportunities were invaluable, allowing me to build strong connections with professionals worldwide. Moreover, I believe that being part of this event contributed to promoting diversity, as Latin America is often underrepresented in international scientific gatherings. To my surprise, some participants approached me to express that I was the first person from Argentina they had met working with scRNA-seq data. This realization filled me with pride and a sense of responsibility, as I hope to see more Latin American scientists, especially women, gain more opportunities and equitable representation in the global scientific community.</p> <h2 id="a-heartfelt-thanks-to-the-obf"><strong>A Heartfelt Thanks to the OBF</strong></h2> <p>None of this would have been possible without the support of the Open Bioinformatics Foundation. I am immensely grateful to the OBF for their generous support, which made my participation in this exceptional event a reality.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/08/photo2-1-768x1024.jpg" alt=""></p> <p>In conclusion, the Human Cell Atlas General Meeting 2023 was an unforgettable experience that broadened my professional and personal horizons. I left the event with new knowledge, invaluable connections, and a renewed determination to contribute to the scientific community.</p>https://www.open-bio.org/2023/07/10/spotlight-on-diversity-jenea-adams/Mon, 10 Jul 2023 21:25:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/07/10/spotlight-on-diversity-jenea-adams/<p>Diversity, inclusion and accessibility (also known as Diversity, Equity and Inclusion, DEI) are a major part of BOSC’s mission and core values, and we pursue these goals in multiple ways. BOSC 2022, for example, included a <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/">panel on Building and Sustaining Inclusive Open Science Communities</a>, with panelists who not only were experts on the topic but also themselves belong to various groups that are typically underrepresented in our community. And with generous support from our <a href="https://www.open-bio.org/events/sponsors">sponsors</a>, each year we provide free registration to 10-20 BOSC participants as part of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship program</a>), which aims to increase diverse participation at events related to open source bioinformatics and open science.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/07/Jenea-Adams-1-1-300x300.png" alt=""></p> <p>Jenea Adams, a Presidential Ph.D. Fellow in Genomics and Computational Biology at the University of Pennsylvania, epitomizes our commitment to fostering diversity and inclusion in the open source bioinformatics community. Jenea served as one of the panelists on the Building and Sustaining Inclusive Open Science Communities panel, and her registration fee and travel expenses were covered by an OBF Event award.</p> <p>Jenea commented, &ldquo;BOSC not only showcased the remarkable strides made in computational biology but also emphasized the power of collaboration and inclusivity. Through my participation in the panel on Building and Sustaining Inclusive Open Science Communities, I witnessed the true potential of harnessing diverse perspectives to drive innovation and create a sustainable foundation for open science.&rdquo;</p> <p>In addition to her PhD studies, Jenea is the Founder and Executive Director of <a href="https://www.blackwomencompbio.org/">The Black Women in Computational Biology Network</a>, which aims to amplify the voices and foster community among Black women in computational biology.  Jenea observed, &ldquo;Having support to attend BOSC 2022 made it possible for me to connect with new and familiar faces in person while providing a platform to share the work and progress of The Black Women in Computational Biology Network.&rdquo;</p> <p>Jenea summed up her thoughts about BOSC &ndash; thoughts we strongly agree with &ndash; as follows: &ldquo;This conference reinforced the notion that by being intentional about accessible science and sharing knowledge, resources, and ideas openly, we can collectively advance the field of computational biology and pave the way for transformative discoveries.&rdquo;</p> <p>We thank Jenea for contributing her knowledge and community-building spirit to BOSC, and wish her the best in all her endeavors!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/11/panel-with-Nomi-1-1024x626.jpeg" alt="Panel on Building and Sustaining Inclusive Open Science Communities: Jason Williams (moderator); panelists Jenea Adams, Monica Munoz-Torres, Rachel Torchet, and Gary Williams; BOSC Chair Nomi Harris"></p> <p>Above: <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/">Panel on Building and Sustaining Inclusive Open Science Communities</a>: Jason Williams (moderator); panelists Jenea Adams, Monica Munoz-Torres, Rachel Torchet, and Gary Williams; BOSC Chair Nomi Harris</p>https://www.open-bio.org/2023/07/05/call-for-event-fellowship-round-2-2023/Wed, 05 Jul 2023 05:05:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/07/05/call-for-event-fellowship-round-2-2023/<p>The call for applications for the OBF Event Fellowship 2023, round 2, is now open. The deadline for this round is <strong>1 August 2023</strong>. Applications should be submitted via <a href="https://forms.gle/8GsspfPaCAVdBPsy9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling out the form – <a href="https://docs.google.com/document/d/1j_v-f1FcOA-ssXtsUdE_YaEOSQKZRms9-P7RGd3vdYA/edit">make a copy of this template</a>.</p> <p>The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from September 2023 to April 2024. <strong><em>These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><img src="https://lh5.googleusercontent.com/MDj2EKTXBJZ3Y3DlJkC03LjLn1zEM_zOlC0oLzxhUDhpFf9VJFlsG3GnOTsWPs_bEvW6QazR1-LVviw1v1PO2qtAP5QL4rR5DD5_fcBcK90HwvjUNSE6Besa8_GX7s68-cEoBgAZOh79iaBKqkYTESY" alt=""><em>Screenshot of our application form information section</em></p> <p><strong>Overview of the round 1 of OBF Event Fellowship 2023</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 7th year. We open three application calls yearly with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In 2023 round 1 (April 2023), we received 23 applications, of which three applicants were awarded this fellowship for various events they were participating in. Congratulations to <strong>Yvonne Ateh Joko Walburga Epse Fru</strong>, <strong>Shirley Salcan</strong> and <strong>Daniela Senra</strong>.</p> <p><strong>Nehemiah Ongeso Mosioma,</strong> who had been previously awarded a fellowship for attending the Vienna BioCenter PhD Program Symposium &ldquo;Pushing Boundaries&rdquo;, but due to visa delays, could not attend the event. The OBF Fellowship Award chairs redirected this award towards attending the Society of Molecular Biology and Evolution (SMBE) 2023.</p> <p>We recently published blog post from two of our latest awardees summarising their experiences attending conferences with help from OBF Event Fellowships:</p> <ul> <li>Winfred Gatua: <a href="https://www.open-bio.org/2023/03/29/winfred-gatua-hybrid-carpentries-workshop/">Winfred Gatua: Hybrid Carpentries workshop supported by OBF Event Fellowship</a></li> <li>Ruth Nanjala: <a href="https://www.open-bio.org/2023/03/21/ruth-nanjala-experience-at-the-ichg-2023-conference/">Ruth Nanjala: My experience attending and participating at the ICHG 2023 conference hosted in the Mother City</a></li> </ul> <p>Congratulations to all of our awardees!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and apply for the fellowship before 1 August 2023</strong>.</p>https://www.open-bio.org/events/sponsors-new-draft-2023/Fri, 28 Apr 2023 22:07:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/sponsors-new-draft-2023/<h1 id="sponsoring-bosc">Sponsoring BOSC</h1> <h2 id="bosc-2023-platinum-sponsor">BOSC 2023 Platinum Sponsor</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="CZI"></a></p> <h2 id="bosc-2023-silver-sponsors">BOSC 2023 Silver Sponsors</h2> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a><a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a><img src="https://www.open-bio.org/wp-content/uploads/2023/04/SSI_PRIMARY-LOGO-300x96.png" alt=""></p> <h4 id="if-youre-interested-in-sponsoring-bosc-2023-please-contact-us-at-">If you’re interested in sponsoring BOSC 2023, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</h4> <hr> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Geraldine-BoF-composite.png" alt="Screenshot from BOSC 2021"></p> <p>Sponsorships from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some conference participants. In 2022, thanks to our sponsors&rsquo; generous support, we were able to grant free registration to 19 participants at <a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a>, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you’re interested in sponsoring BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p>Thanks to our 2021 sponsors, we were able to offer free ISMB/ECCB 2021 registration to 20 participants from all over the world! <iframe loading="lazy" src="https://www.google.com/maps/d/embed?mid=1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width="640" height="480"> </iframe> </p> <h2 id="what-is-bosc">What is BOSC?</h2> <p>BOSC is an annual meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. Whether in-person or online, each BOSC ​includes ​talks,​ ​poster​ ​sessions,​ ​birds-of-a-feather gatherings, and ​lots​ ​of​ ​opportunities​ ​for​ ​networking. It is followed by​ ​collaborative​ ​working​ ​sessions​ ​at the CollaborationFest.​ ​These​ ​events​ ​bring​ ​together​ ​software​ ​engineers,​ ​bioinformaticians,​ ​and​ ​researchers​ ​to collaborate​ ​and​ ​extend​ ​open​ ​source​ ​bioinformatics​ ​tools.</p> <p>Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB). In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>. In July 2020, BOSC again joined forces with GCC to form the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>. Held online, BCC2020 attracted over 600 participants from 62 countries. <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> was part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, and took place July 29-30, 2021 (followed by a two-day <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest</a>).</p> <p><a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> was held July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> in person in Madison, Wisconsin, USA, and simultaneously online.</p> <p><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a>, the 24th annual Bioinformatics Open Source Conference, will take place July 24-25 as part of ISMB/ECCB 2023 in Lyon, France and online. Like last year, we will join forces with Bio-Ontologies for part of a day!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/OBF-BoF-2018-25-300x225.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/43248502932_2395bc3cc6_z-300x200.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2017-panel-1.jpg" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Jason-PeterSelby-FotisPsomopoulos-DhrithiDespande.png" alt=""></p> <p>BOSC​ ​participants​ ​come​ ​from​ ​a​ ​wide​ ​variety​ ​of​ ​research​ ​environments​ ​and​ ​backgrounds:</p> <ul> <li> <p>Biological​ ​researchers,​ ​students,​ ​and​ ​post-docs​ ​who​ ​​ ​are​ ​learning​ ​bioinformatics​ ​analysis tools and techniques</p> </li> <li> <p>Power​ ​bioinformatics​ ​users</p> </li> <li> <p>Bioinformatics​ ​tool​ ​and​ ​workflow​ ​developers</p> </li> <li> <p>Bioinformatics​-focused​ ​principal​ ​investigators​ ​and​ ​researchers</p> </li> <li> <p>Sequencing​ ​core​ ​facility​ ​staff</p> </li> <li> <p>Industry​ ​scientists​ ​and​ ​bioinformaticians</p> </li> <li> <p>Data​ ​producers</p> </li> </ul> <h1 id="previous-events">Previous Events</h1> <p>The​ ​OBF​ ​has​ ​organized​ ​BOSC​ ​ <a href="https://www.open-bio.org/events/bosc/about/">every​ ​year​ ​since​ ​2000</a>.​ From 2000 to 2017 and again in 2019,​ ​BOSC​ ​was ​run​ ​as​ ​part​ ​of​ ​the​ ​large​ ​ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference.​ ​The​ ​OBF​ ​CodeFest​s (now renamed CollaborationFest, or CoFest) have ​been​ ​held​ ​every​ ​year​ after BOSC ​since​ ​2010.</p> <h1 id="sponsorship">Sponsorship</h1> <p>We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to</p> <ul> <li>offer free registration to some BOSC participants</li> <li>support the <a href="https://www.open-bio.org/travel-awards/">OBF&rsquo;s Event Fellowship program</a>, increasing participation from underrepresented groups</li> <li>provide child care at the conference</li> <li>underwrite the cost of conference events such as dinners or refreshments at poster sessions</li> <li>help defray the cost of videography</li> <li>provide space and catering at the CoFest</li> <li>offer honoraria to keynote speakers</li> <li>pay for captioning and translations</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/BOSC2020-party-attendees-e1609719125821.png" alt=""></p> <h2 id="sponsoring-bosc-1">Sponsoring BOSC</h2> <p>Sponsorships from private companies and organizations help to defray some of our costs and allow us to offer registration fee waivers to some attendees. If you are interested in becoming a BOSC sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <h1 id="benefits-of-sponsorship">Benefits of Sponsorship</h1> <p>We acknowledge our sponsors before, during and after the event in multiple ways:</p> <ul> <li>We list our sponsors on the BOSC website</li> <li>Sponsors are thanked and named in the introduction/closing slides during the meeting</li> <li>We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area</li> <li>The sponsors are thanked in selected emails to our mailing list, tweets and blog posts (with your logo) that go out before, during and after the event</li> <li>The sponsors are listed in our published reports after the meeting, e.g., <a href="https://f1000research.com/articles/7-1309/v1">https://f1000research.com/articles/7-1309/v1</a></li> <li>We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.</li> </ul> <h1 id="sponsors-from-previous-years">Sponsors from previous years</h1> <ul> <li> <p>Advanced HPC</p> </li> <li> <p>Alzheimer’s Disease Data Initiative</p> </li> <li> <p>Amazon Web Services</p> </li> <li> <p>Bina</p> </li> <li> <p>BioTeam</p> </li> <li> <p>Brmlab, Prague</p> </li> <li> <p>Broad Institute Data Sciences Platform</p> </li> <li> <p>Curoverse</p> </li> <li> <p>DNADigest</p> </li> <li> <p>Eagle Genomics</p> </li> <li> <p>eLife</p> </li> <li> <p>Elixir</p> </li> <li> <p>F1000 Research</p> </li> <li> <p>FamiLAB</p> </li> <li> <p>GeneVia</p> </li> <li> <p>GigaScience</p> </li> <li> <p>Google</p> </li> <li> <p>Google Cloud</p> </li> <li> <p>Harbinger Partners</p> </li> <li> <p>Hack/reduce</p> </li> <li> <p>Harvard School of Public Health Bioinformatics Core</p> </li> <li> <p>Helicos Biosciences</p> </li> <li> <p>Humboldt University of Berlin Institute of Biology</p> </li> <li> <p>Intel</p> </li> <li> <p>International Society for Biocuration</p> </li> <li> <p>ISCB</p> </li> <li> <p>Jetstream</p> </li> <li> <p>KNIME</p> </li> <li> <p>Lenovo</p> </li> <li> <p>Lifebit</p> </li> <li> <p>Loyola Marymount University Math</p> </li> <li> <p>Massachusetts General Hospital</p> </li> <li> <p>Metalab Hacker Space, Vienna</p> </li> <li> <p>Mozilla Science Lab</p> </li> <li> <p>Oxford University Press</p> </li> <li> <p>PeerJ</p> </li> <li> <p>Phase Genomics</p> </li> <li> <p>PLOS</p> </li> <li> <p>Repositive</p> </li> <li> <p>Seven Bridges</p> </li> <li> <p>Software Sustainability Institute</p> </li> <li> <p>Technology Association of Oregon</p> </li> <li> <p>The Hyve</p> </li> <li> <p>Trinity College, Dublin</p> </li> <li> <p>University of Oregon Bioinformatics and Genomics Program</p> </li> </ul> <p>If you are interested in becoming a sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p>https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/Fri, 14 Apr 2023 21:48:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/<h1 id="bosc-2023-panel-open-and-ethical-data-sharing">BOSC 2023 Panel: Open and Ethical Data Sharing</h1> <p>As a conference that promotes open source and open science, we are big proponents of open data. We love to hear about tools and frameworks (such as FAIR) that promote data sharing and reuse. But sharing data openly also has its challenges: for example, how to securely share data that has personally identifiable health information, or how to ethically obtain and share data from marginalized communities. In this panel discussion, we will delve into some of these intriguing technical and ethical issues, with audience participation encouraged!</p> <h2 id="panelists">Panelists</h2> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Sara-El-Gebali-square-1.png" alt="Sara El-Gebali"></p> <h4 id="sara-el-gebali-scilifelab-datacentre-sweden">Sara El-Gebali (SciLifeLab-DataCentre-Sweden)</h4> <p>Sara El-Gebali is a Project Leader at SciLifeLab-Data Centre in Sweden, where she leads the implementation of technical solutions that facilitate data-driven research on a national scale. She is the founder of <a href="https://www.fairpoints.org/">FAIRPoints</a>, a community driven initiative highlighting pragmatic measures towards the implementing the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. As a member of the steering committee for the FAIR Digital Objects forum, she advocates for inclusive and meaningful engagement practices, as well as the promotion of equitable technical solutions development. She is the founder of OpenCIDER (Open Computational Inclusion &amp; Digital Equity Resource), a knowledge space that highlights communities and resources related to Open Data from a global perspective to ensure equitable and effective engagement from underrepresented groups.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Joseph-Yracheta.png" alt="Joseph Yracheta"></p> <h4 id="joseph-m-yracheta-native-biodata-consortium">Joseph M. Yracheta (Native BioData Consortium)</h4> <p>Joseph M. Yracheta is an Amerindigenous Scientist (P’urhepecha y Raramuri from Mexico) and Executive Director of the Native BioData Consortium within the Cheyenne River Lakota Nation (Sioux). Mr. Yracheta is passionately working to end Amerindigenous Health Disparity by the &ldquo;wearing many research hats&rdquo; of law, ethics, policy, genomics, omics, health outcomes, epidemiology, health care prevention/intervention and allostatic load from systemic racism. Mr. Yracheta believes that ALL data and resources must be seen as unforeseen futures, where their value will constantly change. He feels this data must be secured for Indigenous economic sustainability.</p> <p>The Native BioData Consortium (NBDC) is the first 501(c)(3) nonprofit research institute that is led by Indigenous scientists and tribal community members in the United States. As a biorepository (or “biobank”), it works to ensure that advances in genetics, omics and health research benefit Native Americans and all Indigenous people.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/05/bastian_headshot.png" alt="Bastian Greshake Tzovaras"></p> <h4 id="bastian-greshake-tzovaras-the-alan-turing-institute">Bastian Greshake Tzovaras (The Alan Turing Institute)</h4> <p>Bastian is currently working on the <a href="https://www.turing.ac.uk/research/research-projects/citizen-science-platform-autistica">open source Citizen Science platform</a>. He has a background in biology and a PhD in Bioinformatics from the University of Frankfurt, Germany. Prior to joining the Turing Institute, he was a research fellow at the French National Institute of Health and Medical Research in Paris where he led a research group on facilitating participatory medicine approaches. Bastian is an avid fan of Open (Source|Access|Science|Culture|.*) and thinks that everything is better if you add open in front of it. He co-founded openSNP – a crowdsourced/citizen science open data project that puts personal genetics data into the public domain – in 2011 and was the Director of Research for Open Humans, a non-profit that provides digital and social infrastructure around personal-data driven citizen science and self-research.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/06/Verena-Ras-square-1.png" alt="Verena Ras"></p> <h4 id="verena-ras-university-of-cape-town">Verena Ras (University of Cape Town)</h4> <p>Verena Ras is the Training Coordinator at University of Cape Town for the <a href="https://www.h3abionet.org/">Human Heredity and Health in Africa (H3Africa)&rsquo;s H3ABioNet</a>. She works closely with software development teams and international organizations to develop better training workflows and pipelines and to develop training models that overcome the challenges experienced by developing countries. H3ABioNet offers bioinformatics training all over Africa using various training modalities. Verena also chairs the Sample Collection and Processing Sub-committee of the <a href="https://africanbiogenome.org/">African BioGenome Project</a>, a coordinated pan-African effort to build capacity and infrastructure to generate, analyze and deploy genomics data for the improvement and sustainable use of biodiversity and agriculture across Africa. She manages the ethical sourcing and collection of species/tissue, following international best practises for specimen collection and processing for whole genome sequencing.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Monica_Munoz-Torres-2.jpeg" alt="Monica Munoz-Torres"></p> <h4 id="moderator-monica-munoz-torres-university-of-colorado-anschutz-medical-campus">MODERATOR: Monica Munoz-Torres (University of Colorado Anschutz Medical Campus)</h4> <p>Monica is a Visiting Associate Professor at the University of Colorado. She leads the Standards Core in the BRIDGE Center project of the NIH Bridge to Artificial Intelligence (Bridge2AI) Program, and is the Program Director for the Phenomics First Resource, an NHGRI Center of Excellence in Genomic Science, and for the Monarch Initiative. Monica&rsquo;s expertise, education, and enthusiasm span genomics, biocuration, knowledge representation, and data harmonization – and the development of software tools and standards to advance these fields. Her major motivations are to leverage the wealth of comparative genomics knowledge to advance our understanding of human health and disease with translational and integrative data science, and to continuously improve on socio-technological practices to build and coordinate research communities. In 2022 Monica was recognized as a Kavli Fellow by the National Academy of Sciences.</p>https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/Tue, 11 Apr 2023 15:16:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/<h4 id="this-is-the-schedule-for-bosc-2023">This is the schedule for BOSC 2023</h4> <h6 id="go-to-full-lists-of-the-2023-talks-and-posters"><a href="#talks">Go to full lists of the 2023 talks and posters</a></h6> <h6 id="bosc-2023-keynotes"><a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/">BOSC 2023 Keynotes:</a></h6> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Sara-El-Gebali-square-1.png" alt="Sara El-Gebali"><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Joseph-Yracheta.png" alt="Joseph Yracheta">Sara El-Gebali: A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration Joseph Yracheta: The Dissonance between Scientific Altruism &amp; Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution</p> <h6 id="bosc-2023-panel-open-and-ethical-data-sharing"><a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/">BOSC 2023 Panel: Open and Ethical Data Sharing</a></h6> <h5 id="bosc-2023-schedule-at-a-glance">BOSC 2023 schedule at a glance</h5> <div style="position: relative; padding-top: 90%;"><iframe style="position: absolute; top: 0; left: 0; width:95%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vSFHK2hl0ZBjIPkp_pL09gxbLNRpPuDVy1oy_4zm5zKgG_ybRkZnRL0beiveSwHlMFSLbc7dZ3K4REB/pubhtml?gid=0&amp;single=true&amp;widget=true&amp;headers=false" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h4 id="bosc-2023-talk-schedule">BOSC 2023 Talk Schedule</h4> <div style="position: relative; padding-top: 90%;"><iframe style="position: absolute; top: 0; left: 0; width: 150%; height: 99%;" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vSFHK2hl0ZBjIPkp_pL09gxbLNRpPuDVy1oy_4zm5zKgG_ybRkZnRL0beiveSwHlMFSLbc7dZ3K4REB/pubhtml?gid=1729310258&single=true" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h4 id="bosc-2023-posters">BOSC 2023 Posters</h4> <div style="position: relative; padding-top: 85%;"><iframe style="position: absolute; top: 0; left: 0; width: 120%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vSFHK2hl0ZBjIPkp_pL09gxbLNRpPuDVy1oy_4zm5zKgG_ybRkZnRL0beiveSwHlMFSLbc7dZ3K4REB/pubhtml?gid=1094351563&single=true" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h6 id="last-year"><a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXYotvWZLnKd9rcNMb6r9tjf">Last year&rsquo;s BOSC 2022 talk and poster videos on YouTube</a></h6>https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/Sat, 01 Apr 2023 05:03:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/<h1 id="bosc-2023-keynotes">BOSC 2023 Keynotes</h1> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Sara-El-Gebali-square-1.png" alt="Sara El-Gebali"></p> <h3 id="sara-el-gebali-scilifelab-datacentre-sweden">Sara El-Gebali (SciLifeLab-DataCentre-Sweden)</h3> <h6 id="a-new-odyssey-pioneering-the-future-of-scientific-progress-through-open-collaboration"><em>A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration</em></h6> <p>_Join us in humanity&rsquo;s quest for knowledge and understanding, on a transformative odyssey of scientific progress, fueled by the power of open collaboration. This presentation will navigate the realms of scientific discovery, exploring the profound impact of globally inclusive and collaborative efforts that have the potential to revolutionize the very fabric of scientific advancement. _</p> <p><em>As we embark on this journey, we will delve into the principles of diverse global alliances and pioneering scientific institutions, illustrating how their values align with real-world initiatives that promote open science, and provide examples of the groundbreaking opportunities that arise when individuals from various backgrounds, disciplines, and experiences unite in pursuit of a common goal.</em></p> <p><em>In the spirit of &ldquo;Infinite Diversity in Infinite Combinations,&rdquo; this presentation will showcase inspiring examples of collaboration and inclusivity in action, demonstrating how community building, mentorship programs, and grassroots movements play an essential role in fostering inclusive scientific communities.</em></p> <p><em>These initiatives empower individuals from underrepresented backgrounds to overcome barriers, access valuable resources, and contribute their unique perspectives to the scientific conversation. By nurturing a culture of inclusivity and support, we can create a flourishing environment that encourages the exchange of ideas and accelerates the pace of scientific discovery. Join us as we chart a course toward a brighter, more inclusive future, where the collective power of diverse minds and open collaboration propels us forward into the uncharted territories of scientific discovery.</em></p> <p>Sara El-Gebali is a Project Leader at SciLifeLab-Data Centre in Sweden, where she leads the implementation of technical solutions that facilitate data-driven research on a national scale. She is the founder of <a href="https://www.fairpoints.org/">FAIRPoints</a>, a community driven initiative highlighting pragmatic measures towards the implementing the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. As a member of the steering committee for the FAIR Digital Objects forum, she advocates for inclusive and meaningful engagement practices, as well as the promotion of equitable technical solutions development.</p> <p>With a strong background in life science and a PhD in cancer research, Sara is a passionate community builder and an outspoken advocate for the inclusion of historically marginalized groups in STEM and Open Science. She is the founder of OpenCIDER (Open Computational Inclusion &amp; Digital Equity Resource), a knowledge space that highlights communities and resources related to Open Data from a global perspective to ensure equitable and effective engagement from underrepresented groups.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/04/Joseph-Yracheta.png" alt="Joseph Yracheta"></p> <h3 id="joseph-m-yracheta-native-biodata-consortium">Joseph M. Yracheta (Native BioData Consortium)</h3> <h6 id="the-dissonance-between-scientific-altruism--capitalist-extraction-the-zero-trust-and-federated-data-sovereignty-solution"><em>The Dissonance between Scientific Altruism &amp; Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution</em></h6> <p>_The history that led to the roadbuilding of Open Data’s current pathway is a murky one and one that isn’t fully transparent as to causes, sponsors or decision makers. The philosophical underpinnings and moral obligation of Open Data is flawed and over prioritizes funding commitments and scientists’ rights to data rather than the privacy, development and implementation obligations that are often left to the unjust realm of commercial capitalization. Mr. Yracheta will discuss from the USA’s American Indian perspective (as sovereign Domestic Dependent Nations) and their relationship with states’ and federal governments. Several U.S. policy documents and legislative acts that were created in and out of consultation with American Indian nations will be shared and discussed. Key gaps in the moral obligation to society at large will be demonstrated via this special relationship with tribes. Where possible, Mr. Yracheta will employ game theory to move the Open Data argument into a more socially just and philosophically robust posture. Interrogated are two possible pathways to our current landscape 1) Is the current Open Data environment well intended but ignorant? Neglectful? Aligned with or against the Belmont Principle of Non-Coercion? Or 2) Is the current Open Data environment obfuscatory, purposely predatory and extractive? The answers to either position will determine the timing and delivery of benefits to societies and individuals. _</p> <p>Joseph M. Yracheta is an Amerindigenous Scientist (P’urhepecha y Raramuri from Mexico) and Executive Director of the Native BioData Consortium within the Cheyenne River Lakota Nation (Sioux). Mr. Yracheta has been a scientist since 1990; he started as a bench biotechnician and worked across many disciplines. In 2014 he graduated from UW Seattle with a master’s in Pharmaceutics and Bioethics under Drs. Ken Thummel and Wylie Burke. He is currently finishing a DrPH in Environmental Health and Engineering from Johns Hopkins under Drs. Ana Navas-Acien and Paul Locke.</p> <p>Mr. Yracheta is passionately working to end Amerindigenous Health Disparity by the &ldquo;wearing many research hats&rdquo; of law, ethics, policy, genomics, omics, health outcomes, epidemiology, health care prevention/intervention and allostatic load from systemic racism. Mr. Yracheta believes that ALL data and resources must be seen as unforeseen futures, where their value will constantly change. He feels this data must be secured for Indigenous economic sustainability.</p> <hr> <h4 id="bosc-keynote-speaker-selection-process">BOSC keynote speaker selection process</h4> <p>BOSC usually includes two or three keynote talks given by prominent individuals or emerging leaders who are accomplished in areas relevant to the bioinformatics open source community and who represent a diversity of backgrounds and ideas. Please see our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker rubric</a> for more information about our keynote speaker selection process and criteria.</p>https://www.open-bio.org/2023/03/29/winfred-gatua-hybrid-carpentries-workshop/Wed, 29 Mar 2023 15:15:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/03/29/winfred-gatua-hybrid-carpentries-workshop/<p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/Winfred_BWCB.png" alt=""></p> <p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Winfred Gatua,</em></strong> <em><strong>Doctor of Philosophy, Bristol Medical School</strong></em> <strong><em>, was awarded an OBF Event Fellowship to organize</em></strong> <em><strong>a Hybrid Carpentries workshop at Laikipia University, Kenya.</strong></em></p> <p>Hosting and facilitating a hybrid carpentries workshop in my home country is an excellent highlight for me. I am very grateful to have received the OBF Event Fellowship 2022.</p> <p>Among my goals is mentorship and training of younger researchers in Kenya, especially those in remote Kenyan universities with no access to many resources; instead, being stuck in the traditional way of doing research, including contracting experts to do the data analysis for them; a costly ordeal. However, I wanted to change the narrative and open these scientists to the world view of data, how to make their research work reproducible, and shed insights into what is open science and collaborations.</p> <p>Despite spending my time as a volunteer instructor in institutions abroad, I have always wanted to host and run a carpentries-based workshop in some institutions in Kenya. However, the cost associated with running any workshop is immense; therefore, when I saw the call for an OBF event fellowship, this was a perfect opportunity for me to try it.</p> <p>Upon receiving an award email, I was excited and eager to carry on with the workshop to ensure that students know in advance bioinformatics, open science, and reproducible research before they leave their bachelor’s studies.</p> <p>With the assumption that since the pandemic, institutions have adapted to online teaching, I designed the training to be exclusively online while applying for funding. Upon assessing the resources available, I decided to adopt a hybrid workshop with a resident helper at the University helping the students. In contrast, other instructors/helpers of the workshop joined online and taught modules online.</p> <p>While all participants were novices when we began the workshop, by the close, the participants were excited to explore careers in bioinformatics and data science, including access to advanced training. This workshop allowed my colleagues and me to share our broad knowledge of data science and inspire students to carry on with collaborative, open, and reproducible research in the future.</p> <p>I want to thank the instructors and helpers who worked tirelessly with me through the five days of the workshop. I appreciate the Laikipia University administration’s support during the preparation and workshop. A big shout out to the OBF event fellowship for the award; without your support, the workshop would not have succeeded.</p> <p>The next step includes applying for funding from other organizations to facilitate sharing of knowledge around data science and open and reproducible research practices in Kenya and Africa.</p> <p>Below is a photo of the workshop in progress, a screenshot showing virtual participants, and a group photo at the end of the workshop.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/DSC_0380-1024x683.jpg" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2023/03/Zoom_screenshot-1024x530.jpeg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/IMG_5250-3-1024x683.jpg" alt=""></p>https://www.open-bio.org/events/bosc/sponsors-2025/Mon, 27 Mar 2023 19:05:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc/sponsors-2025/<h3 id="2025-platinum-sponsor">2025 Platinum Sponsor:</h3> <p><a target="_new" href="https://chanzuckerberg.com/science/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:60%" alt="CZI" /></a></p> <center>The aim of CZI’s Open Science program is the universal and immediate open sharing of all scientific knowledge, processes, and outputs. </center> <br/> <h4 id="2025-gold-sponsor">2025 Gold Sponsor:</h4> <p><a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" style="width:50%" alt="Seqera" /></a></p> <center><small>Seqera, developed by the creators of Nextflow, empowers researchers to develop and deploy scalable bioinformatics pipelines faster</small></center> <p align="center"><iframe src="https://drive.google.com/file/d/1V1BbVcCPQHWN-8eMr4-yZ19xAK1p0Tfd/preview" width="640" height="480" allow="autoplay" ></iframe></p> <p><strong>2025 Silver Sponsor:</strong></p> <p><a target="_new" href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" style="width:30%" alt="GigaScience" /></a></p> <br/> <div class="well"> <h3 id="sponsoring-bosc-2025">Sponsoring BOSC 2025</h3> <div class="splitbox"><div class="left"> <p>Sponsorships from companies and non-profit organizations help to defray some of our costs and enable us to offer free registration for some conference participants. In 2024, thanks to our sponsors’ generous support, we were able to grant free registration to 15 participants, offer honoraria to keynote speakers, and cover other expenses.</p> <h4 id="interested-in-sponsoring-bosc">Interested in sponsoring BOSC?</h4> <h4 id="please-contact-us-at-">Please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</h4> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Nomi-by-BOSC2024-poster.jpg" alt="Nomi by BOSC 2024 poster"></p> </div><div style="clear:both"></div></div> </div> <h2 id="what-is-bosc">What is BOSC?</h2> <p>BOSC is an annual meeting organized by the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation (OBF)</a>, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>Each BOSC ​includes ​talks,​ ​poster​ ​sessions,​ ​panel, and ​lots​ ​of​ ​opportunities​ ​for​ ​networking. It is followed by​ ​collaborative​ ​working​ ​sessions​ ​at the <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a>.​ ​These​ ​events​ ​bring​ ​together​ ​software​ ​engineers,​ ​bioinformaticians,​ ​and​ ​researchers​ ​to collaborate​ ​and​ ​extend​ ​open​ ​source​ ​bioinformatics​ ​tools.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt="Panel at BOSC 2015"></p> <p>BOSC​ ​participants​ ​come​ ​from​ ​a​ ​wide​ ​variety​ ​of​ ​research​ ​environments​ ​and​ ​backgrounds:</p> <ul> <li>Biological​ ​researchers,​ ​students,​ ​and​ ​post-docs​ ​who are​ ​learning​ ​bioinformatics​ ​analysis tools and techniques</li> <li>Power​ ​bioinformatics​ ​users</li> <li>Bioinformatics​ ​tool​ ​and​ ​workflow​ ​developers</li> <li>Bioinformatics​-focused​ ​principal​ ​investigators​ ​and​ ​researchers</li> <li>Sequencing​ ​core​ ​facility​ ​staff</li> <li>Industry​ ​scientists​ ​and​ ​bioinformaticians</li> <li>Data​ ​producers</li> </ul> <h2 id="previous-events">Previous Events</h2> <p>BOSC​ has been held <a href="https://www.open-bio.org/events/bosc/about/">every​ ​year​ ​since​ ​2000</a>.​ Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB).</p> <p>In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>. In July 2020, BOSC again joined forces with GCC to form the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>. Held online, BCC2020 attracted over 600 participants from 62 countries.</p> <p><a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> was part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, and took place July 29-30, 2021 (followed by a two-day <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest</a>).</p> <p><a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> was held July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> in person in Madison, Wisconsin, USA, and simultaneously online.</p> <p><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a> took place July 24-25, 2023 as part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> in Lyon, France and online. Like the previous year, we joined forces with Bio-Ontologies for part of a day!</p> <p><a href="https://www.open-bio.org/events/bosc-2024/">BOSC 2024</a>, the 25th annual Bioinformatics Open Source Conference, took place July 15-16, 2024 as part of <a href="https://www.iscb.org/ismb2024/home">ISMB 2024</a> in Montreal, Canada and online. It was followed by <a href="https://www.open-bio.org/events/bosc-2024/ismb-collaborationfest-2024/">CoFest 2024</a>.</p> <p><a href="https://www.open-bio.org/events/bosc-2025/">BOSC 2025</a> will be held in Liverpool, UK, as part of the large <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a> conference. This year, for the first time, <a href="https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/">CollaborationFest</a> will be part of the main ISMB/ECCB conference and will be open to all.</p> <p><a href="https://www.open-bio.org/events/bosc/about" class="btn btn-lg btn-primary">More about BOSC</a></p> <br/> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Seqera-booth-2024.jpg" alt="Seqera booth at BOSC 2024"></p> <h2 id="benefits-of-sponsorship">Benefits of Sponsorship</h2> <p>Sponsoring BOSC increases your visibility in the bioinformatics community. We acknowledge our sponsors before, during and after the event in multiple ways:</p> <ul> <li>We list our sponsors on the BOSC website</li> <li>Sponsors are thanked and named in the introduction/closing slides during the meeting</li> <li>We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area</li> <li>The sponsors are thanked in selected emails to our mailing list and social media posts (with your logo) that go out before, during and after the event</li> <li>The sponsors are listed in our published reports after the meeting, e.g., <a href="https://f1000research.com/articles/7-1309/v1">https://f1000research.com/articles/7-1309/v1</a></li> <li>Platinum sponsors can show a short video before the first keynote</li> <li>Gold sponsors can show a short video some time during the conference</li> <li>We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <h2 id="how-sponsorships-help-bosc">How sponsorships help BOSC</h2> <p>We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to</p> <ul> <li>offer free registration to some BOSC participants</li> <li>support the <a href="https://www.open-bio.org/event-awards/">OBF&rsquo;s Event Fellowship program</a>, increasing participation from underrepresented groups</li> <li>provide child care at the conference</li> <li>underwrite the cost of conference events such as dinners or refreshments at poster sessions</li> <li>help defray the cost of videography</li> <li>provide space and catering at the CollaborationFest</li> <li>offer honoraria to keynote speakers</li> <li>pay for captioning and translations</li> </ul> <div class="well"> <p>In 2021, sponsorships enabled us to offer free registration to 20 participants from all over the world! <iframe loading="lazy" src="https://www.google.com/maps/d/embed?mid=1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width="640" height="480"> </iframe> </p> </div> <h1 id="sponsors-from-previous-years">Sponsors from previous years</h1> <h2 id="2024-platinum-sponsors">2024 Platinum Sponsors:</h2> <p><a target="_new" href="https://seqera.io/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/Logo_Seqera-Color.png" style="width:75%" alt="Seqera" /></a></p> <center>Seqera makes complex data analysis accessible at any scale</center> <p><a target="_new" href="https://chanzuckerberg.com/science)"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:65%" alt="CZI" /></a></p> <div class="splitbox"><div class="left"> <br/> <p><strong>2024 Gold Sponsor:</strong></p> <p><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2024/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Data Science"></a></p> </div><div class="right"> <br/> <p><strong>2024 Silver Sponsor:</strong></p> <div class="splitbox"><div class="left"> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a></p> </div><div class="right"> </div><div style="clear:both"></div></div> </div><div style="clear:both"></div></div> <br/> <h2 id="bosc-2023-platinum-sponsor">BOSC 2023 Platinum Sponsor</h2> <p><a target="_new" href="https://chanzuckerberg.com/science)"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:60%" alt="CZI" /></a></p> <h3 id="bosc-2023-silver-sponsors">BOSC 2023 Silver Sponsors</h3> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a><a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a><a href="https://www.software.ac.uk/"><img src="https://www.open-bio.org/wp-content/uploads/2023/04/SSI_PRIMARY-LOGO-300x96.png" alt="SSI logo"></a></p> <h2 id="bosc-2022-platinum-sponsors">BOSC 2022 Platinum Sponsors</h2> <p><a target="_new" href="https://chanzuckerberg.com/science"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" style="width:60%" alt="CZI" /></a></p> <br/> <p><a target="_new" href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" style="width:35%" alt="AWS" /></a></p> <h2 id="bosc-2022-gold-sponsors">BOSC 2022 Gold Sponsors</h2> <p><a target="_new" href="https://www.broadinstitute.org/data-sciences-platform"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/Broad-DSP-logo-1.png" style="width:50%" alt="Broad" /></a></p> <p><a target="_new" href="https://datascience.nih.gov"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/NIH-ODSS_Horizontal_1Color-653.jpg" style="width:70%" alt="NIHODSS" /></a></p> <h3 id="bosc-2022-silver-sponsors">BOSC 2022 Silver Sponsors</h3> <p><a href="https://arvados.org"><img src="https://www.open-bio.org/wp-content/uploads/2022/05/ArvadosCurii.png" alt="Arvados, supported by Curii"></a><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="Gigascience"></a></p> <br/> <div class="well"> <center> <p><b>If you are interested in becoming a BOSC sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</b></p> </center> </div>https://www.open-bio.org/2023/03/22/mailing-lists-to-paid-hosting/Wed, 22 Mar 2023 16:07:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/03/22/mailing-lists-to-paid-hosting/<p>We&rsquo;re sharing some important news with you regarding our mailing lists. From early on, we’ve maintained a self-hosted Mailman server for any OBF project that needs a mailing list, including our member roster list. After careful consideration, we have decided we need a solution that keeps track more reliably with current and emerging spam-fighting technologies and standards, and that simultaneously requires much less administration time and know-how. Specifically, we are planning to migrate the lists to paid hosting, possibly Mailchimp.</p> <p>As an open-source community, we understand the importance of using open solutions whenever possible. However, in this case, we feel that switching to a paid provider is the right call for our organization. Mailchimp will offer us a simpler solution  with features that should significantly improve the overall user experience for our members. Additionally, it will be easier for us to maintain and manage the mailing lists, which will free up resources for other important initiatives.</p> <p>We understand that open-source solutions are important to many of our members, but having a stable, reliable, user-friendly, and cost-effective mailing list is essential to our community&rsquo;s success. If you have personal experience with another mailing list provider that you believe would provide similar or better functionality than Mailchimp, and that is more open, we’d love to hear about it – please contact us by Monday 3 April 2023. You can submit your suggestions by leaving comments in <a href="https://github.com/OBF/obf-docs/issues/114">this GitHub issue</a>, or contact us in the <a href="https://join.slack.com/t/open-bio/shared_invite/zt-1pnswao9y-8igcckVxBXhQHCMweHt_NA">OBF Slack</a>.</p>https://www.open-bio.org/2023/03/21/ruth-nanjala-experience-at-the-ichg-2023-conference/Tue, 21 Mar 2023 16:32:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/03/21/ruth-nanjala-experience-at-the-ichg-2023-conference/<p><img src="https://lh6.googleusercontent.com/81b1Vw9GP-Bimj8BknvbmoKN1ABWtA9jiidU__Lk5Znu9M4SCq1HYm24l5duwWa2B9QF1unBf5FrqViiy1uY9nGHDZwPof5bWPw3mSh0TITA0bU1JIz-mgQ7HNII7egFPLj0OJGmRE83" alt=""></p> <p><strong><em>The</em></strong> <a href="https://www.open-bio.org/travel-awards"><strong><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></strong></a> <strong><em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Ruth Nanjala, a DPhil student in Cellular and Molecular Medicine at the University of Oxford, was awarded an OBF Event Fellowship to attend the</em></strong> <a href="https://www.ichg2023.com"><strong><em>International Congress of Human Genetics (ICHG) 2023</em></strong></a> <strong><em>conference.</em></strong></p> <p>Earlier in 2022, I received the Open Bioinformatics Foundation (OBF) Event Fellowship for participating and promoting open science at the American Society of Human Genetics (ASHG) 2022 conference in Los Angeles. However, I could not travel to ASHG due to unavoidable circumstances. Fortunately, OBF gave me a second chance by facilitating my travel to the International Congress of Human Genetics (ICHG) 2023 conference hosted at home (Africa is considered the cradle of humankind) between the 22nd and 26th of February.</p> <p><img src="https://lh5.googleusercontent.com/t0YzIrVivPm7UuWqaYPNOuCeRgyLTFpVncqziSrg8JD009-vxDXkKqsPBm4BOZQYtHgS6s82Ap9i3H2WqUWKjc7cUFasO7SjkdTgmc1u1Rn3x1GDaIOGHZkYCwUW4WlmDYsNPCNW2ZrEEYO569ZKwA" alt=""></p> <p><strong><em>Image: First day of poster presentations at the Cape Town International Convention Centre</em></strong></p> <p>My research focused on evaluating different programs, reference panels, and genotyping arrays used to predict HLA alleles from the highly polymorphic human Major Histocompatibility Complex region. The workflow was written using the open-source software, Nextflow and published on GitHub <a href="https://github.com/nanjalaruth/MHC-Imputation-Accuracy">https://github.com/nanjalaruth/MHC-Imputation-Accuracy</a>. For those interested in learning more, the preprint can be accessed at the link: <a href="https://pubmed.ncbi.nlm.nih.gov/36747714/.">https://pubmed.ncbi.nlm.nih.gov/36747714/.</a></p> <p>Aside from presenting a poster of my work, I was able to attend and engage in other conference sessions. Below, I highlight take-home messages from each day:</p> <p><strong>Day 1</strong> The keynote on Genomics and anthropology set the tone for the day as insights were shared on human settlement patterns and migration patterns in Africa. The continent is widely considered the birthplace of modern humans. During this day, Prof. Nicola Mulder proposed the setup of a network of Genomic Centres of Excellence in Africa with the aim of reducing the access gap for genomic technologies.</p> <p><strong>Day 2</strong> Karoline Kuchenbaecker from University College London showed that diversity in genetic investigations promotes gene prioritization, causal inference, precise mapping, and locus identification. Andrew Morris from the University of Manchester demonstrated the effectiveness of heterogeneous populations for Genome-Wide Association Studies discovery and application.</p> <p><strong>Day 3</strong> A captivating session was chaired by Athena, which focused on overcoming obstacles to studying diversity in global genetics. The session presenters, Adebowale, Krystal, and Lerato pointed out strategies that can be adopted to improve diversity.</p> <p><strong>Day 4</strong> An interesting session was on the “Southern African Population structure, Admixture and Adaptation,” as I got insights on the changes in skin color in southern Africa, Khoisan gene flow and its significance for genetic research, and the intricate patterns of mixing and population migrations during the Bantu expansion.</p> <p>The conference was then closed by the ICHG conference team led by Prof. Michele Ramsay, who handed over the planning for the next conference in 2026 to the Mexico team.</p> <p><img src="https://lh4.googleusercontent.com/IND_tgHCmknXDXUwmVK-IxpHuGndNgWBA6asSZlt-uwMV2_LmXQDzwPIVkizK9tpanA3c_Px5ZL46se929xKEXqMWxS1hxzYH5LdYCkWhP-g_VCA4aEu63koTF3FeJAn1V_VUFHPkaffUG38FWuTuA" alt=""> <strong><em>Image: Aerial view of Cape Town. Table Mountain (left), Lion’s head (right)</em></strong></p> <p>Attending my first ICHG conference has been an incredible experience and an excellent opportunity to network with diverse scientists in human genetics. As a researcher interested in enhancing diversity in human genetics research and promoting open science, I found most talks enlightening. I am extremely grateful to OBF and the team members that made it possible for me to attend the ICHG conference, which is hosted every four years.</p>https://www.open-bio.org/2023/03/17/hannah-wei-webinar-video-now-available/Fri, 17 Mar 2023 23:50:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/03/17/hannah-wei-webinar-video-now-available/<p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/Moni-moderating-questions-for-Hannah-Wei-1-266x300.png" alt=""></p> <p>On March 14, 2023, we held a webinar (hosted by <a href="https://www.iscb.org/iscbacademy">ISCBacademy</a>) about &ldquo;Re-Thinking the Patient’s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative&rdquo; presented by Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative. See <a href="https://www.open-bio.org/2023/03/07/iscbacademy-webinar-on-patient-led-research/">the webinar announcement</a> for a full description.</p> <p>BOSC organizing committee member Monica Munoz-Torres introduced Ms. Wei and fielded a lively Q&amp;A session. The webinar recording is available on YouTube at <a href="https://youtu.be/M2vAotWKd_Q">https://youtu.be/M2vAotWKd_Q</a>.</p> <p>The <a href="https://www.iscb.org/iscbacademy">ISCBacademy</a> is a series of free webinars offered by the <a href="https://www.iscb.org/">ISCB</a>, which runs the annual ISMB conference, through the ISCB Communities of Special Interest (COSIs), which include BOSC/OBF. Each COSI gets two webinar slots per year, so watch for our next one in fall 2023!</p>https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/Tue, 14 Mar 2023 21:53:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/<h1 id="collaborationfest-2023">CollaborationFest 2023</h1> <p>In conjunction with our annual meeting, <a href="https://www.open-bio.org/events/bosc-2022/">B</a> <a href="https://www.open-bio.org/events/bosc-2023/">O</a> <a href="https://www.open-bio.org/events/bosc-2022/">SC</a>, the OBF runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you.</p> <p>The 2023 BOSC CoFest, which will <strong>precede</strong> ISMB/ECCB 2023, will take place July 22-23, and will be hybrid (online + in person at <a href="http://www.ens-lyon.fr/en/campus-life/campus-tour/">ENS Lyon</a>, France). We encourage you to register for the conference, but the CoFest itself is free. Three easy steps to sign up:</p> <ul> <li>add yourself to this <a href="https://docs.google.com/spreadsheets/d/1BxvvMHieousC9Gl-15UIK5Igoo2pT4I-JHcA3l4xLhc/edit#gid=0">spreadsheet</a> to help us gauge interest, coordinate topic groups and more importantly order lunches (food will be offered to all in-person attendees),</li> <li>add your project ideas in this <a href="https://docs.google.com/document/d/1D7FtwmpPEWddbJEk8sqgbg9O7CBBDmSbVvvY_qOI2Nw/edit">document</a> if you have something in mind,</li> <li>join the #cofest channel in the <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">BOSC Slack</a>!</li> </ul> <p>Please register in advance to help us set up everything!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/codefest-big-group-on-steps.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h2 id="date">Date</h2> <p>Saturday July 22nd to Sunday 23rd, from 9am to 5.30pm.</p> <h2 id="location">Location</h2> <p>The 2023 BOSC CoFest will take place in Condorcet meeting room, at the ENS Lyon:</p> <p>Address: <a href="https://goo.gl/maps/9qEpK8smZ8TpDFFh9">1, place de l’École <br> 69007 Lyon <br> France </a> GPS coordinates: (45.729846881035385, 4.828230822514165)</p> <p>Detailed access instructions are available <a href="https://www.open-bio.org/wp-content/uploads/2023/07/how_to_come_to_CoFest_2023.pdf">here</a></p> <h2 id="public-transports">Public transports</h2> <ul> <li>metro line B, Deboug station,</li> <li>tramway T1, ENS Lyon stop.</li> </ul> <h2 id="sponsors">Sponsors</h2> <p><a href="https://www.ixxi.fr/"><img src="https://www.ixxi.fr/ixxi/configuration/fiche-de-configuration-charte-ENS/@@images/logo_site" alt=""> <br> Complex Systems Institute</a></p> <p><a href="http://www.ens-lyon.fr"><img src="https://www.open-bio.org/wp-content/uploads/2023/06/ens_logo.png" alt=""> <br> École Normale Supérieure de Lyon</a></p> <p><a href="http://www.ens-lyon.fr/RDP/"><img src="https://www.open-bio.org/wp-content/uploads/2023/06/ens_rdp_logo.jpeg" alt=""> <br> Laboratoire Reproduction et Développement des Plantes</a></p> <p><a href="http://www.ens-lyon.fr/RDP/"><img src="https://www.france-bioinformatique.fr/wp-content/uploads/logo-ifb-couleur.svg" alt=""></a> Thanks to the support from <a href="https://www.france-bioinformatique.fr/en/home/">French Institute of Bioinformatics</a> and <a href="http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil">PSMN</a>, virtual machines will be available to attendees.</p> <h2 id="history">History</h2> <p>This will be the 14th annual pre- or post-BOSC collaboration fest. Previous fun and successful events were <a href="https://www.open-bio.org/wiki/Codefest_2010">Codefest 2010</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> in Vienna, <a href="https://www.open-bio.org/wiki/Codefest_2012">Codefest 2012</a> in Los Angeles, <a href="https://www.open-bio.org/wiki/Codefest_2013">Codefest 2013</a> in Berlin, <a href="https://www.open-bio.org/wiki/Codefest_2014">Codefest 2014</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2015">Codefest 2015</a> in Dublin, <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a> in Orlando, <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> in Prague, <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC Collaboration Fest 2018</a> in Portland, <a href="https://www.open-bio.org/events/bosc/bosc-2019-collaborationfest">Collaboration Fest 2019</a> in Basel, and the last two worldwide virtual editions <a href="https://www.open-bio.org/events/bosc-2020/bosc-2020-collaborationfest/">BOSC 2020 CollaborationFest</a>/ <a href="https://bcc2020.github.io/cofest/">BCC2020 CollaborationFest</a> (online) and <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">Collaboration Fest 2021</a> (online). The <a href="https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/">2022 CollaborationFest</a> was hybrid (virtual + in person).</p> <h2 id="code-of-conduct">Code of Conduct</h2> <p>This event is under the <a href="https://www.open-bio.org/code-of-conduct/">OBF Code of Conduct</a>.</p>https://www.open-bio.org/2023/03/09/bosc-early-poster-acceptance/Thu, 09 Mar 2023 17:57:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/03/09/bosc-early-poster-acceptance/<p>ISMB/BOSC is around the corner! We can hardly wait for the abstracts to start pouring in!</p> <p>We realize that some people can’t get conference travel approval from their institution until they get confirmation that their abstract has been accepted for a presentation.</p> <p>To help you, this year we have decided to offer <strong>Early Poster Acceptance</strong>: if you <a href="https://www.open-bio.org/events/bosc-2023/submit/">submit your abstract</a> by March 31, we will let you know by April 6 whether it has been accepted or not for (at least) a poster. (The regular abstract submission deadline is April 20, and authors who submit in that round will be informed of poster/talk acceptance on May 11.)</p> <p>When you submit your abstract, you can choose to only apply for a poster, or to apply for a poster and a talk. If you choose poster+talk, then after the Early Poster Acceptance round your abstract will stay in the pool for the regular review round and you will find out on May 11 whether you got a talk slot.</p> <p>Ready your keyboards, and good luck!</p> <p>Key dates March 31: Early Poster Acceptance submission deadline April 6: Notification of poster acceptance April 20: Regular submission deadline May 11: Notification of talk and/or poster acceptance</p> <h3 id="faq">FAQ</h3> <p>Q: How do I submit my abstract for the Early Poster Acceptance round? A: The same way all abstracts are submitted to BOSC: see <a href="https://www.open-bio.org/events/bosc-2022/submit/">/events/bosc-2022/submit/</a> for instructions and submission link.</p> <p>Q: Can I submit in the Early Poster Acceptance round if I want to be considered for a talk? A: Yes, though you won’t get early notification about whether your abstract was chosen for a talk. All abstracts submitted early will be reviewed for possible talk acceptance in the regular review round, and you will be informed whether you got a talk on May 11.</p> <p>Q: Will I get a full review of my submission in the Early Poster Acceptance round? A: No, you will just get “accepted for poster” or “declined for poster”. However, your abstract will get a full review in the regular round, and the reviews will be sent to you on May 11.</p> <p>Q: What are the criteria for poster acceptance in the Early Poster Acceptance round? A: Please see <a href="https://www.open-bio.org/events/bosc-2022/submit/">/events/bosc-2022/submit/</a> for the criteria, but note that early submissions will receive a streamlined review in the Quick Check round. They will go through a full review in the regular round.</p> <p>Q: What are the possible outcomes in this Early Poster Acceptance round? A: 1. Accepted for poster (to be considered for talk in the regular round, if you requested a talk) 2. Declined 3. Deferred (we can’t decide; you will need to wait for a full review in the regular round). (We do not expect many submissions to fall into category #3.)</p> <p>Q: Can I present a talk AND a poster at BOSC? A: Yes! In fact, all abstracts accepted for talks are also invited to present a poster on the same topic. This is unaffected by early submission.</p> <p>Q: Are other COSIs also doing an Early Poster Acceptance round? A: We don’t know; you’d have to check with them. (But it was BOSC’s idea first.:-)</p>https://www.open-bio.org/2023/03/07/iscbacademy-webinar-on-patient-led-research/Tue, 07 Mar 2023 10:53:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/03/07/iscbacademy-webinar-on-patient-led-research/<p>Date and Time: Tuesday, March 14, 11am EDT/ 15:00 (not 16:00!) UTC Location: <a href="https://iscb.junolive.co/Nucleus/live/mainstage/iscbacademycosi79">Online webinar</a> hosted by ISCB and free to the public. (Video now available at <a href="https://youtu.be/M2vAotWKd_Q">https://youtu.be/M2vAotWKd_Q</a>)  Speaker: Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative Topic: Re-Thinking the Patient&rsquo;s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative</p> <blockquote> <p>The ISCB, which runs the annual ISMB conference, is offering a series of <a href="https://www.iscb.org/iscbacademy">ISCBacademy webinars</a> hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are now open to the public; you&rsquo;ll just need to create an ISCB Nucleus account to <a href="https://iscb.junolive.co/Nucleus/live/mainstage/iscbacademycosi79">register for the webinar</a>.</p> </blockquote> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/02/Hannah_Wei_Profile.jpg" alt="Photo of Hannah Wei"></p> <p>So often, a patient’s role in research has been limited to the donor of data and receiver of care, limiting the possibilities in between for participatory methodologies and open science collaboration.</p> <p>This webinar will be a case study of the patient-led research model. We will explore how the model was formed under the context of those with COVID-19 developing their own research capacity to study Long COVID, or Post-Acute Sequelae of COVID (PASC). We will present the levels of patient-involvement, data ownership and access principles, and accommodations for disabled contributors from our community. We will further discuss how patient-generated data can guide research direction and inform research hypotheses, while patients’ lived experiences, experiments and own research can enrich a learning health system. We will suggest ways to incorporate patient-led research models into open science innovations.</p> <p>The talk will be delivered by Hanna Wei, a patient-researcher, co-founder and technologist at the Patient-Led Research Collaborative, a multi-disciplinary, patient-run organization dedicated to placing patient voices at the forefront of Long COVID research.</p> <blockquote> <p>Hannah Wei is a co-founder at the Patient-Led Research Collaborative, an international organization of Long-COVID patient-researchers and advocates at the forefront of the Long COVID patient-led movement.</p> <p>Since the beginning of the pandemic, PLRC has brought together an interdisciplinary team of patients with backgrounds in medicine, neuroscience, participatory design, public policy, cognitive science, research engineering, data science, biostatistics, virology, psychiatry, neurology, pediatrics, and social epidemiology. PLRC has collaborated with the Long COVID taskforce at the WHO, CDC and co-authored over a dozen papers, including the paper on Characterizing long COVID in an international cohort: 7 months of symptoms and their impact published in the <a href="https://www.thelancet.com/journals/eclinm/article/PIIS2589-5370(21)00299-6/fulltext">Lancet</a>.</p> <p>Hannah&rsquo;s background is in computer science and leading data-driven products for the technology industry. Before the pandemic, Hannah was running field research in frontier communities of West Africa and Southeast Asia for product innovation teams at Fortune 500 tech companies. She became a Long COVID patient after getting infected on an airplane in March 2020. Since then, she has dedicated her efforts to running projects PLRC and innovating on the patient-led research model.</p> </blockquote> <p><strong><a href="https://iscb.junolive.co/Nucleus/live/mainstage/iscbacademycosi79">Register for the free webinar</a></strong></p>https://www.open-bio.org/2023/02/20/obf-event-fellowship-2023-1-call/Mon, 20 Feb 2023 03:09:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/02/20/obf-event-fellowship-2023-1-call/<p>The call for applications for the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> 2023, round 1, is now open. <strong>The deadline for this round is 1 April 2023.</strong> Applications should be submitted via <a href="https://forms.gle/r5BB6W6tL1hrwV426">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling the form – <a href="https://docs.google.com/document/d/1j_v-f1FcOA-ssXtsUdE_YaEOSQKZRms9-P7RGd3vdYA/edit">make a copy of this template</a>.The OBF Event Fellowship program aims to increase diverse participation at events that promote open source bioinformatics and/or open science. We invite applications from candidates who are seeking financial support to attend or host relevant scientific events from May 2023 to April 2024. <strong><em>These events can be conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><img src="https://lh6.googleusercontent.com/Gb9qZTiZuW75jMnWKMfms0sid9dT2K9EHJ3DTjsmIQW4cyZdt0TLFF4Ry5n1QgfNT-dbRioQuGEUAVaAqOe8yL1wjqVVlOukoApW68B_IT717K9NI5-qLBd7IiqMzz7l6NK45nn5lz1ddTSMkACLAps" alt=""></p> <p><em>Screenshot of our application form information section</em></p> <p><strong>Overview of the round 2 of OBF Event Fellowship 2022</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> is now in its 8th year. In the last year, we had two calls for applications, with deadlines on 1 April and 1 October in 2022. Starting in 2023, <strong>we will open three calls for applications</strong> with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>In 2022 round 2 (October 2022), we received 23 applications, of which three applicants were awarded this fellowship for various events they were participating in. Congratulations to <strong>Winfred Gatua</strong>, <strong>Luise Rauer,</strong> and <strong>Ruth Nanjala</strong>.</p> <p><strong>Nehemiah Ongeso Mosioma</strong> was also approved to attend Vienna BioCenter PhD Program Symposium &ldquo;Pushing Boundaries&rdquo;, but due to admin oversight, they could not attend the event. The OBF Fellowship Award chairs are discussing how we can redirect this award towards another event the awardee might be able to attend.</p> <p>We have recently published a blog post from one of our latest awardees summarising their experience attending a conference with help from an OBF Event Fellowship:</p> <ul> <li><a href="https://www.open-bio.org/2022/12/29/microbiome-knights/">Luise Rauer: Microbiome (k)nights</a></li> </ul> <p>Congratulations to all of our awardees!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and apply for the fellowship before 1 April 2023</strong>.</p>https://www.open-bio.org/2023/02/10/bosc-2023-keynote-comment-period/Fri, 10 Feb 2023 22:44:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/02/10/bosc-2023-keynote-comment-period/<p>We asked the community to <a href="https://www.open-bio.org/2023/02/02/nominate-keynote-speaker-for-bosc-2023/">nominate potential BOSC keynote speakers</a>, and we were pleased with all the great suggestions! Now it’s time for the next phase of our process: we’re giving the community a chance to let us know if there is anything that makes any of the nominated individuals NOT appropriate as BOSC keynote speakers.</p> <p>Our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker process and rubric</a> gives examples of some possible reasons for exclusion. <strong>If you have concerns about any of the people on our list, please let us know (with as much specificity as you feel comfortable providing) via <a href="https://docs.google.com/forms/d/e/1FAIpQLSegBn3b6_6_7DDxpjoayMhjCChVw07o8CVldXP54HzVuwcDlw/viewform">this anonymous form</a> no later than February 16, 2023.</strong></p> <p><strong>The nominees (in alphabetical order by first name) are&hellip;</strong></p> <ul> <li>Anne E. Carpenter (Broad Institute)</li> <li>Bérénice Batut (University of Freiburg / Open Life Science)</li> <li>Emma Hodcroft (University of Bern)</li> <li>Ishwar Chandramouliswaran (NIH)</li> <li>Joseph Yracheta (NativeBioData)</li> <li>Kevin Matthew Byrd (University of North Carolina, NIH/NIDCR, and the American Dental Association Science &amp; Research Institute)</li> <li>Kizzmekia Corbett (Harvard T.H. Chan School of Public Health)</li> <li>Laurie Goodman (GigaScience)</li> <li>Maria Nattestad (Google Health)</li> <li>Mark Robinson Rechavi (University of Zurich and Swiss Institute of Bioinformatics)</li> <li>Meag Doherty (National Institutes of Health)</li> <li>Michael R. Crusoe (Common Workflow Language project)</li> <li>Nico Matentzoglu (semanticly)</li> <li>Nicolás Palopoli (University of Quilmes, Argentina)</li> <li>Sara El-Gebali (SciLifeLab Data Centre, FAIRPoints)</li> <li>Sofia Forslund (ECRC (MDC &amp; Charité joint center), Berlin)</li> <li>Stephen Klusza (Clayton State University)</li> <li>Susanna Sansone (University of Oxford)</li> </ul> <p>After the community comment period closes on February 16, the BOSC organizing committee will draw on this list to extend invitations to potential keynote speakers. Since we cannot know in advance who will accept the invitation, we may have to go beyond the list of those nominated. In that case, we will not rerun this process, but community members are always encouraged to inform the Organizing Committee if any speaker does not meet our standards.</p>https://www.open-bio.org/2023/02/02/nominate-keynote-speaker-for-bosc-2023/Thu, 02 Feb 2023 06:06:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2023/02/02/nominate-keynote-speaker-for-bosc-2023/<p>BOSC usually includes two or three keynotes. We want these invited speakers to be prominent individuals or emerging leaders who are accomplished in their fields, and whose work is likely to be informative and of interest to the bioinformatics open source community. Please see our <a href="https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md">invited speaker rubric</a> for more information about our keynote speaker selection process and criteria.</p> <p>We would like to assemble a diverse list of potential BOSC 2023 keynote speakers. <strong>We invite the community to nominate keynote speakers using <a href="https://docs.google.com/forms/d/13DxXJsufZV63APAhlYaZ0304GsIyHgJNtvj2lEp5WZg/viewform">this form</a> by February 9.</strong></p> <p>We seek candidates who:</p> <p>Work on topics relevant to the bioinformatics research community Can contextualize their work with the open source bioinformatics community Have gained acclaim in their field Can inspire the BOSC community with new ideas and/or challenge them to think deeply about new topics Offer diversity in terms of gender, ethnicity, or geographical location</p> <p>Please <a href="https://docs.google.com/forms/d/13DxXJsufZV63APAhlYaZ0304GsIyHgJNtvj2lEp5WZg/viewform">submit your keynote speaker nominations</a> by 2023-02-09!</p>https://www.open-bio.org/2022/12/29/microbiome-knights/Thu, 29 Dec 2022 20:21:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/12/29/microbiome-knights/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Luise Rauer, a PhD student at the Technical University of Munich, was awarded an OBF Event Fellowship to participate virtually in the <a href="https://ihmc2022.jp/">9th International Human Microbiome Consortium (IHMC) conference</a> in November 2022.</em></p> <p>What do a total lunar eclipse and the 9th International Human Microbiome Consortium (IHMC) conference have in common? While they are both exciting and rare events that started in Kobe, Japan, on 8th November 2022, they also happened in the very early morning for any spectator from Europe. With the IHMC conference starting at 1 a.m. for me as a virtual participant based in Central Europe, my very unique preparation for this conference included changing my sleeping rhythm to become a nighthawk for 3 days and nights. But it was worth it!</p> <p><img src="https://lh3.googleusercontent.com/xPHSave0sB4wnINy1FmDgZAMppudbf8Awe7QF-gBnQZhum0Ie-XRHDoNhzZ3HcIuX6wqVAewQXL7itzJJtQvwc0SRI7ELIh7jtwJanqLnRdHrDRf6Vq1gWeV95oykU3qluSyb9X5_3mjw2pkW7AIXwiVsQoRnvPsu1DHNelSIth2VOayGXjyh_dFOe2-fQ" alt=""></p> <p>Lunar eclipse during the IHMC conference in Kobe, Japan. Copyright: <a href="https://twitter.com/ihmc2022/status/1589938303465558019">IHMC2022Kobe on Twitter: https://t.co/fcZmwRyDXr / Twitter</a></p> <p><img src="https://lh5.googleusercontent.com/eBwU2DmRmdXjggB4DpT4PpCnaNHKrujY9X1Q6Ld33LTTmVLFv9tRR7hN4IEHEuCiTjFtZphEkTHvBr4XrApHiy47jYuJKWotlfTfM7L3Q0Z3AIPgfhKiR8s5BH3Crf7iLml3ZKujLUBiZmMAMmWxMD9VetwaGUC_bGzIGE-KCgUqAyXjr-eRdmBHCPMTUw" alt=""></p> <p>IHMC conference venue in Kobe, Japan. Copyright: <a href="https://twitter.com/ihmc2022/status/1589797866792710144">IHMC2022Kobe on Twitter: https://t.co/gyksCdOLuK / Twitter</a></p> <p>The great selection of talks at the IHMC conference showed that microbiome research is really starting to fulfill its expectations. Kjersti Aagaard summarized a decade of her research on preterm birth in Malawi, which is prevented by supporting beneficial bacteria in the mouth microbiome with a specific chewing gum at the other end of the body. Similarly, Eran Segal reported successful stool transplants in atopic dermatitis – or in simple words, receiving other people’s poop treats your skin disease. Isn’t that amazing?</p> <p>While we learned that stool transplants are working in relieving some diseases, it is still unclear which bacteria are actually doing the job. An alternative idea – and probably a more appealing solution to patients – is using defined bacterial communities without the attached dark matter, as presented by Bernat Olle. The prospect of treating bacterial infections with <em>pro</em> biotics ( = living bacteria) instead of <em>anti</em> biotics ( = killing bacteria) is the way of positive thinking that I like.</p> <p>As a methodology enthusiast, I particularly enjoyed the talks by Ami Bhatt, promoting absolute abundance data and investigating how sample storage affects microbiome results, and by Jun Terauchi, presenting recent harmonization efforts in the microbiome field. In the same vein, I presented my two posters on methodological challenges in microbiome research, and how to tackle them using open-source software for quality control and the power of <a href="https://www.go-fair.org/fair-principles/">FAIR</a> data and research. Therefore, one of my personal highlights was the keynote presentation by Rob Knight, impressively summarizing his long-standing contribution to the field, starting from early methodological work on diversity measures to the more recent development of open science data platforms.</p> <p><img src="https://lh5.googleusercontent.com/zoNUspJTAv5k0YAM1xDDYkj0GFEfG69_A57y0z92Jh-uhMPClZHlH3vBkLwK3W_O8lMiNiSZVXuqoiRhkubOWEjSQXZf3tqu4uzQPzMLFWckEbGGky85TT51OIUsA04zLyU6Wdj6II-ev9aJLjOlCg7kTozOy0JX659JwqjkF-xhs01d45ndEVfl-vjCOA" alt=""></p> <p>Rob Knight’s keynote presentation at the IHMC conference in Kobe, Japan. Copyright: <a href="https://twitter.com/ihmc2022/status/1590290658887360512">IHMC2022Kobe on Twitter: https://t.co/0nJwbV4rg5 / Twitter</a></p> <p>While microbiome researchers have been caring a lot about microbial diversity ever since, geographic and ethnic diversity of the sampled humans have only started to be considered, as <a href="https://www.science.org/content/article/studies-human-microbiome-ignored-developing-world-potentially-compromising-treatments">illustrated earlier in 2022</a>. But science is moving forward: Projects like the Microbiota Vault aim to collect microorganisms across human cultures for sustainable microbiome health, data sharing practices are increasingly enforced by scientific journals, and hybrid events like the IHMC conference allow a wider inclusion of researchers in the scientific exchange through remote participation. While I really enjoyed following the talks from the distance, it would have been great to be able to exchange directly with other remote and onsite participants. Can the just announced next IHMC conference 2024 in Rome further foster interaction between all attendants, e.g. by providing digital sessions or hybrid interaction spaces?</p> <p>To sum it up, the IHMC conference did not only provide me with an exciting overview on new microbiome research around the globe, but also illustrated the importance of fair, inclusive, open science to me once more. Starting at a small scale, I want to contribute to this development in microbiome research by further providing open-source code on my <a href="https://github.com/LuiseRauer">Github account</a> and by promoting open science practices in my work environment. Therefore, I highly appreciate the work of the OBF, and would like to thank them again for awarding me with the OBF Event Fellowship for attending the IHMC conference.</p>https://www.open-bio.org/events/bosc-2023/Fri, 23 Dec 2022 00:09:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2023/<h1 id="bosc-2023">BOSC 2023</h1> <p><strong>BOSC 2023</strong>, the 24th annual Bioinformatics Open Source Conference, took place July 24-25 as part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> in Lyon, France and online. The <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-schedule/">program included presentations by 45 speakers;</a> <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/">keynotes</a> by Sara El-Gebali and Joseph M. Yracheta; a joint session with <a href="https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting">Bio-Ontologies</a>, and a <a href="https://www.open-bio.org/events/bosc-2023/bosc-2023-panel/">panel discussion about Open and Ethical Data Sharing</a>.</p> <p><a href="https://www.open-bio.org/2023/08/14/bosc-2023-report/">BOSC 2023 report</a> <a href="http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/">BOSC/ISMB 2023 report</a> from one of our sponsors, <a href="https://academic.oup.com/gigascience">GigaScience</a> How BOSC supports diversity, inclusion, and accessibility</p> <p>BOSC has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. The 25th annual conference, <a href="https://www.open-bio.org/events/bosc-2024/">BOSC 2024</a>, will be part of ISMB 2024 in Montréal, Canada (and online).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/11/panel-with-Nomi-1.jpeg" alt="BOSC 2022 panelists with chair Nomi Harris"></p> <h2 id="key-dates-for-2023">Key Dates for 2023</h2> <ul> <li>March 31: <a href="https://www.open-bio.org/2023/03/09/bosc-early-poster-acceptance/">Early Poster Acceptance</a> submission deadline</li> <li>April 20: Regular abstract submission deadline (talks and posters)</li> <li>May 11: Notification to authors</li> <li>May 18: Late poster submission deadline</li> <li>May 25: Late poster acceptance notification</li> <li>July 22-23: Pre-BOSC <a href="https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/">CollaborationFest</a></li> <li>July 23-27, 2023: <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> (Lyon, France and online)</li> <li>July 24-25, 2023: <strong>BOSC 2023</strong> (part of ISMB/ECCB)</li> </ul> <h2 id="topics">Topics</h2> <p>BOSC covers all aspects of open source bioinformatics software and open science, including (but not limited to) these topics:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Data Access and Visualization</li> <li>Open Approaches to Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach and Training</li> </ul> <h3 id="sponsors">Sponsors</h3> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image1.jpg" alt="Photo from BOSC 2022"></p> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some presenters. Thanks to our sponsors, we were able to grant free registration to 19 participants at BOSC 2022, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you&rsquo;re interested in sponsoring BOSC 2023, please see our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors page</a>!</p> <h2 id="bosc-2023-platinum-sponsor-chan-zuckerberg-initiative">BOSC 2023 Platinum Sponsor: Chan Zuckerberg Initiative</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="CZI"></a></p> <h3 id="bosc-2023-silver-sponsors">BOSC 2023 Silver Sponsors</h3> <p><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="GigaScience"></a> <a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a> <a href="https://www.software.ac.uk/"><img src="https://www.open-bio.org/wp-content/uploads/2023/04/SSI_PRIMARY-LOGO-300x96.png" alt="SSI logo"></a> &lt;</p> <h3 id="overview">Overview</h3> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, which was part of ISMB/ECCB 2021 online, took place July 29-30, 2021. The <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">BOSC 2021 talks and posters are listed here</a>, and <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">videos of all the talks are on our YouTube channel.</a></p> <p>BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <p>BOSC is usually preceded or followed by what we now call <a href="https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/">CollaborationFest (CoFest</a> for short), a two-day community development session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. All are welcome to attend CoFest, whether or not you attend BOSC!</p> <p><a href="https://www.open-bio.org/events/bosc/about/">More about BOSC&hellip;</a></p> <h2 id="registration">Registration</h2> <p>To participate in BOSC 2022, you will need to <a href="https://www.iscb.org/ismb2022">register for ISMB 2022</a>. If the registration fee is a barrier, those who submit abstracts can request a fee waiver on the submission form, and we will provide other ways for those who aren&rsquo;t submitting abstracts to request fee assistance.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/12/Jason-online-presentation-with-slide-1.jpeg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2023/03/BOSC2023-org-committee-square.jpeg" alt="BOSC 2023 Organizing Committee members"></p> <h2 id="bosc-2023-organizing-committee">BOSC 2023 Organizing Committee</h2> <p><strong>Chair: Nomi L. Harris</strong> (Lawrence Berkeley National Laboratory)</p> <p>Karsten Hokamp (Trinity College Dublin) Jason Williams (Cold Spring Harbor Laboratory) Hervé Ménager (Institut Pasteur) Jessica Maia (BD) Deepak Unni (SIB Swiss Institute of Bioinformatics) Radhika Khetani (Harvard T.H. Chan School of Public Health) Chris Fields (University of Illinois, Champaign-Urbana) Monica Munoz-Torres (University of Colorado Anschutz Medical Campus)</p> <h3 id="review-committee">Review Committee</h3> <p>Arpita Joshi, Aziz Khan, Chris Fields, David Twesigomwe , Deepak Unni*, Gianluca Della Vedova, Harsh Sharma, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, Jenea Adams, Kai Blin, Karsten Hokamp*, Konstantin Okonechnikov, Luis Pedro Coelho, Milen Nikolov, Monica Munoz-Torres, Rachel Torchet, Radhika Khetani, Seth Carbon, Surya Saha*, Swapnil Sawant, Tazro Ohta, Tyrone Chen, Varsha Khodiyar \* Also reviewed Late Poster abstracts</p> <h2 id="previous-boscs">Previous BOSCs</h2> <p><a href="https://www.open-bio.org/events/bosc/about#Past_BOSCs">BOSC has been held yearly since 2000.</a> <a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> was held July 13-14, 2022, as part of the hybrid <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> (in person in Madison, Wisconsin, USA and online).</p> <p>BOSC 2022 summaries:</p> <p><a href="https://f1000research.com/articles/11-1034/v1">Report at F1000Research</a> <a href="http://gigasciencejournal.com/blog/birthday-at-ismb2022/">GigaScience blog post</a> <a href="https://www.open-bio.org/2022/08/16/crowdsourced-highlights-from-bosc-2022/">Geraldine Van der Auwera&rsquo;s blog post</a> <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXYotvWZLnKd9rcNMb6r9tjf">Talk and poster videos</a></p> <p><a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021, which was part of</a> <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021 online</a>, took place July 29-30, 2021. In 2020, <a href="https://bcc2020.github.io/">BCC2020</a>, the Bioinformatics Community Conference, brought together the Galaxy Community Conference (GCC) and <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2020</a> in a joint online meeting.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/11/BOSC-participants-with-Moni-1.jpeg" alt="Photo from BOSC 2022"></p> <h1 id="code-of-conduct">Code of Conduct</h1> <p>As part of ISMB/ECCB 2023, BOSC 2023 will be covered by the <a href="https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct">ISMB/ECCB Code of Conduct.</a></p>https://www.open-bio.org/2022/09/29/obf-public-board-meeting-2022-10-21/Thu, 29 Sep 2022 17:33:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/09/29/obf-public-board-meeting-2022-10-21/<h2 id="date-time-and-how-to-join"><strong>Date, Time, and How to Join</strong></h2> <ul> <li>Date and time: 2022-10-21, 15:00 UTC (8am PT / 11am ET / 4pm UK)</li> </ul> <h2 id="agenda">Agenda</h2> <h3 id="board-officer-elections">Board Officer Elections</h3> <ul> <li>Chris Fields wishes to step down as Secretary, and Nomi Harris is standing for election to this role</li> <li>This will be an electronic ballot of the current board members</li> </ul> <h3 id="elections-to-the-board">Elections to the Board</h3> <ul> <li>Iddo Friedberg, running for Board member at-large ( <a href="https://www.open-bio.org/wp-content/uploads/2022/10/OBF-Statement-Iddo-Friedberg.pdf">statement of interest</a>)</li> <li>This will be an electronic ballot of the current board members</li> </ul> <h3 id="bylaw-changes">Bylaw Changes</h3> <ul> <li>We periodically review our bylaws</li> <li>Changes must formally approved by the Board at a public board meeting</li> <li>We plan minor changes to avoid gendered language, including subsuming the Secretary role (with historical gendered associations) into a Vice President role.</li> <li>Proposed changes expressed as a <a href="https://github.com/OBF/obf-docs/pull/102">Pull Request</a></li> </ul> <h3 id="minutes">Minutes</h3> <p>After the meeting, the meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs/tree/master/minutes">obf-docs GitHub repository</a>.</p>https://www.open-bio.org/2022/08/18/bhki-sponsorship/Thu, 18 Aug 2022 14:30:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/08/18/bhki-sponsorship/<p>The OBF Community Support Sponsorship scheme aims to sponsor small open-source-focused events like a scientific meeting, small conference, training workshop, hackathon, or time-limited series like monthly seminars. See <a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">details in this post</a>. One application was funded under this program to prototype the workflow, with OBF offering financial support for a <a href="https://bhki.org/2022/08/17/empowering-our-community-with-bioinformatics-data-management-and-soft-skills/">seminar series hosted by the Bioinformatics Hub Kenya</a>. Congratulations to Michael Kofia Landi for leading this application and working collaboratively with the BHKi team – Pauline Karega, David Kiragu, Margaret Wanjiku and Festus Nyasimi – and OBF Board including Treasurer Heather Wiencko, to help establish a process for this new type of OBF funding.</p> <p><a href="https://bhki.org/2022/08/17/empowering-our-community-with-bioinformatics-data-management-and-soft-skills/"><img src="https://www.open-bio.org/wp-content/uploads/2022/08/Bioinformatica_Hub_Logo-918x1024.png" alt=""></a></p>https://www.open-bio.org/2022/08/16/crowdsourced-highlights-from-bosc-2022/Tue, 16 Aug 2022 00:08:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/08/16/crowdsourced-highlights-from-bosc-2022/<p>Going home after attending BOSC was a little bittersweet. It&rsquo;s my favorite conference because it brings together such a welcoming group of people, and the lineup of talks typically offers a great balance of technical learning and community-building insights. So on my flight home, I was coasting on dopamine from the good times, but also getting a little sad that it was over for this year. With the help of a few fellow BOSC enthusiasts (special shout-out to Nomi Harris for the event summary notes, photos and help recruiting contributors), I put together this little recap of the conference, with highlights and personal accounts contributed by a number of other participants. I couldn&rsquo;t fit everything people shared into the blog post, but you can find the full quotes in <a href="https://docs.google.com/document/d/1yAciaYC94qN2WF1gaLueqs0xByOW75mgU9wTG55cdJg/edit#">the original google doc</a>.</p> <h2 id="the-4-1-1-on-bosc-2022"><strong>The 4-1-1 on BOSC 2022</strong></h2> <p>If you&rsquo;re not already familiar with it, BOSC stands for Bioinformatics Open Source Conference, and we just completed the 23rd edition — <a href="http://open-bio.org/events/bosc-2022">BOSC 2022</a> — as a &ldquo;COSI&rdquo; track, or Community Of Special Interest, within the <a href="https://www.iscb.org/ismb2022">ISMB</a> meeting of the International Society for Computational Biology (ISCB). It was a hybrid conference, with the in-person component hosted in beautiful Madison, Wisconsin (USA). Presenters are encouraged to publish their slides and/or posters as part of the <a href="https://f1000research.com/collections/bosc">BOSC collection on F1000 Research</a>. This year&rsquo;s BOSC included two joint keynotes with the Education and Bio-Ontologies COSIs, which multiple people highlighted as some of their favorite parts of the conference. Given the overlaps in terms of interests and methodologies between these COSIs, I thought it was especially great that the Education COSI itself took place the day before the BOSC COSI. To my delight I was able to catch a number of their talks without having to make tough track-preference decisions. (I loved to see how many people are creating portable materials using Jupyter Notebooks, in some cases with the explicit goal of distributing them on the cloud.)</p> <h2 id="day-1-education-standards-tools-and-more"><strong>Day 1: Education, standards, tools and more</strong></h2> <p>The first day of BOSC proper kicked off with a welcome from chair Nomi Harris and an overview of BOSC’s parent organization, the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a>, by Chris Fields, who highlighted some opportunities to get involved with the OBF. I may have volunteered to be the new OBF Newsletter editor; you&rsquo;ll know it&rsquo;s for real if I ever manage to get the post-BOSC newsletter out!<img src="https://www.open-bio.org/wp-content/uploads/2022/08/image3.jpg" alt="BOSC 2022 chair Nomi Harris giving the opening remarks">Next was a joint keynote (BOSC/Education COSI) by Jason Williams entitled &ldquo;Riding the bicycle: Including all scientists on a path to excellence&rdquo;. Jason discussed principles for making short-format training (aka “bootcamps”) more effective and persistent. Next was a joint keynote (BOSC/Education COSI) by Jason Williams entitled &ldquo;Riding the bicycle: Including all scientists on a path to excellence&rdquo;. Jason discussed principles for making short-format training (aka “bootcamps”) more effective and persistent. <img src="https://www.open-bio.org/wp-content/uploads/2022/08/image5-858x1024.jpg" alt="Jason Williams delivered one of the keynote talks at BOSC 2022">Let me do you a big favor here and point you to a <a href="https://youtu.be/f75XR_zAydc">recorded version of the same talk</a> that Jason posted on Youtube, because googling &ldquo;jason williams riding the bicycle&rdquo; will not give you the results you&rsquo;re looking for (unless you&rsquo;re into stories about cycling for charity — but it&rsquo;s a different Jason). You should also check out Jason&rsquo;s <a href="https://lifescitrainers.org/2022/07/14/july-2022-community-discussion-the-bicycle-principles-for-effective-inclusive-and-career-spanning-short-format-training/">blog post on lifesciencetrainers.org</a>, which summarizes the concept of the &ldquo;Bicycle Principles&rdquo; and calls for community involvement. As Hilmar Lapp commented, &ldquo;Jason Williams set the perfect tone with his keynote: trying to be as professional as you can about whatever your pursuit is matters, for yourself and those who your work affects, and don’t ever forget to regularly laugh and have fun while doing it. A timely reminder after both got increasingly crowded out by a pandemic of other concerns.&ldquo;After the keynote, BOSC had themed sessions about “Standards and Practices for Open Science”, “Analysis tools &amp; approaches”, “Data access and visualization”, and “Standards for Open Science”. There were too many great talks to mention all of them, but I will say I was excited to see that several talked explicitly about leveraging <a href="https://www.ga4gh.org/">GA4GH</a> standards. Brian Repko, echoing this sentiment, called out the <a href="https://phenopacket-schema.readthedocs.io/en/v2/">Phenopackets schema</a> in particular, which provides a human and machine-readable way to structure phenotypic data about a patient or individual. As Monica Munoz-Torres announced joyfully in her talk, <a href="https://www.ga4gh.org/news/phenopackets-v2-expands-utility-to-provide-a-more-complete-medical-picture">Phenopackets version 2.0 was released earlier this year</a> as a major upgrade to the original schema, which represents the culmination of a huge amount of work — so congratulations to the Phenopackets team on their achievement!During the lunchtime poster session, participants checked out 42 BOSC posters and learned about a variety of bioinformatics tools and initiatives. Connections were made, cards and emails were exchanged, and perhaps next year we&rsquo;ll hear talks about new collaborations that were sparked here.<img src="https://www.open-bio.org/wp-content/uploads/2022/08/image6-1024x815.jpg" alt="Festus Nyasimi presented a poster at BOSC 2022"></p> <h2 id="day-2-workflows-ontologies-and-inclusion"><strong>Day 2: Workflows, ontologies and inclusion</strong></h2> <p>The second day of BOSC started with a session about “Workflow Management Systems”, including a number of talks related to CWL, aka the Common Workflow Language that grew out of a BOSC CodeFest in 2014. In that same session, I gave a talk about WDL, the Workflow Description Language that grew out of the Broad Institute&rsquo;s GATK pipeline engineering group and is now stewarded by the <a href="https://openwdl.org/">OpenWDL community project</a>. Check out my <a href="https://terra.bio/deciphering-a-mystery-workflow-written-in-wdl/">blog post and recording</a> (+ <a href="https://f1000research.com/slides/11-877">slides on F1000</a>) if you&rsquo;re interested in a method for deciphering any WDL workflow handed to you by a perfect stranger. The workflows session was delayed by some technical issues, but session chair Hervé Ménager kept his cool throughout the back and forth with the local A/V team. Hervé himself commented &ldquo;Despite the many technical issues we had with running the Workflow Management Systems session of BOSC, I was really impressed with the patience and understanding of the audience and the speakers, who all went out of their way to try and keep us on track, so that every presenter could get the opportunity to speak.&rdquo; And it&rsquo;s true, the BOSC crowd stayed pretty chill when things went, uh, pear-shaped. Ahem. The session after lunch was a joint session with the Bio-Ontologies COSI, featuring a keynote by Melissa Haendel, “The open data highway: turbo-boosting translational traffic with ontologies.” Melissa discussed ways to bridge the translational divide by leveraging semantics and robust ontologies  — with the caveat that in most cases, if you think you need to invent a new ontology, you actually don’t. Her talk was very well received and highlighted by multiple people as a conference favorite; though for my money, Brian Repko said it best: &ldquo;My internal notes for Melissa’s keynote literally says &lsquo;HOLY COW THIS IS GREAT&rsquo;&quot;. <img src="https://www.open-bio.org/wp-content/uploads/2022/08/image8-632x1024.jpg" alt="Melissa Haendel delivered one of the BOSC 2022 keynotes">BOSC ended with a panel entitled “Building and Sustaining Inclusive Open Science Communities” moderated by Jason Williams, with a fantastic roster of panelists known for their work advancing diversity and inclusion. Being themselves members of groups that are underrepresented in our field, they spoke eloquently of challenges and opportunities that we can all tackle as a community. As Nicole Vasilevsky noted, &ldquo;Jason did a great job facilitating and the discussion was very thought provoking&rdquo;. Among key takeaways, &ldquo;the panel reminded us that we all have much more agency than we think in making spaces welcoming to everyone who wants to enter,&rdquo; reflected Hilmar.<img src="https://www.open-bio.org/wp-content/uploads/2022/08/image1-1024x366.jpg" alt="Jason Williams moderates the panel discussion, “Building and Sustaining Inclusive Open Science Communities”">The high level of enthusiasm for the panel was palpable both during the event and in the comments we collected afterward. I read this as a clear sign that the majority of the participants genuinely care about inclusion, which in itself suggests that this community is on the right track. As a long-time community member, Nomi commented, &ldquo;I’m pretty sure this was the first BOSC, maybe even the first ISMB, where one of the attendees was a [service] dog. Which of course is great regardless, but more seriously, it represents tangible progress in our efforts to make BOSC more inclusive and accessible.&rdquo; Early feedback from newcomers certainly seems encouraging. &ldquo;As someone who got into bioinformatics just before the pandemic, it was great to finally be around &lsquo;my people&rsquo;&rdquo; wrote Bhavesh Patel, first-time BOSC participant, adding &ldquo;All the talks were great, but I especially loved the panel discussion on diversity and inclusion. It is a wonderful initiative and I hope it becomes a frequent occurrence at all conferences.&ldquo;And that is a really nice note to end a conference on, isn&rsquo;t it?</p> <h2 id="add-on-1-scheduled-dinners"><strong>Add-on #1: Scheduled dinners</strong></h2> <p>But wait, there&rsquo;s more! BOSC folks are a surprisingly social group, for a bunch of bioinformatics nerds (no offense y&rsquo;all). So in addition to the daytime conference programming, the organizing committee had organized (as they do) two outdoor dinners for BOSC participants to get together and keep the conversations going. <img src="https://www.open-bio.org/wp-content/uploads/2022/08/image2-1024x562.jpg" alt="Some of the attendees at a BOSC 2022 dinner">Just about everyone who attended the dinners raved about how great they were, to a point that might be borderline obnoxious to anyone who didn&rsquo;t go; but I can tell you from first-hand experience it&rsquo;s all justified. And to be clear, it was &ldquo;pay-your-own-way&rdquo; (aka BYO wallet), so the enthusiasm wasn&rsquo;t about getting a free meal on the dime of some corporate sponsor — it was all about the friendly company and congenial atmosphere. &ldquo;The dinner was [&hellip;] a great opportunity to interact with other participants in a laid-back setup,&rdquo; wrote Bhavesh. As Nomi noted, we were very lucky with the weather, so we were able to hang out, dine and socialize on the outdoor patios until well after nightfall. <img src="https://www.open-bio.org/wp-content/uploads/2022/08/image7.jpg" alt="Attendees at the second of two informal BOSC 2022 dinners">There was definitely a sense that this felt especially good because we had all been deprived of this kind of interaction for over two years. Nomi shared that for her, &ldquo;the best moments [of the conference] were not the talks (though of course those were great!) but the personal interactions that I have missed so much the last few years.&rdquo; As Hilmar pointed out, &ldquo;The BOSC socials and CoFest showed how much it is worth even to just be together again. Not that we didn’t know, but knowing and understanding are not always the same thing.&rdquo; This sentiment, which almost everyone who was there in person echoed in some way, does raise the question of how we can provide quality social interaction for those in our community who cannot yet come back to in-person events — or for those who have never been able to do so due to the circumstances of their lives or their geography. As Tazro Ohta remarked eloquently, &ldquo;What I learnt during the pandemic was: The power of online meetings that connect people and the power of time differences that prevents me from attending them helding in a western time zone.&rdquo; That is a topic I expect we will have to explore as we iterate on the hybrid event models that are likely to shape the future of scientific gatherings.</p> <h2 id="add-on-2-collaboration-fest-cofest"><strong>Add-on #2: Collaboration Fest (CoFest)</strong></h2> <p>Ok we&rsquo;re almost done, but I still have to tell you about <a href="https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/">CoFest</a>, a two-day &ldquo;collaboration fest&rdquo; that takes place informally after the conference, in which a subset of BOSC participants stick around for a couple of days to work together on some projects. Those projects can involve coding, but also documentation or other non-coding activities, so anyone can contribute regardless of their technical background. In fact, for my CoFest project, I started working on the <a href="https://github.com/OBF/newsletter/blob/newsletter-2022-07/newsletters/2022-07.md">upcoming OBF newsletter issue</a>. You can see the full set of projects that were undertaken at this year&rsquo;s CoFest in the <a href="https://docs.google.com/presentation/d/1HHUdnXvtEpC16R1hDvK0-McZGVd0XJlrqTpBw3jJrg4">status update slide deck</a>. Out of the six projects that were proposed this year, three were worked on by remote CoFest participants while the other three were worked on by the in-person group. Those of us who attended CoFest in person worked at the Madison Public Library on the first day, and we had ourselves a nice little sunset social on the waterfront with beer and brats. On the second day, we relocated to the airport to accommodate the group&rsquo;s wide range of departure times, and &ldquo;cofested&rdquo; variously from the pre-security lounge, from our respective gates, and from the air, because sometimes it&rsquo;s just that hard to let a good thing go. <img src="https://www.open-bio.org/wp-content/uploads/2022/08/image4.jpg" alt="In-person participants at the 2022 CollaborationFest"><em>In-person CoFesting from the Madison airport lounge. Don&rsquo;t judge me, I only took off my mask for the photo!</em> In my experience, CoFest is as much about community building as it is about making progress on a project. As Bhavesh, our BOSC first-timer who also attended CoFest, observed, “The cofest was my favorite part as it provided a very informal setting to get to know all the participants on a personal level. It also gave me a unique opportunity to discuss personally with experts of the field and get one-on-one feedback on my work.” In fact, he added, &ldquo;I would highly recommend anyone new to BOSC to join the cofest!&ldquo;So don&rsquo;t miss your opportunity to get in on the fun, and make sure to add BOSC to your must-go list of conferences for next year (whether remotely or in-person). BOSC 2023 will be part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> and will be held in Lyon, France between July 23-27 (exact dates TBD).I hope to see you there/onscreen!</p>https://www.open-bio.org/2022/08/12/obf-event-fellowship-2022-round2/Fri, 12 Aug 2022 05:27:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/08/12/obf-event-fellowship-2022-round2/<p>The call for applications for the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> 2022, round 2 is now open. <strong>The deadline for this round is 1 October 2022.</strong> Applications should be submitted via <a href="https://forms.gle/Rt7Si7eT2MuTqrQZ9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling the form – <a href="https://docs.google.com/document/d/1tgzkHS84L8m3RwYoL7X86Axb6p_OiqNWaoJpiV4q8S0/">make a copy of this template</a>.</p> <p>We invite applications from candidates who are seeking financial support to attend or host relevant scientific events from late October 2022 to April 2023. <strong><em>These events can be conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. For more details, please read our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Event Fellowship policy document</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/07/image.png" alt="OBF Event Fellowship Application DEADLINE for next round: October 1, 2022 The Open Bioinformatics Foundation (OBF) offers the OBF Event Fellowship program aimed at increasing diverse participation at events promoting open science practices such as open source bioinformatics resource development and dissemination in the biological research community. These fellowships are available to support both in-person and remote (virtual) participation at events such as conferences, workshops, training courses or collaborative development sprints. "></p> <p><em>Screenshot of our application form information section</em></p> <p><strong>Overview of the round 1 of OBF Event Fellowship 2022</strong></p> <p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to support and encourage diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. Each year we open two calls for applications, the deadlines for which are 1 April and 1 October.</p> <p>In 2022 round 1, we received 17 applications, of which six applicants were awarded this fellowship for various events they were participating in. Congratulations <strong>Jemima Becker, Furkan M. Torun, Xi Zhang, Festus Nyasimi, Omar Ahmed, Emmanuel Adamolekun</strong>.</p> <p><strong>Confidence Goji Vandu</strong> was also granted their application to attend BOSC 2022, but due to admin oversight, they could not attend the event. The OBF Fellowship Award chairs are discussing how we can redirect this award towards another event the awardee might be able to attend.</p> <p>Here, we have recently published blog posts from a few awardees summarising their experience from attending these conferences:</p> <ul> <li>Furkan Torun: <a href="https://www.open-bio.org/2022/06/17/furkanmtorun-pycon2022/">Furkan M. Torun: Highlights of my participation at PyCon IT 2022</a></li> <li>Jemima Becker: <a href="https://www.open-bio.org/2022/06/23/obf-fellow-jemimabecker2022/">My trip to the EMBO neural stem cells workshop</a></li> <li>Festus Nyasimi: <a href="https://www.open-bio.org/2022/08/01/obf-event-fellow2022-fnyasimi/">Festus Nyasimi: Journey to the ISMB/BOSC 2022 conference</a></li> </ul> <p>Congratulations to each of them!  We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.</p> <p><strong>Please share this post and apply for the fellowship before 1 October 2022</strong>. Also, read the <a href="https://www.open-bio.org/2022/02/07/obf-event-fellowship-update/(opens%20in%20a%20new%20tab)">updates from the OBF Event Fellowship chairs</a>.</p>https://www.open-bio.org/2022/08/01/obf-event-fellow2022-fnyasimi/Mon, 01 Aug 2022 15:45:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/08/01/obf-event-fellow2022-fnyasimi/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Festus Nyasimi, A co-founder and lead of the <a href="https://www.bhki.org">Bioinformatics Hub of Kenya Initiative (BHKi)</a>, attended the <a href="https://www.open-bio.org/events/bosc-2022/">ISMB/BOSC conference 2022</a>, supported by this fellowship granted to him in the first round of 2022.</em></p> <p>In mid-May, I attended a different conference where I shared my experience with community building in the bioinformatics space with one of the attendees. I had a chance to brief them about the BHKI community we are building and growing in Africa. Immediately they suggested I should check out the ISMB/BOSC conference happening on July 11th - 14th, 2022.</p> <p>I looked into it immediately, and I was lucky to find the late abstract submission round was still on. I sent in an abstract on our community, its activities, and the progress we have made in the region. A few weeks later, our abstract was strongly accepted for poster presentation and iced up with free registration. Bam!!! This felt like a Lebron James slam dunk or Steph Curry swish three point shot. Never felt this happy to go share our work with a larger bioinformatics community.</p> <p><img src="https://lh5.googleusercontent.com/bhsN-q42r2FwsPRQshfkWxsjP9QkttreS4kx3gUGgxXoHCp5Up_1VCsGbEnKP3pdy_g38WYvdvOLnxyC7EIZ688VgOPltUtNLksWKj4y8JE6LNJjc_Pqe6UmgRQCxeJ6CZZGUB0E5L-hRdVLlSuomeE" alt=""></p> <p>In the happy moment, the rush to plan for the conference set in; this included travel, accommodation and misc stuff. The rest of the team and I worked on the presentation alongside our training activities; this is one amazing team. Considering we are a young and growing community mostly running training through volunteering and small grants to cater for the training, we had to find a source of funding to cater for the conference fee and that’s where the OBF Event fellowship showed up perfectly. Honestly, I least expected this but I didn’t discount myself and gave it a shot; I always tell myself, <em>“ <strong>if I don’t knock, I will never know the answer</strong>”.</em></p> <p>Fast forward, here I am at the conference; I got to attend some sessions i.e. BioInfo Core, NetBio, Varl, MLCSB and Educational COSI, where I learnt many new skills in Bioinformatics the BOSC track started. Some of the things I learned I will propose to the organizing team we develop tutorials for the community to learn from. The opening day of BOSC was the peak of the conference for me; I had an opportunity to learn more about open-source software, how to efficiently contribute to ongoing projects and how to help communities grow. I also had a chance to join the GA4GH VRS hackathon at the conference. I had a good opportunity to represent the BHKI community on what we are doing and received great responses from attendees who visited my poster. The light was shining on our community; I hope the spotlight will be on and attract more collaborators to help us achieve our mission of a collaborative and inclusive hub.</p> <p><img src="https://lh4.googleusercontent.com/LE_vl3pKIFuweLbd8pAXB7vT9XOm9VWAOAOCU9hcDPEFGsack9AzVKWpHklMxX35CiA4X7Ksa7LHPWUDeZtKX3j2DSyavX_THyI4Bz6Ptfu-G-3-di6QONsM1f8kh40qELlynJWr7X-qV9ti8hvbV6M" alt=""> Some of the cool people I meet at BOSC: <em>panelist Jenea Adams and keynote speaker Jason Williams</em>.</p> <p>I learned how to advocate for our community to grow well towards achieving Diversity, Equity and Inclusion (DEI) goals; these are necessary for a strong, welcoming and collaborative community. Interacting with attendees at the conference provided me with an opportunity to learn more about leadership and how to be a good leader from a different perspective. I look forward to keeping in touch with other communities to grow further collaborations, especially in community empowerment.</p> <p>Generally, the whole conference turned out to be the best one I have attended in many months through the pandemic, and I am so thankful to OBF, all organisations and team members who made it possible for me to attend the conference. Looking forward to more of these sweet moments.</p> <p>This <a href="https://twitter.com/Festus_nyasimi/status/1547547465737437184">Twitter post</a> got my notifications blowing a trumpet! While you are here, check out the <a href="http://www.bhki.org">BHKI website</a> and <a href="https://twitter.com/BioinfoHub_KE">Twitter</a> we have some cool stuff. :)</p>https://www.open-bio.org/2022/07/25/reflections-malvika-2022/Mon, 25 Jul 2022 19:34:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/07/25/reflections-malvika-2022/<p><img src="https://www.open-bio.org/wp-content/uploads/2022/07/aaron-burden-zunGugEsJCE-unsplash.jpg" alt="A simple post card on the table with the &lsquo;Thank you&rsquo; written on it. Next to it is an ink pen."></p> <p><em>Thank You. Photo by Aaron Burden on Unsplash</em></p> <p>I have reached the end of my term after working with the OBF board members since 2019 and have stepped down from the board. It is bittersweet! I will miss seeing my colleagues from OBF in monthly calls, but also, this comes with an opportunity to make space for new voices to come into the leadership role of the Open Bioinformatics Foundation.</p> <p>Over the last years, one of my main focuses has been the OBF Event Fellowship, previously managed by Nomi Harris and Farah Zaib Khan ( <a href="https://www.open-bio.org/2020/08/22/obf-event-fellowship-round-2-2020/">previously called travel fellowship</a>). Having benefited from this programme, I personally value the opportunity for small funding that researchers with low or non-existent travel budgets can use for attending international conferences. Scientific events are extremely valuable for researchers to build new connections, share their research and often find their next career opportunities. You can see my post-event blog from 2019 here: <a href="https://www.open-bio.org/2019/08/27/tips-for-informal-discussions/">/2019/08/27/tips-for-informal-discussions/</a>.</p> <p>Since joining, I managed and coordinated the programme (see <a href="https://github.com/OBF/obf-docs/issues/95">the task list</a>) and built rubrics to review applications ensuring fair evaluation and avoiding biases that unexplicit scoring can lead to (see <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md#review-process">review process</a>). Primarily motivated by the travel restrictions experienced due to the pandemic, in collaboration with the OBF board members, I <a href="https://github.com/OBF/obf-docs/pull/79">revised the travel fellowship documents</a> to adapt to the need for supporting online participation. So far, I have managed six rounds of Event Fellowships (over three years) and supported one OBF-BOSC Event Support Fund, which together was awarded to 28 individuals (see <a href="https://www.open-bio.org/2020/08/22/obf-event-fellowship-round-2-2020/">all announcements</a>). Of course, none of this could be possible without the timely review and thoughtful advice given by Bastian Greshake, Chris Fields, Hilmar Lapp, Nomi Harris, Peter Cock, Yo Yehudi and our wonderful treasurer Heather Wienco.</p> <p>Earlier this year, I <a href="https://www.open-bio.org/2022/02/07/obf-event-fellowship-update/">onboarded two newly elected members</a>, Caleb Kibet and Hilyatuz Zahroh, as co-chairs of the Event Fellowship. They will continue in this position and will take forward the programme. I am really excited for the OBF community to see further improvement in the Event Fellowship programme supporting our commitments to open science and strengthening the participation of diverse researchers in bioinformatics events ( <a href="https://github.com/OBF/obf-docs/pull/94">see discussion</a>).</p> <p>Since the event fellowship is an individual award, we received many applications from event hosts asking for financial support for their attendees. This was unfortunately not in scope for this scheme. However, it led to many internal discussions with the OBF Board members to build pathways for the grassroots communities and identify support for their ongoing activities. I contributed to drafting the <a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">OBF Community Support Fund</a> proposal, which is being led by Peter Cock.</p> <p>I also drafted a Code of Conduct adopted from The Carpentries for the OBF community in collaboration with the board members, especially Bastian Greshake and Yo Yehudi, who along with me are listed as the members for report handling. Started in 2020, the Code of Conduct was approved in January 2022. This was a long process for a good reason, as we could reflect on the scope, extent and enforcement procedure carefully. The complete <a href="https://github.com/OBF/obf-docs/tree/master/code-of-conduct">Code of Conduct document</a> is available on the OBF GitHub repository and applies to the OBF community including the board.</p> <p>OBF’s annual conference, Bioinformatics Open Source Conference (BOSC) was my entry into the open science community in bioinformatics  in 2012 ( <a href="https://www.open-bio.org/2019/08/27/tips-for-informal-discussions/">mentioned in the third paragraph</a>). This community has a special place in my heart and I was grateful to be involved in the <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> planning committee, which was chaired by Nomi Harris. At that conference, we featured the first bilingual keynote lecture, discussed the rubrics and honoraria for invited speakers to align our workflow with the intention to build an inclusive community and facilitated an OBF-BOSC Event Support Fund for BOSC attending from underrepresented communities. See the full report: Harris, N. L., Cock, P. J. A., Fields, C. J., Hokamp, K., Maia, J., Munoz-Torres, M., Sharan, M., Williams, J. (2021). BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference. F1000Research, 10(1054), 1054. DOI: <a href="https://f1000research.com/articles/10-1054">10.12688/f1000research.74074.1</a>.</p> <p>My path has diverged – I no longer work in bioinformatics. Over the last years, I moved countries, changed jobs, co-launched Open Life Science, transitioned to co-leading The Turing Way, became involved in various open science communities and established a team of Community Managers at The Alan Turing Institute. My limited time and energy are now being directed towards building people-centric resources and community infrastructure, which I am sure will continue to cross paths with OBF, even beyond my time on the OBF board.</p> <p>With immense gratitude towards all members of the OBF board, previous member Yo Yehudi who nominated me for election, and various collaborative projects I was involved in, I am bidding my farewell to the OBF board. Please look out for the call for the next election and nominate yourself, or someone who would like to give back to the open source communities in bioinformatics through an opportunity to support the ongoing projects or propose new ideas for the OBF.</p> <p>You are very welcome to find details about my work and connect with me: <a href="https://malvikasharan.github.io/">https://malvikasharan.github.io/</a>.</p> <p>With best wishes,</p> <p>Malvika</p>https://www.open-bio.org/2022/06/23/obf-fellow-jemimabecker2022/Thu, 23 Jun 2022 22:04:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/06/23/obf-fellow-jemimabecker2022/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Jemima Becker, DPhil student at Merton College, University of Oxford, attended the <a href="https://meetings.embo.org/event/21-neural-stem-cells">EMBO workshop: “Neural stem cells: From basic understanding to translational applications&quot;</a>, supported by this fellowship granted to him in the first round of 2022.</em></p> <p>This June, I had the opportunity to travel to the EMBO workshop: “Neural stem cells: From basic understanding to translational applications”. There, I presented a poster documenting the first six months of my PhD work on long noncoding RNAs (lncRNAs) in the postnatal ventricular-subventricular (V-SVZ): “Long noncoding RNAs in the Ventricular-Subventricular zone: what have we learnt from single cell transcriptomics?”.</p> <p><img src="https://lh5.googleusercontent.com/z-pNd6B0_0jByEfOAgydy_CLhx33lUvdLoB-x_dKsNto7HKwHjimxJ0IcRb1fwg0DOI0XuiD00Jk2IgyQQD0s09XtR6prjJ7ysguMKluXSSfXWWxJTWJd502XxCzaqXXfqsMbJqo_fxrjtK1rg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/06/jb1.png" alt=""></p> <p><em>Images: My supervisor Francis Szele and I after the end of the first poster session (left). Sunset on the first evening at the conference (right).</em></p> <p>This work was a broad meta-analysis of single cell RNAseq papers, in conjunction with ChIP-seq data in order to identify candidate genes for functional studies into the role of V-SVZ lncRNAs. I presented my computational logic and workflow for this study, linking back to how open access data and code can be used to construct a robust prediction of regulatory genes. I made the argument that, particularly in the stem cell field, a lot of redundant data is generated; during the process of this project I found many overlapping studies – by making use of online data to identify candidates for further study we can save time, expense, and resources by narrowing down the pool of molecules to investigate in vitro or in vivo. Through the results of this analysis, I have started mechanistic investigations into two select lncRNAs and the role they may be playing in V-SVZ neurogenesis in vivo.</p> <p>The conference was an invaluable experience, as it provided me with not only the opportunity to meet and discuss my work with others working in high resolution’ omics, but also allowed me to network with researchers tackling similar problems using divergent approaches.</p> <p><strong>Day 1</strong></p> <p>The first day of the conference began with an early flight from London to Athens, followed by a coach journey to a beautiful venue on the coast. The first keynote talk of the conference was given by Malin Parmar, discussing the applicability and translational capacity of stem cell studies in treatment of human neurodegenerative disease. A fascinating aspect of this talk was the use of scRNAseq to analyse the survival and development of tissue grafts, linking high resolution molecular description to gross changes in motor performance.</p> <p><strong>Day 2</strong></p> <p>On my second day in Kyllini, I attended four sessions totalling 15 talks and was able to present my poster in the evening. Of great excitement to me was a talk from Ana Martin-Villalba regarding a single cell triple-omics approach to analyse stem cell trajectories. The first of two poster sessions took place this evening from 8:30pm, and I found enough people interested in discussing my approach that I stayed at the session until midnight! It was incredibly valuable to be able to talk to other people, as many approaches to finding novel regulatory genes in the V-SVZ (or other tissues) take into account a limited amount of data; by comparing different datasets to identify consistent trends I had been able to find a large number of candidate genes, and was able to discuss the strengths and difficulties of my strategy.</p> <p><strong>Day 3</strong></p> <p>The third day focused on bioengineering of neural stem cells and 3D human models of neural stem cells. One talk that I found particularly interesting was from Marisa Karow, which focused on the utilisation of SNP maps to identify the allelic origin of individual transcripts in sequencing data. I have previously worked on this with mouse-derived tissue, although I found difficulties with my approach when examining low-abundance transcripts such as lncRNAs, so hearing about Professor Karow’s strategy was very useful.</p> <p><strong>Day 4</strong></p> <p>The fourth and final day of the conference consisted of three sessions, with a focus on translational capacity and patient care. I enjoyed a talk from Noelia Urban Avellaneda examining the spectrum of stem cell states within the V-SVZ. This was particularly relevant to my work, as something I have noticed in the papers whose scRNAseq data I have examined is that the number of and criteria for different V-SVZ stem cell states is apparently defined on a paper-by-paper, rather than universal basis. Dr Urban Avellaneda proposed a fluid model in which stem cells exist within a complex topology, rather than a single trajectory, of developmental potential.</p> <p>Overall, my first conference has been an unforgettable opportunity and a fantastic introduction to the wider world of neural stem cells. An especially valuable element, for me, was the chance to meet more women working in bioinformatics – the bulk of my interactions within local computational biology as an undergraduate consisted of male-dominated classes, a trend which has persisted through my classes and workshops as a graduate student. The combination of meeting a greater diversity of scientists alongside the chance to share and discuss my ideas was highly rewarding, and I look forward to taking up more opportunities like this in the future.</p> <p>I would like to express my gratitude to the Open Bioinformatics Foundation for making this experience possible, and thank them for their support.</p>https://www.open-bio.org/2022/06/17/furkanmtorun-pycon2022/Fri, 17 Jun 2022 16:34:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/06/17/furkanmtorun-pycon2022/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. <a href="https://furkanmtorun.github.io/">Furkan M. Torun</a>, Data Scientist at OmicEra Diagnostics &amp; Computational Biologist, attended the <a href="https://pycon.it/en">PyCon Italia 2022</a>, supported by this fellowship granted to him in the first round of 2022.</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_1-1024x712.jpeg" alt=""></p> <h3 id="background"><strong>Background</strong></h3> <p>As it is shown in the surveys of the programming languages used and the latest publications in the field of bioinformatics/computational biology, Python has experienced unprecedented growth. Meanwhile, to spread knowledge, learn from each other, and make new networks for Pythonistas, several Python conferences (“PyCon”), are held annually by <a href="https://pycon.org/">the international communities worldwide</a>.</p> <p>A while ago I came across the <a href="https://pycon.it/en">PyCon Italia 2022</a> and I hoped to attend this conference as it is fairly close to me and easy to travel. Moreover, I was thrilled to see the speakers and titles of the talks when I reviewed the schedule of the conference. Personally, I have been using Python for several years to develop bioinformatics pipelines, machine learning projects, and other data analyses for my computational biology research. Then, I decided to attend the conference and make it for my first PyCon. However, unfortunately, due to my nation’s currency meltdown against foreign currencies, I was facing a tough problem of finding enough financial support for myself to attend such an event in Europe that unites many developers and scientists from a wide range of disciplines. I applied to the Open Bioinformatics Foundation and was awarded the Event (Travel) Fellowship! So, this opportunity provided by OBF enabled me to afford my expenses including conference ticket, traveling, and accommodation! Excellent news!</p> <h3 id="now-lets-focus-on-the-talks"><strong>Now, let’s focus on the talks!</strong></h3> <p>When I entered the hotel where the conference was hosted, it started to excite me as all attendees were already chatting! After 2 years of pandemics without any in-person conference, we all looked forward to such events! Then, I learned that more than 700 participants were at the conference. So, after getting my badge, I had a chance to get to know people, including another bioinformatician, share my skills and experiences, and learn from them!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_2-768x1024.jpeg" alt=""></p> <p>The schedule of the first day was so exciting. I had already planned what talk to attend as there were several talks going in parallel. The first talk I participated in was “Building data pipelines with Apache Airflow” since I am interested in creating repeatable and reliable workflows in Python, which is an emerging problem in bioinformatic pipelines. Then, I followed the Data Science and Machine Learning tracks as I would like to pursue my future career in those domains. So, overall the talks I attended inspired me and enabled me to make my future work better!</p> <p>Also, I listened to the keynote talk entitled “Pro tips for writing great unit tests” by Raymond Hettinger and it emphasized the test concepts and writing of unit tests in a readable, fast, clear way.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_3.jpeg" alt=""></p> <p>Afterwards, I joined the next keynote talk entitled “Inclusive community leadership” delivered by Jessica Greene which gave insights into how a community can continue growing and evolving by staying true to its principles.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_4-1024x786.jpeg" alt=""></p> <p>In the next days, I was also inspired by another talk namely “Python&rsquo;s Life of the Brain”. In this talk, several open-source Python libraries developed by brain research enthusiasts were presented to analyze, process, and visualize the data coming from the neurons and simulate the whole brain <em>in silico</em>, even in a Jupyter notebook!</p> <p>Also, another really exciting talk was about source code optimisation and code efficiency where I learned how to write faster code in Python 3, which will help me a lot while developing new pipelines for my future projects!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_5-1024x772.jpg" alt=""></p> <p>Last but not least, there was another fabulous talk delivered by the CEO of Jina AI, Dr. Han Xiao, with the title “DALL·E Flow: when neural search meets generative art”. We all know that the use of deep learning has become ubiquitous in almost every area. But, how about generating an image based on the text user provided? Yes, in this talk, it is demonstrated with examples and here are the some of them (the text on the left-hand side of the image was given and the image on the right was generated based on that text provided):</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_7-1024x685.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/08/image_6-1024x744.jpg" alt=""></p> <h3 id="to-sum-up"><strong>To sum up…</strong></h3> <p>Overall, I really enjoyed the conference and had a chance to meet and socialize with developers, engineers, and scientists while listening to their experiences and challenges!</p> <p>I was very lucky that I had a chance to meet with the creator of the project that I contributed to last month by sending a <a href="https://github.com/furkanmtorun/PyScript_Bioinformatics_Tool">Pull Request for a bioinformatics application</a>!</p> <p>So, again, I am thankful to both the organizers of the PyCon Italia 2022 and the Open Bioinformatics Foundation for awarding me this Event (Travel) Fellowship!</p> <p>For the next steps, I will advocate open-source software development (especially in bioinformatics/computational biology fields) and open science <a href="https://furkanmtorun.github.io/">over my social media channels</a>! Moreover, I will be applying my new learnings to the future open-source projects I publish on <a href="http://github.com/furkanmtorun">my GitHub account.</a></p>https://www.open-bio.org/2022/06/09/post-bosc-cofest-will-be-online/Thu, 09 Jun 2022 18:31:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/06/09/post-bosc-cofest-will-be-online/<p>&rsquo;ello Co-Fest Friends!</p> <p>After failing to find a good spot for an in-person <a href="https://www.open-bio.org/2022/05/17/collaborationfest-2022/">CoFest</a>, we decided to have the CoFest remotely! I was really excited to meet you all at this event (and have you all meet each other) in the real world, but we&rsquo;ll have to settle for doing that at BOSC (for those who are there).</p> <p>By all means, don&rsquo;t let this stop your in-person innovations! Want to meet up and work at a café? Do it! Hotel room? It&rsquo;s your room! Get some of your newest friends together and collaborate!</p> <p>In order for that to happen, I&rsquo;d LOVE (and so would others) to see what the projects are planning to be this year. If you are looking to help a project OR lead one, please add your name to the <a href="https://docs.google.com/spreadsheets/d/1h5woYd0URjgUKInWA2sozDwfThUlQbQQ9xbjdEdQQXk/edit#gid=0">participation spreadsheet</a> and your project idea to <a href="https://docs.google.com/presentation/d/1x0YW49aUG7FKL1vZh62Ct0rTW-0jH-ipIDWzoFs9_nc/edit?usp=sharing">The Slides</a>!</p> <p>We&rsquo;ll put together an agenda in the #cofest channel of the <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">BOSC Slack</a> (which everyone should join) and make that our main point of communication moving forward.</p> <p>Thank you all for taking part and increasing the spirit of collaboration!</p> <p>&ndash;Thomas Schlapp, CoFest 2022 organizer</p>https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule-2/Tue, 24 May 2022 19:50:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule-2/<h4 id="bosc-2022-schedule-at-a-glance">BOSC 2022 schedule at a glance</h4> <p>(Scroll down to see the full lists of talks and posters.)</p> <h4 id="bosc-2022-talk-schedule">BOSC 2022 Talk Schedule</h4> <p><strong>Coming soon!</strong></p>https://www.open-bio.org/2022/05/17/collaborationfest-2022/Tue, 17 May 2022 18:53:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/05/17/collaborationfest-2022/<h4 id="guest-post-by-thomas-schlapp-cofest-organizer">Guest post by Thomas Schlapp, CoFest organizer</h4> <p>This year we&rsquo;re looking to have another post-BOSC <a href="https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/">CoFest</a>! Last year (my first year being involved in BOSC at all) showed me just how collaborative and innovative this community can be. I&rsquo;d absolutely LOVE to see more of it again. Last year we saw six very fascinating projects see progress (look them over <a href="https://docs.google.com/presentation/d/10blW3DVEIUArq12mrKf-PIJQNn01GOSmGOH8d7sCUWo/edit?usp=sharing">HERE</a>!). Let&rsquo;s see if we cannot do just a few more in the name of innovation and collaboration!</p> <p><a href="https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/">CoFest 2022</a> will take place the two days after BOSC/ISMB: July 15-16, 2022. We are trying to determine whether there is sufficient interest in holding the CoFest in person in Madison, Wisconsin; if not, it will be virtual.</p> <p>Please please please <a href="https://docs.google.com/spreadsheets/d/1h5woYd0URjgUKInWA2sozDwfThUlQbQQ9xbjdEdQQXk/edit#gid=0">REGISTER</a> if you want to be a part of this awesome community remote or on-site! Do you have a project to add? Great! Are you alone but want to help in some way? Equally awesome! Head over to this set of slides ( <a href="https://docs.google.com/presentation/d/1x0YW49aUG7FKL1vZh62Ct0rTW-0jH-ipIDWzoFs9_nc/edit?usp=sharing">Submissions!</a>) and add yourself or your project!</p> <p>Thank you again BOSC community for allowing me the opportunity to help CoFest manifest.</p>https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/Sat, 07 May 2022 22:43:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/<h1 id="bosc-2022-panel-building-and-sustaining-inclusive-open-science-communities">BOSC 2022 Panel: Building and Sustaining Inclusive Open Science Communities</h1> <p>Building open source software is a great start, but to maximize the impact, it’s also necessary to put effort into maintaining it. Similarly, open source / open science communities don’t just need to be built; they also need to be maintained and expanded. We’ve seen increasing calls for inclusion and diversity, but once you’ve reached out to a new community, attracted new contributors, or recruited a new team member, how do you go beyond surface-level changes and achieve meaningful and sustainable inclusion? What difficult work, self-education, and research is needed to make more diverse groups thrive?</p> <p>This panel and audience discussion will focus on what needs to come after initial steps to diversify. Wherever you are on your path to building inclusion in your open-source project, we invite you to offer your questions and thoughts on how we can do better. Diversity and inclusion isn&rsquo;t achieved in a single success, but rather by maintaining continued success.</p> <h3 id="panelists">Panelists</h3> <h5 id="jenea-adams-black-women-in-computational-biology-network">Jenea Adams (Black Women in Computational Biology Network)</h5> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Jenea_Adams.jpg" alt="Jenea Adams"></p> <p>Devoted to promoting Black women in computational biology, <a href="https://www.jeneaiadams.com/">Jenea Adams</a> is currently a Ph.D. Candidate at the University of Pennsylvania in the Perelman School of Medicine&rsquo;s Genomics and Computational Biology program. She is a member of the Yi Xing Lab at the Children&rsquo;s Hospital of Philadelphia Center for Computational and Genomic Medicine.</p> <p>A Janssen Oncology Scholar, Penn Presidential PhD Fellow, and a dual Master&rsquo;s Student in Statistics and Data Science, Jenea is experienced in developing and improving computational tools that leverage RNA biology for targeted cancer immunotherapy, and she is a recognized community advocate for minoritized computational biologists. Jenea founded the <a href="https://www.blackwomencompbio.org/">Black Women in Computational Biology (BWCB) Network</a>, an intersectional community of Black women who are working toward (or interested in) a career that combines computational and quantitative sciences with biology. BWCB has grown from a small collective to an internationally-recognized professional development community for broadening participation in computational biology for Black women across the diaspora.</p> <h5 id="andrew-hasley-north-carolina-state-university">Andrew Hasley (North Carolina State University)</h5> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Andrew-Halsey.png" alt="Andrew Hasley"></p> <p>Andrew (Drew) Hasley is currently a Postdoctoral Teaching Scholar in the Biotechnology Program at North Carolina State University. He teaches courses in fundamental biotechnology skills, professional development, biotechnology ethics, and environmental DNA analysis and applications to ecology and environmental science. Dr. Hasley co-managed BioQUEST&rsquo;s Universal Design for Learning (UDL) initiative. This initiative focuses on providing professional development for undergraduate biology faculty at 2- and 4-year institutions to help them adopt and apply a UDL approach to their teaching.</p> <p>Dr. Hasley earned a Ph.D. in genetics from University of Wisconsin - Madison in 2016. In addition to his genetics research, Dr. Hasley has devoted substantial effort to outreach and research on strategies for making biology, especially quantitative biology, education more accessible for students with disabilities. This focus has broadened to an interest in Universal Design for Learning, a framework for creating instructional environments that are usable by, accessible to, and inclusive of, as many students as possible. Dr. Hasley can provide a, sadly, rare perspective to discussions of UDL in biology education as he is himself a blind biologist who has been blind since birth.</p> <h5 id="monica-munoz-torres-university-of-colorado-anschutz-medical-campus">Monica Munoz-Torres (University of Colorado Anschutz Medical Campus)</h5> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Monica_Munoz-Torres-2.jpeg" alt="Monica Munoz-Torres"></p> <p>Dr. Munoz-Torres, an Associate Research Professor in the School of Medicine at the University of Colorado Anschutz Medical Campus, is the Program Manager for the Translational and Integrative Sciences Lab (TISLab) and currently serves as Director of Operations for the Phenomics First Resource, an NHGRI Center of Excellence in Genomic Science. Curating genomes sparked Dr. Munoz-Torres&rsquo;s scientific path, and she now manages software development projects aimed at facilitating how we draw insight from genomic and phenomic data across species. She is an experienced project manager, specializing in bioinformatics and genome curation efforts, and has been very successful in building and growing communities around genome curation.</p> <p>Dr. Munoz-Torres strives to improve diversity in representation within the genomics and bioinformatics research workforces. She has actively participated in the Equity, Diversity, and Inclusion Committees for the Global Alliance for Genomics and Health (GA4GH), where she contributes to effort towards a more inclusive approach to the development of standards in genomics and health data sharing; for the International Society for Biocuration, where she spearheaded efforts to ensure that planning for their annual conference includes steps to increase diversity in the speaker roster; and has also volunteered as a member of the ISCB EDI committee.</p> <h5 id="gary-mcdowell-lightoller-llc">Gary McDowell (Lightoller, LLC)</h5> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Gary.png" alt="Gary McDowell"></p> <p>Gary McDowell is the founder of Lightoller LLC, a consultancy providing expertise on early career researchers, with the goal of ensuring that future generations of researchers can reach their potential to solve problems for society. Originally from Northern Ireland, Gary has a Masters in Chemistry and PhD in Oncology from the University of Cambridge, U.K. He carried out postdoctoral research at Boston Children’s Hospital then Tufts University and helped organize a symposium in Boston in 2014 to give a voice to early career researchers (resulting in the White Paper, “Shaping the Future of Research: a perspective from junior scientists”). In 2016 he co-founded and became Executive Director of the nonprofit “Future of Research&quot;, and since 2019 he has worked as a consultant through Lightoller LLC focusing on advising institutions on how to better support future generations of researchers, and to provide early career researchers with tools and strategies to effect change. He has worked on the role of early career researchers in journal article peer review, paying particular attention to the hidden yet vital role they play in the process, shedding a light on ghostwriting in journal peer review and the lack of access to authentic training experiences.</p> <h5 id="rachel-torchet-institut-pasteur">Rachel Torchet (Institut Pasteur)</h5> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Rachel-Torchet.jpg" alt="Rachel Torchet"></p> <p>Research Engineer Rachel Torchet does web and interface development in the Bioinformatics and Biostatistics HUB at Institut Pasteur. From a multidisciplinary background - from wet lab technician to computational biologist and finally a UX developer - she has always worked in diverse professional universes, which helped her to understand the needs of users, scientists, and colleagues. Based on that experience she came up with the idea of creating an internal professional community to promote diversity, equality, and inclusion at the Institut Pasteur, which included animating an online community, co-hosting a Feminist Café, being part of a Gender Month organization committee, and more.</p> <p>Along with PI Hanna Julienne, Ms. Torchet co-supervised a Master student in social science with the intention of investigating how to create the proper conditions for a gender-equal expression in scientific conferences through an evidence-based and mixed-method study, the <a href="https://research.pasteur.fr/en/project/jobim-2021-pilot-project-gender-speaking-differences-in-academia/">JOBIM 2021 pilot project – Gender Speaking Differences in Academia</a>. One of the deliverables of this project is a leaflet of guidelines for STEM conference organizers.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Jason-Williams-1.jpeg" alt="Jason Williams"></p> <h5 id="moderator-jason-williams-cold-spring-harbor-laboratory"><strong>Moderator:</strong> Jason Williams (Cold Spring Harbor Laboratory)</h5> <p><a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-keynotes/">Jason&rsquo;s bio</a></p>https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/Thu, 21 Apr 2022 20:55:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/<h1 id="collaborationfest-2022">CollaborationFest 2022</h1> <p>In conjunction with our annual meeting, <a href="https://www.open-bio.org/events/bosc-2022/">BOSC</a>, the OBF runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you.</p> <p>The 2022 BOSC CoFest, which will follow ISMB 2022, will take place July 15-16, and will be hybrid (online + in person at the Madison Public Library). We encourage you to register for the conference, but the CoFest itself is free.</p> <p>Please add yourself to this <a href="https://docs.google.com/spreadsheets/d/1h5woYd0URjgUKInWA2sozDwfThUlQbQQ9xbjdEdQQXk/edit?usp=sharing">spreadsheet</a> to help us gauge interest and coordinate topic groups, and join the #cofest channel in the <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">BOSC Slack</a>!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/codefest-big-group-on-steps.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h2 id="history">History</h2> <p>This will be the 13th annual pre- or post-BOSC collaboration fest. Previous fun and successful events were <a href="https://www.open-bio.org/wiki/Codefest_2010">Codefest 2010</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> in Vienna, <a href="https://www.open-bio.org/wiki/Codefest_2012">Codefest 2012</a> in Los Angeles, <a href="https://www.open-bio.org/wiki/Codefest_2013">Codefest 2013</a> in Berlin, <a href="https://www.open-bio.org/wiki/Codefest_2014">Codefest 2014</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2015">Codefest 2015</a> in Dublin, <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a> in Orlando, <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> in Prague, <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC Collaboration Fest 2018</a> in Portland, <a href="https://www.open-bio.org/events/bosc/bosc-2019-collaborationfest">Collaboration Fest 2019</a> in Basel, and the last two worldwide virtual editions <a href="https://www.open-bio.org/events/bosc-2020/bosc-2020-collaborationfest/">BOSC 2020 CollaborationFest</a>/ <a href="https://bcc2020.github.io/cofest/">BCC2020 CollaborationFest</a> (online) and <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">Collaboration Fest 2021</a> (online).</p>https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule/Mon, 21 Mar 2022 00:14:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule/<h6 id="go-to-full-lists-of-talks-and-posters"><a href="#talks">Go to full lists of talks and posters</a></h6> <h6 id="see-talk-and-poster-videos-on-youtube"><a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXYotvWZLnKd9rcNMb6r9tjf">See talk and poster videos on YouTube</a></h6> <h5 id="bosc-2022-schedule-at-a-glance">BOSC 2022 schedule at a glance</h5> <div style="position: relative; padding-top: 90%;"><iframe style="position: absolute; top: 0; left: 0; width:95%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vQf1fc-iJHGE8HlQGu9zIDkEhxAxBpbXTUiWYI9rxVzfY6PNijbPP2J5mkqccgy9JUkRX1Bt-Z9ZZq7/pubhtml?gid=0&amp;single=true&amp;widget=true&amp;headers=false" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h6 id="keynotes"><a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-keynotes/">Keynotes:</a></h6> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Jason-Williams-1.jpeg" alt="Jason Williams"><img src="https://www.open-bio.org/wp-content/uploads/2022/03/Melissa-Haendel-cropped.jpg" alt="Melissa Haendel">Jason Williams (joint keynote with Education COSI): Riding the bicycle — including all scientists on a path to excellence Melissa Haendel (joint keynote with Bio-Ontologies COSI): The open data highway: turbo-boosting translational traffic with ontologies</p> <h6 id="panel-building-and-sustaining-inclusive-open-science-communities"><a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/">Panel: Building and Sustaining Inclusive Open Science Communities</a></h6> <h6 id="see-talk-and-poster-videos-on-youtube-1"><a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXYotvWZLnKd9rcNMb6r9tjf">See talk and poster videos on YouTube</a></h6> <h4 id="bosc-2022-talk-schedule">BOSC 2022 Talk Schedule</h4> <div style="position: relative; padding-top: 90%;"><iframe style="position: absolute; top: 0; left: 0; width: 150%; height: 99%;" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vQf1fc-iJHGE8HlQGu9zIDkEhxAxBpbXTUiWYI9rxVzfY6PNijbPP2J5mkqccgy9JUkRX1Bt-Z9ZZq7/pubhtml?gid=1729310258&single=true" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h4 id="bosc-2022-posters">BOSC 2022 Posters</h4> <p>Posters will be presented on July 13 from 12:30-2:30pm CT. <a href="https://www.iscb.org/ismb2022-program/posters">More info&hellip;</a></p> <div style="position: relative; padding-top: 85%;"><iframe style="position: absolute; top: 0; left: 0; width: 120%; height: 100%" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vQf1fc-iJHGE8HlQGu9zIDkEhxAxBpbXTUiWYI9rxVzfY6PNijbPP2J5mkqccgy9JUkRX1Bt-Z9ZZq7/pubhtml?gid=1094351563&single=true" allowfullscreen="allowfullscreen" frameborder="0"></iframe></div> <h6 id="see-talk-and-poster-videos-on-youtube-2"><a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXYotvWZLnKd9rcNMb6r9tjf">See talk and poster videos on YouTube</a></h6>https://www.open-bio.org/adding-projects/Sat, 12 Mar 2022 10:13:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/adding-projects/<p>This page provides the OBFs affiliated project policy, alongside an FAQ around what it means to be a member project.</p> <p>You can always find <a href="https://github.com/OBF/obf-docs/blob/master/Affiliated-Project-Policy.md">the binding documents on our official Git repo</a> (alongside <a href="https://github.com/OBF/obf-docs/blob/master/Affiliated-project-FAQ.md">the FAQ</a>).</p> <h2 id="contents">Contents</h2> <!-- TOC start (generated with https://github.com/derlin/bitdowntoc) --> <ul> <li><a href="#background">Background</a></li> <li><a href="#motivation">Motivation</a></li> <li><a href="#project-affiliation-types">Project affiliation types</a></li> <li><a href="#community-voting-on-project-status">Community voting on project status</a></li> <li><a href="#maintenance-of-affiliation-status">Maintenance of affiliation status </a></li> <li><a href="#projects-with-grandfathered-affiliation-status">Projects with grandfathered affiliation status</a></li> <li><a href="#dispute-and-board-veto">Dispute and Board Veto</a></li> <li><a href="#faq">FAQ</a></li> </ul> <!-- TOC end --> <h2 id="background">Background</h2> <p>The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>OBF originally grew out of the volunteer projects BioPerl, BioJava and Biopython. Later BioRuby, BioSQL, BioLib, DAS, MOBY, EMBOSS, and OBDA joined the OBF umbrella, primarily as a consequence of requiring project hosting support, existing community relationships, and through informal consensus among members of OBF&rsquo;s Board of Directors. OBF has since become hesitant to include new projects under the official umbrella, in part because the growth in OBF-hosted project resources has reached the capacity of OBF servers, and in part because of OBF&rsquo;s mission and scope as an organization. Furthermore, the OBF Board resolved that the listing of projects related to OBF use affiliation categories that are based on a formal definition, and a community process for attaining them that is consistent with the OBF&rsquo;s values of transparency and fostering community.</p> <h2 id="motivation">Motivation</h2> <p>This policy formalizes criteria and a community-driven, transparent process by which open-source software projects can gain, lose, and maintain certain types of affiliation with the OBF.</p> <p>Establishing an affiliation between an open source software project and the OBF is intended to have value for both the project and the OBF. It stands to promote a project&rsquo;s overall health and long-term sustainability, which is among the OBF&rsquo;s primary objectives. The user and developer communities of affiliated projects constitute the primary pool of volunteers for OBF as an umbrella organization.</p> <p>That notwithstanding, it is not the OBF&rsquo;s mission to serve primarily as a project hosting or resource provider for bioinformatics open-source projects. Instead, as an umbrella organization the OBF&rsquo;s focus is on projects that serve, or have the potential to serve, a large variety of bioinformatics research applications and users. Therefore, the group of projects with some status of affiliation with the OBF is expected to always be limited in number. In keeping with the potential benefits of affiliation for a project, the criteria formalized here aim to maintain OBF&rsquo;s focus and mission.</p> <p>Projects differ in terms of their activity, community, audience, and wider impact on bioinformatics. Also, over time, projects change, become more active, or less relevant and even dormant. This policy aims to provide mechanisms through which projects&rsquo; affiliations can reflect such dynamics.</p> <h2 id="project-affiliation-types">Project affiliation types</h2> <h3 id="affiliated-obf-projects">Affiliated OBF projects</h3> <p>Affiliated OBF projects are bioinformatics open-source initiatives with an active developer and/or user community. Affiliated OBF Projects include mature long-standing projects with a broad user base, as well as projects in earlier phases of adoption, a smaller user base, or a narrow focus. In either case, their focus will be highly relevant to the stated mission of the OBF.</p> <p>To be an Affiliated OBF Project, a project should show all of the following:</p> <ul> <li>A developer and user community, with defined project leadership. A project must also be active when seeking to become an Affiliated OBF project. Evidence of this could include recent pull requests being reviewed / accepted, blog posts, or community events/conferences.</li> <li>An Open Source licence, either OSI-approved or one that was agreed upon by the OBF Board as compatible.</li> <li>A community culture welcoming newcomers and a diverse group of users and contributors. Specifically, the project must have or adopt a Code of Conduct, either that of the OBF, or another one found acceptable by the OBF. Other evidence of a welcoming culture will usually include an informative, up-to-date, and inviting web presence; documented guidelines for how to contribute; and instructions for how to ask for help.</li> <li>Being an active member of the OBF organization. Evidence of this includes active participation by project members in OBF flagship events, such as contributing to BOSC and GSoC, or in OBF leadership.</li> </ul> <h3 id="candidate-obf-projects">Candidate OBF Projects</h3> <p>Candidate OBF Projects have the aspiration and promise to develop themselves into an Affiliated OBF Project. They may already meet most or even all expectations for Affiliated Project status, except, for example, for not yet having been active members of the OBF organization.</p> <p>This status is the path for projects previously unaffiliated with the OBF to attain official affiliation. Candidate OBF Projects will be in this status for only a limited amount of time, typically one year, and no more than 3 years in a row. A project that loses Candidate OBF Project status due to exceeding this limit can re-apply for Candidate OBF Project status later.</p> <h3 id="other-projects">Other projects</h3> <p>Projects other than those under the stated affiliation categories may have a de-facto relationship with OBF or one of its official member projects, but they do not have a recognized affiliation status. As such, their status is not voted on.</p> <p>These projects may include student projects with OBF community participation, including projects executed under the OBF umbrella, and other projects considered active and interesting to the wider bioinformatics community. They may be listed and described on the OBF website so long as it is evident that they do not have an official affiliation with the OBF as per the ones defined here.</p> <h2 id="community-voting-on-project-status">Community voting on project status</h2> <h3 id="explanation">Explanation</h3> <p>Projects can change or attain an affiliation status once a year by a vote of the OBF community.</p> <p>The OBF community for the purposes of this policy may be represented by, but need not be limited to the OBF membership. For example, the collective attendees of a BOSC meeting, or of similar OBF-endorsed events, also qualify as representative of the OBF community. Voting may be by electronic means, or simply by physical signs such as raising hands. The exact details of voting are intentionally left to the OBF volunteers organizing the process in a given year so long as the process is reasonably consistent between subsequent years.</p> <h3 id="ballot-preparation">Ballot preparation</h3> <p>The group of OBF members overseeing the ballot preparation for the annual OBF community vote will conduct the following steps at least 14 days before voting is scheduled to take place:</p> <ul> <li>Identify currently affiliated projects (i.e., in Affiliate or Candidate status) that may warrant a status change.</li> <li>Identify currently unaffiliated projects that seek Candidate OBF Project status.</li> <li>Solicit mission, scope, and metrics from project leads as suitable for each project to be voted on.</li> <li>Compile this information online, disseminate it to the OBF membership as well as the larger developer and user community, and solicit feedback from these communities.</li> <li>Incorporate feedback as suitable into the online documentation.</li> </ul> <h3 id="voting">Voting</h3> <p>A group of OBF members overseeing the voting process for the annual OBF community vote will in general conduct the following steps:</p> <ul> <li>Ensure that the OBF community to cast votes is aware of the projects on the ballot, and the argument(s) for or against the status changes that are on the ballot.</li> <li>Ensure an opportunity for each project on the ballot to present its viewpoint, not to exceed five (5) minutes per project.</li> <li>Organize and execute the voting.</li> </ul> <p>For an affiliation status change on the ballot to become effective, a majority of 70% or more of the cast ballots must be in favor of the change.</p> <h4 id="projects-seeking-affiliated-obf-project-status">Projects seeking Affiliated OBF Project status</h4> <p>To become an Affiliated OBF Project a project has to have had Candidate OBF Project status for at least one (1) year, and it must be active. A Candidate OBF Project failing to achieve Affiliated OBF Project status will remain a Candidate OBF Project unless it has reached the maximum time a project can remain in that status, in which case the project will lose their Candidate OBF Project status as a consequence of the vote.</p> <h4 id="projects-seeking-candidate-obf-project">Projects seeking Candidate OBF Project</h4> <p>A project not currently affiliated with OBF can seek to attain Candidate OBF Project status. A project failing to achieve the necessary majority in favor of becoming a Candidate OBF Project can be on the ballot again the following year, unless it has failed three (3) times in a row.</p> <h4 id="removal-of-affiliation-status">Removal of affiliation status</h4> <p>The ballot can include a vote on removing OBF affiliation from a project. Possible reasons for such a vote include consistent failure to meet expectations for OBF affiliated projects; consistent failure to adhere to OBF&rsquo;s Code of Conduct; and a project being no longer maintained.</p> <h2 id="maintenance-of-affiliation-status">Maintenance of affiliation status</h2> <p>The status of Affiliated and Candidate OBF Projects that are not voted on stays the same, unless one of the following conditions occurs:</p> <p>A Candidate OBF Project has reached the maximum consecutive length of time that Candidate status can be held. This will result in the project automatically losing its OBF affiliation status.</p> <p>An Affiliated OBF Project is no longer actively maintained. In addition to the possible evidence for demonstrating that a project is active (see above), evidence of a project&rsquo;s active maintenance includes the following:</p> <ul> <li>A maintainer attends yearly OBF public board meetings or BOSC to provide a project update.</li> <li>Posting a project update on the OBF blog.</li> <li>Updates on the project&rsquo;s main code repository or website.</li> <li>Participation in GSoC, whether under the OBF umbrella or not.</li> </ul> <p>Affiliated OBF projects that have not been actively maintained for over twelve months may have their affiliation status archived as a result of a review by the OBF Board of Directors. The OBF Board of Directors will conduct such reviews in regular intervals, and will make reasonable efforts to contact the project maintainers before taking action.</p> <h2 id="projects-with-grandfathered-affiliation-status">Projects with grandfathered affiliation status</h2> <p>The projects considered OBF member projects prior to enactment of this policy are grandfathered to Affiliated OBF Project status. These projects are the so-called Bio* Projects, which consist of BioPerl, Biopython, BioJava, BioRuby, BioSQL; DAS (Distributed Annotation System); and EMBOSS (European Molecular Biology Open Software Suite).</p> <p>Other projects that existed prior to enactment of this policy can be grandfathered to Affiliated or Candidate OBF Project status as well upon approval by the OBF Board of Directors. It is expected that the Board will do so in public session. For pre-existing projects grandfathered to Candidate OBF Project status the minimum waiting period for seeking Affiliate OBF Project status is waived.</p> <h2 id="dispute-and-board-veto">Dispute and Board Veto</h2> <p>Any dispute on votes or current affiliation status of a project must be brought before the OBF Board of Directors, who will arbitrate, if necessary by public meeting and vote. The Board&rsquo;s decision is final and binding.</p> <p>The OBF Board of Directors may, at its discretion, veto, instate, or terminate a project&rsquo;s official affiliation status, if the Board determines the need to do so. It is expected that the Board will do so in public session, whether at an annual Board meeting, or at a specifically convened one.</p> <h2 id="faq">FAQ</h2> <h3 id="how-do-i-apply-to-become-an-affiliated-or-candidate-obf-project">How do I apply to become an Affiliated or Candidate OBF Project?</h3> <p>Assuming your project meets, or intends to soon meet, all of the requirements in our affiliated project policy, please create a GitHub issue with the following details:</p> <ul> <li>URL of the project</li> <li>Contact information for the project maintainers</li> <li>Proof of compliance with Affiliate Status requirements where possible, e.g. licence, code of conduct, etc. or plan to implement any missing requirements in the near future.</li> </ul> <p>Filling out and submitting this issue template constitutes a formal request to be put on the next ballot for voting on OBF affiliation status. If your project has not previously been affiliated with the OBF, your application is for attaining Candidate OBF Project status. If your project is currently a Candidate OBF Project, then your application is for attaining Affiliated OBF Project status.</p> <p>You can also feel free to drop us a line if you have questions about your eligibility before applying.</p> <h3 id="why-apply-for-affiliate-status-are-there-benefits-or-obligations">Why apply for affiliate status? Are there benefits or obligations?</h3> <p>The benefits of affiliate status include access to umbrella resources such as domain / site hosting, mailing list hosting, a community of active open source developers, and a tremendous pool of open-source collaborative development know-how. Furthermore, affiliate status officially signifies that a project has met certain requirements promoting community and collaboration, which may improve its ability to attract more users as well as potential developers. Finally, OBF, through its fiscal sponsor SPI, can sustainability hold assets on behalf of a project, such as domain names, and financial assets, in a way that is robust to changes in the project&rsquo;s (and even OBF&rsquo;s) leadership, and that does not risk tax implications for an individual.</p> <p>The obligations of affiliate status are few - primarily projects must remain active and maintain a good standing within the community, e.g. by enforcing their code of conduct if necessary.</p> <h3 id="can-i-sign-my-project-over-to-the-obfs-ownership">Can I sign my project over to the OBF&rsquo;s ownership?</h3> <p>The OBF is primarily a home for projects that are actively maintained. If you fear your project doesn&rsquo;t have enough community contributors we can share a call for contributors within the OBF community, but the OBF does not provide software maintenance services.</p> <p>If by signing over ownership you only mean assigning intellectual property rights (in particular, copyright) for a project&rsquo;s source code artifacts to the OBF, please contact the OBF Board. Note that due to OBF&rsquo;s current status as an SPI-associated project, this would have to mean to assign copyright to the SPI. Note also that currently OBF does not own any intellectual property rights in any of its member projects, neither directly nor through the SPI.</p> <h3 id="im-interested-in-taking-donations-for-my-project-or-ive-recently-received-a-grant-can-the-obf-handle-my-cash-flow">I&rsquo;m interested in taking donations for my project, or I&rsquo;ve recently received a grant. Can the OBF handle my cash flow?</h3> <p>The OBF can accept donations and grants on behalf of its member projects through SPI, the OBF&rsquo;s fiscal sponsor. The OBF also can, again through SPI, request the disbursement of funds earmarked for a member project. Management of cash flow with a high rate of transactions, will, however, likely exceed the capacity of SPI&rsquo;s (almost entirely volunteer) financial administrators, and we therefore advise projects expecting this need to apply independently for fiscal sponsorship. Organisations providing fiscal sponsorship for software projects include SPI, Software Freedom Conservancy, NumFocus, and OpenCollective.</p>https://www.open-bio.org/2022/03/02/bosc-and-bio-ontologies-joint-session/Wed, 02 Mar 2022 04:52:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/03/02/bosc-and-bio-ontologies-joint-session/<p><img src="https://www.open-bio.org/wp-content/uploads/2022/03/ISMB-Bio-Ontologies-BOSC.jpg" alt=""></p> <p>We are excited to announce that <a href="https://www.open-bio.org/events/bosc-2022/">BOSC</a> and <a href="https://www.bio-ontologies.org.uk/ismb-annual-meeting">Bio-Ontologies</a> will join forces for part of a day at <a href="https://www.iscb.org/ismb2022">ISMB 2022</a>. The joint session will include talks chosen from abstracts submitted to BOSC or Bio-Ontologies, plus a keynote speaker who is well known in both the ontology and open science communities!</p> <p>BOSC and Bio-Ontologies are two of the longest-running COSIs (Communities of Special Interest) at ISMB: BOSC started in 2000 and Bio-Ontologies in 1998. <a href="http://www.bio-ontologies.org.uk/">Bio-Ontologies</a> focuses on the FAIR development and application of ontologies and other Linked Open Data resources and the organization and dissemination of knowledge in biomedicine and the life sciences; <a href="https://www.open-bio.org/events/bosc-2021/about/">BOSC</a> covers the full spectrum of open source, open science, open data and open standards in the life sciences.</p> <p>You can submit relevant abstracts to either <a href="https://www.open-bio.org/events/bosc-2022/submit/">BOSC</a> or <a href="https://www.bio-ontologies.org.uk/ismb-annual-meeting">Bio-Ontologies</a> (please do not double-submit the same abstract); the Program Chairs of both COSIs will consider appropriate abstracts for the joint session.</p> <p>Both BOSC and Bio-Ontologies will take place July 13-14, 2022. The time and date of the joint session will be announced in May.</p>https://www.open-bio.org/events/bosc-2022/bosc-2022-keynotes/Tue, 01 Mar 2022 05:49:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/bosc-2022-keynotes/<h1 id="bosc-2022-keynotes">BOSC 2022 Keynotes</h1> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/03/Melissa-Haendel-cropped.jpg" alt="Dr. Melissa Haendel"></p> <h3 id="melissa-haendel-university-of-colorado-anschutz-medical-campus">Melissa Haendel (University of Colorado Anschutz Medical Campus)</h3> <h5 id="joint-keynote-bosc-and-bio-ontologies">Joint keynote, BOSC and Bio-Ontologies</h5> <h6 id="the-open-data-highway-turbo-boosting-translational-traffic-with-ontologies"><em>The open data highway: turbo-boosting translational traffic with ontologies</em></h6> <p><em>Addressing complex scientific challenges requires a roadmap of data from diverse sources, organisms, contexts, formats, and granularities. Building a coherent holistic view of the data landscape to address any given problem is non-trivial. Often in the aggregation process, many of the original connections within the data are lost and it is difficult to make new (inferred) connections. Novel data integration strategies that leverage semantic technologies such as ontologies, knowledge graphs, and common modeling strategies can help span disciplinary boundaries. However, it takes the people too; robust interdisciplinary collaboration and improved data licensing and access can advance progress and innovation, turbo-boosting the open data highway.</em></p> <p>Melissa Haendel is the Chief Research Informatics Officer and Marsico Chair in Data Science at University of Colorado Anschutz Medical Campus, and the Director of the Center for Data to Health (CD2H). Her background is molecular genetics and developmental biology as well as translational informatics, with a focus over the past decade on open science and semantic engineering. Dr. Haendel’s vision is to weave together healthcare systems, basic science research, and patient-generated data through development of data-integration technologies and innovative data capture strategies. Dr. Haendel’s research has focused on integration of genotype-phenotype data to improve rare-disease diagnosis and mechanism discovery. She also leads and participates in international standards organizations to support improved data sharing and utility worldwide.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/05/Jason-Williams-1.jpeg" alt="Jason Williams"></p> <h3 id="jason-williams-cold-spring-harbor-laboratory">Jason Williams (Cold Spring Harbor Laboratory)</h3> <h6 id="riding-the-bicycle--including-all-scientists-on-a-path-to-excellence"><em>Riding the Bicycle — Including All Scientists on a Path to Excellence</em></h6> <p><em>Life science is rapidly increasing in interdisciplinarity, making career-spanning learning critical. New methods and deeper research questions requires scientists and educators to traverse widening skill gaps to remain competent. Short-format training (SFT) — including workshops, bootcamps, and short courses — is a solution many turn to. However, the effectiveness of SFT is lower than many realize. Overall, SFT is delivered without sufficient grounding in evidence-based pedagogy, and systemic inequity limits inclusion of all learners (see</em> <em><a href="https://www.science.org/doi/10.1126/science.abn9515">my recent Science paper</a> about this).</em></p> <p><em>I will describe the work of an international group of scientist-educators to develop a new construct — the “Bicycle Principles”. The Principles assemble education science and collective experience into a framework for improving SFT through two cyclic (hence bi-cycle) and iterative processes:</em></p> <p><em>- “Core Principles” (“Best Evidence”, “Catalytic”, Effective”, and “Inclusion”) apply to all SFT and are grounded in research and work in education, diversity, equity, and inclusion.</em> <em>- “Community Principles” (“Reaching”, “Scaling”, and “Sustaining”) apply when SFT is organized by groups to achieve the objectives of a community (e.g., science discipline, institution, career stage).</em></p> <p>_Community refinement, adoption, and adaptation of the Bicycle Principles will help accelerate scientific progress by making SFT more effective, inclusive, and career-spanning for all. _</p> <p><a href="https://jasonjwilliamsny.github.io/profile/">Jason Williams</a> has worked at Cold Spring Harbor Laboratory since 2004, first at the bench in the Plant Science group and currently as an Assistant Director at the lab’s <a href="https://www.cshl.edu/dna-learning-center/">DNA Learning Center</a>. Jason is on numerous Advisory Boards and Diversity/Equity/Inclusion committees for organizations including the Earth BioGenome Project, Data Dryad, Global Alliance for Genomics and Health, BioData Catalyst, and ELIXIR UK. In 2020, he was chosen as a Kavli Frontiers of Science Fellow by the National Academy of Sciences, and won the <a href="https://www.cshl.edu/jason-williams-wins-nsf-2026-idea-machine-competition/">NSF 2026 Idea Machine Competition</a>.</p> <p>Jason feels that helping scientists keep up with changing technology is one of the most important things we can do to accelerate research. He believes this can be sustainably achieved by building, supporting, and promoting the people who do this training - hence his founding of the group <a href="https://lifescitrainers.org/">Life Science Trainers</a>, a global community of practice for short-format training in the life sciences.</p>https://www.open-bio.org/2022/02/23/watch-the-recording-of-the-iscbacademy-webinar-on-growing-open-source-communities/Wed, 23 Feb 2022 08:27:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/02/23/watch-the-recording-of-the-iscbacademy-webinar-on-growing-open-source-communities/<p>Yesterday we <a href="https://www.open-bio.org/2022/01/20/iscbacademy-webinar-feb-22-yo-yehudi/">hosted the OBF/BOSC contribution to the ISCBacademy webinar</a>. Our former OBF-board member and <em>Open Life Science</em> co-lead <a href="https://twitter.com/yoyehudi/">Yo Yehudi</a> presented how internship programs such as <em>Google Summer of Code</em> or <em>Outreachy</em> can be a great way to grow your open source community. If you missed the event, you can now <a href="https://www.youtube.com/watch?v=h4GVFMlUnMc">watch the recording on YouTube</a>.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share; fullscreen" loading="eager" referrerpolicy="strict-origin-when-cross-origin" src="https://www.youtube.com/embed/h4GVFMlUnMc?autoplay=0&amp;controls=1&amp;end=0&amp;loop=0&amp;mute=0&amp;start=0" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" title="YouTube video"></iframe> </div> <p>Lalit Narayan, who is an undergraduate student at the Indian Institute of Technology Mandi, was a first-time webinar attendee:</p> <blockquote> <p>&ldquo;This was my first time attending a webinar from OBF and I enjoyed it. Yo was a really great speaker and it was fun to get guidance from them. I had done industrial internships in the past but not any formal research internships. I really liked the idea of getting connected to like-minded people and working together in a team to work on an interesting research idea. In a team environment we learn from peers and spend time together which eventually leads to a great network.&rdquo;</p> </blockquote>https://www.open-bio.org/2022/02/07/obf-event-fellowship-2022-round1/Mon, 07 Feb 2022 16:56:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/02/07/obf-event-fellowship-2022-round1/<p><em>Announcement drafted by Malvika Sharan, Caleb Kibet and Hilya Zahroh, with the OBF Board&rsquo;s input.</em></p> <p>The call for applications for the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship</a> 2022, round 1 is now open. <strong>The deadline for this round is 1 April 2022.</strong> Applications should be submitted via <a href="https://forms.gle/Rt7Si7eT2MuTqrQZ9">this Google Form</a>. We have provided a Word template to help you draft the application locally before filling the form – <a href="https://docs.google.com/document/d/1tgzkHS84L8m3RwYoL7X86Axb6p_OiqNWaoJpiV4q8S0/">make a copy of this template</a>.</p> <p>We invite applications from candidates who are seeking financial support to attend or host scientific events in 2022. <strong><em>These events can be conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events</em></strong>. The selected awardees can use the OBF Event Fellowship to cover conference registration fees and potentially additional expenses associated with attending or hosting the event. Please <a href="https://github.com/OBF/obf-docs/blob/event-fellowship-rubric/Travel_fellowships.md#what-does-the-event-fellowship-cover">read details</a> about what this fellowship award will and will not cover. For instance, group applications are not in scope, but if multiple members of the same group would like to attend the same event, each member should send their application separately. If members of an organising committee would like to apply for support for hosting an event, the application should be sent by one person (preferably the lead organiser). More details regarding the fellowship application, review, and reimbursement process can be found on our website: <a href="https://www.open-bio.org/event-awards/">/event-awards/</a>.</p> <h2 id="your-application-with-required-details-allows-reviewers-to-make-informed-decisions">Your application with required details allows reviewers to make informed decisions!</h2> <p>Our efforts with this fellowship are to support members from underrepresented demographic groups including but not limited to diverse ethnic backgrounds, career stages, sexuality, gender identity and expression, people with disabilities and members from low-income backgrounds (such as from developing nations). The goal is to create opportunities for exposure to open science practises in bioinformatics and enhance collaboration among diverse researchers by covering participation costs for attendees from underrepresented groups.</p> <p>In the previous rounds, we received many applications that did not provide us with sufficient information to allow us to make informed decisions about what applicants hoped to gain from the conference they selected to attend, and how their participation contributes to the overall goals of the OBF Event fellowship programme. We encourage all applicants to read our review process before drafting their applications. We have also added our rubrics for review to keep the process transparent and supportive for our applicants, <a href="https://github.com/OBF/obf-docs/blob/event-fellowship-rubric/Travel_fellowships.md#review-process">read them here</a>.</p> <p>We have recently announced that Caleb Kibet and Hilyatuz Zahroh will join Malvika Sharan as co-chairs of the OBF Event Fellowship ( <a href="https://www.open-bio.org/2022/02/07/obf-event-fellowship-update/">read details</a>). We have also announced a <a href="https://www.open-bio.org/2022/02/07/2021-obf-fellowship-roundup/">round-up from the 2021 fellowship</a>.</p> <p>If you have questions, please contact the OBF board by emailing <a href="mailto:board@open-bio.org">board@open-bio.org</a>.</p> <p>C <em>over photo by <a href="https://unsplash.com/@brett_jordan?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText">Brett Jordan</a> on <a href="https://unsplash.com/s/photos/apply?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText">Unsplash</a></em>.</p>https://www.open-bio.org/2022/02/07/2021-obf-fellowship-roundup/Mon, 07 Feb 2022 16:55:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/02/07/2021-obf-fellowship-roundup/<p>The <a href="https://www.open-bio.org/event-awards/">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to support and encourage diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. Each year we open two calls for applications, deadlines for which are 1 April and 1 October.</p> <p>In 2021, we received 15 applications, of which three applicants, Sona Charles (Indian Institute of Spices Research, India), Anshika Sah (Institute of Home Economics, India) and Rupesh Gelal (Nepal Engineering College, Nepal) were awarded funding across the two open calls.</p> <p>In addition, in the spirit of the OBF Event Fellowship, we made it easier to attend our own conference with <a href="https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/">the BOSC-OBF Event Support Fund</a>, which received 9 applications, all of which were granted fee waivers for their participation in BOSC 2021, which took place online as a part of ISMB 2021. These awardees are David Twesigomwe (Sydney Brenner Institute for Molecular Bioscience – South Africa), Gemma Turon (University of Arkansas, USA), Ariel Mundo (University of Arkansas, USA), Paula Roxana Reyes Pérez (UNAM, Mexico), Fortune Ogo-ndah Awala (University of Port Harcourt, Nigeria), Wishah Mohammednour Ahmed Mohammednour (Omdurman Islamic University, Sudan), Menegbe Zibo (Université Félix Houphouët-Boigny, Ivory Coast –NH), Priyanka Sarkar (Deen Dayal Upadhyaya University, India) and Gloria Umutesi (EDAM Ontology Intern, Rwanda).</p> <p>Here, I have compiled blog posts from a few of these awardees summarising their experience from attending these conferences:</p> <ul> <li><strong>Sona Charles:</strong> <a href="https://www.open-bio.org/2021/06/07/sona-charles-glbio2021/">Summary of my participation at the GLBIO-2021 conference</a></li> <li><strong>Rupesh Gelal:</strong> <a href="https://www.open-bio.org/2021/12/17/riscv-summit-rgelal-2021">My virtual participation at the RISC-V 2021 summit</a></li> <li><strong>Gemma Turon</strong>: <a href="https://www.open-bio.org/2021/08/31/gemma-turon-obf-bosc-2021/">Highlights of my participation at the BOSC-2021</a></li> <li><strong>David Twesigomwe</strong>: <a href="https://www.open-bio.org/2021/09/07/david-twesigomwe-bosc2021/">My BOSC 2021 Experience</a></li> <li><strong>Ariel Mundo Ortiz</strong>: <a href="https://www.open-bio.org/2021/09/08/ariel-mundo-ortiz-bosc2021/">My participation at BOSC 2021</a></li> </ul> <p>Congratulations to each of them!  We are delighted to support their participation as the OBF Event Fellowship and BOSC-OBF Event support fund awardees and wish them all the best for their future work.</p> <p>We have receently opened the call for the first round of applications for 2022; <a href="https://www.open-bio.org/2022/02/07/obf-event-fellowship-2022-round1/">read details</a> and <strong>apply before 1 April 2022</strong>. Also, read the <a href="https://www.open-bio.org/2022/02/07/obf-event-fellowship-update/(opens%20in%20a%20new%20tab)">updates from the OBF Event Fellowship chairs</a>.</p> <p><em>Cover photo by <a href="https://unsplash.com/@brandsandpeople?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText">Brands&amp;People</a> on <a href="https://unsplash.com/s/photos/award?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText">Unsplash</a></em></p>https://www.open-bio.org/2022/02/07/obf-event-fellowship-update/Mon, 07 Feb 2022 16:51:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/02/07/obf-event-fellowship-update/<p>We are delighted to announce that <a href="https://www.open-bio.org/2021/10/06/two-new-members-elected-to-obf-board/">Caleb Kibet and Hilyatuz Zahroh, two members who recently joined the OBF board</a>, will be joining <a href="https://malvikasharan.github.io/">Malvika Sharan</a> as the co-chairs of the <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowship program</a>. Inviting contributions from the OBF board members, as well as bringing insights from their lived experiences, Caleb, Hilya and Malvika will re-evaluate how we can manage the OBF Event fellowship more effectively going forward.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/02/obf-ef-chairs-1024x488.png" alt=""></p> <p>There is a growing body of evidence, including the report from BOSC 2021, that virtual events are indeed more equitable for our colleagues from the Global South (see references: <a href="https://f1000research.com/articles/10-1054">[1]</a> &amp; <a href="https://www.nature.com/articles/s41893-021-00823-2#Fig1">[2]</a>), who were inadvertently excluded from most international events which required expensive travelling before the pandemic. However, in 2021, we saw a decline in applications to the Event Fellowship where we specifically accepted applications requesting funding for online conferences. We suspected that, after a year of the pandemic, most people working remotely must have managed the basic setup to attend virtual events.  It is also possible that many potential applicants might consider the expense for participation trivial enough that they didn’t want to spend time writing proposals or dealing with the admin workload of requesting fee assistance, and instead pay it out of their own pockets. Furthermore, online events are often free and/or provide free recordings to watch after the event – removing the need to pay a registration fee.</p> <p>The goal of the OBF Event fellowship programme is to create opportunities for exposure to open science practises in bioinformatics and enhance collaboration among diverse researchers by covering participation costs for attendees from underrepresented groups. Considering the recent evolution of scientific events, there is a need to assess how we continue to support participants who represent their local research, exchange knowledge and benefit communities more widely through their participation in international scientific events.</p> <p>With the new co-chairs on board, we will reflect on changes we can make in this programme that benefits members from marginalised groups and low-income backgrounds through learning, sharing and networking opportunities – potentially helping them advance their careers and impact the directions of bioinformatics research at the international level. We encourage you to participate in the discussion via this GitHub issue: <a href="https://github.com/OBF/obf-docs/issues/88">https://github.com/OBF/obf-docs/issues/88</a>.</p> <p>We have just opened the call for the first round of Event Fellowship applications for 2022; <a href="https://www.open-bio.org/2022/02/07/obf-event-fellowship-2022-round1/">read details</a> and <strong>apply before 1 April 2022</strong>.</p> <p><strong>References:</strong></p> <p>[1] Harris, N.L., Cock, P.J.A., Fields, C.J. <em>et al.</em> BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]. <em>F1000Research</em> 2021, <strong>10</strong>(ISCB Comm J):1054. <a href="https://doi.org/10.12688/f1000research.74074.1">https://doi.org/10.12688/f1000research.74074.1</a></p> <p>[2] Skiles, M., Yang, E., Reshef, O. <em>et al.</em> Conference demographics and footprint changed by virtual platforms. <em>Nat Sustain</em> (2021). <a href="https://doi.org/10.1038/s41893-021-00823-2">https://doi.org/10.1038/s41893-021-00823-2</a></p>https://www.open-bio.org/2022/01/28/google-summer-of-code-2022-time-for-project-ideas/Fri, 28 Jan 2022 01:38:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/01/28/google-summer-of-code-2022-time-for-project-ideas/<p>Hi everyone!</p> <p>My name is Melissa and I’m happy to be collaborating with OBF as lead GSoC admin this year along with support from Yo Yehudi. I had a great (virtual) time at BOSC 2021 as an Outreachy intern and am glad to be supporting another internship program this year.</p> <p>It’s time to start coming up with GSoC project ideas again! Below is some info that should help with that.</p> <p><strong>To refresh your mind…</strong></p> <p>These were last year’s projects: <a href="https://summerofcode.withgoogle.com/archive/2021/organizations/6326136019091456#projects-list">https://summerofcode.withgoogle.com/archive/2021/organizations/6326136019091456#projects-list</a></p> <p>In that link you will find short project descriptions and the work developed by students.</p> <p><strong>2022 project ideas</strong></p> <p>This year, projects can be medium-sized (~175 hours) or large-sized (~350 hours).</p> <p>There is something new compared to previous years: projects can now take 12-22 weeks to complete. From GSoC’s website:</p> <p>“Rather than a mandatory 12-week program that runs from June – August with everyone required to finish their projects by the end of the 12th week, we are opening it up so mentors and their GSoC Contributors can decide together if they want to extend the deadline for the project up to 22 weeks”.</p> <p>Please add your project ideas to the following document by THURSDAY FEBRUARY 17 (using suggest mode):</p> <p><a href="https://docs.google.com/document/d/1lUnIfd115DtGS-9wO2VpuM7osZj_M_sz7PZ-LtLxFtQ/edit?usp=sharing">https://docs.google.com/document/d/1lUnIfd115DtGS-9wO2VpuM7osZj_M_sz7PZ-LtLxFtQ/edit?usp=sharing</a></p> <p>- you can add ideas after this if needed, but we need as many fully fleshed ideas as possible already online for the organization review phase.</p> <p><strong>Time commitment + have co-mentors!</strong></p> <p>Mentors should expect a commitment of at least 5-8 hours per week during the coding phase. However, there’s an exploration and student application period, when they may (and probably will) start contacting the projects they’re interested in. Mentors should be able to answer questions during that time and also be available for 3 weeks of “community bonding”. Scroll down to see the timeline: <a href="https://summerofcode.withgoogle.com/how-it-works">https://summerofcode.withgoogle.com/how-it-works</a></p> <p>Communicate with students! Once the project starts, ideally mentors and students should have at least one video conference contact hour per week, plus likely at least twice that in email/chat during the week.</p> <p>Make sure you have 2-3 mentors for every project idea to cover you in case something comes up (such as covid-related downtime, illness, caring, or anything else).</p> <p>If you&rsquo;re interested in helping us with org admin duties, we&rsquo;d love to have you on board and are willing to provide you support and mentoring while you learn how to do it. Email <a href="mailto:obf-gsoc-admins@googlegroups.com">obf-gsoc-admins@googlegroups.com</a> to discuss it.</p> <p><strong>Please subscribe to OBF GSoC mailing lists!</strong></p> <p>If you haven’t already, please join both lists below - mentors and general. The mentors list will be used until (if) we&rsquo;re accepted as an organization, as well as to send reminders of actions required. The general list will become more active once (if) we have any students.</p> <p><a href="https://groups.google.com/g/obf-gsoc-mentors">https://groups.google.com/g/obf-gsoc-mentors</a></p> <p><a href="https://groups.google.com/g/obf-gsoc-general">https://groups.google.com/g/obf-gsoc-general</a></p> <p><strong>Code of Conduct</strong></p> <p>The OBF has recently voted to adopt the code of conduct presented here: <a href="https://github.com/OBF/obf-docs/tree/master/code-of-conduct">https://github.com/OBF/obf-docs/tree/master/code-of-conduct</a></p> <p>Please take a few minutes to read it, as it should also provide guidelines for this year’s OBF’s participation in GSoC.</p> <p><strong>Any questions?</strong></p> <p>If you have any questions please email either the mentor group ( <a href="mailto:obf-gsoc-mentors@googlegroups.com">obf-gsoc-mentors@googlegroups.com</a>) or the admin group ( <a href="mailto:obf-gsoc-admins@googlegroups.com">obf-gsoc-admins@googlegroups.com</a>). You can also reach out on <a href="https://twitter.com/melissablck">Twitter</a> to schedule a call.</p> <p>Thank you,</p> <p>Melissa</p>https://www.open-bio.org/2022/01/27/approved-by-obf-membership-vote/Thu, 27 Jan 2022 23:08:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/01/27/approved-by-obf-membership-vote/<p>As previously described, during the November 2021 public Board meeting, <a href="https://www.open-bio.org/2022/01/04/obf-membership-referendum/">the OBF announced two new initiatives to be voted on by the OBF membership</a>. Both of these <a href="https://vote.heliosvoting.org/helios/e/obf-coc-css">received a large majority of votes</a>:</p> <ol> <li>OBF Community Support Sponsorship (53 for, 3 against, 2 abstaining)</li> <li>OBF Code of Conduct (54 for, 2 against, 1 abstaining)</li> </ol> <p>The work to set up the new Community Support Sponsorship is <a href="https://github.com/OBF/obf-docs/issues/86">underway</a>. The new Code of Conduct is now available on the <a href="https://www.open-bio.org/code-of-conduct/">OBF website.</a></p>https://www.open-bio.org/2022/01/20/iscbacademy-webinar-feb-22-yo-yehudi/Thu, 20 Jan 2022 22:12:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/01/20/iscbacademy-webinar-feb-22-yo-yehudi/<p>Date &amp; Time: Tuesday, February 22, 2022, 15:00 UTC / 11am EDT</p> <p>Location: online webinar hosted by ISCB</p> <p>Speaker: Yo Yehudi, Open Life Science (former OBF board member and Google Summer of Code admin &amp; mentor)</p> <p>Topic: Growing open source communities with internships</p> <p>The ISCB, which runs the annual ISMB conference, is offering a series of <a href="https://www.iscb.org/iscbacademy-webinars">ISCBacademy webinars</a> hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are free to ISCB members.</p> <p>If you are not an ISCB member but would like to register to attend this webinar, and the <a href="https://www.iscb.org/iscb-membership-dues">fee (which ranges from $5-$135)</a> is a barrier, <strong><a href="https://docs.google.com/forms/d/e/1FAIpQLSf-8YnrYfB2vFpiRjvcMChJOk_KSNEmgsPwF_8Ffxlz0NvpXQ/viewform">please fill out our application for a fee waiver</a></strong>.</p> <p>Building communities for your open source computational tooling requires more than just technical expertise, and often isn&rsquo;t as straightforward as building the tool itself. Having a community of contributors and users can make a big difference in many ways - additional community members will spot opportunities and bugs in your code that previously you didn&rsquo;t notice, and may be able to offer unique skill sets to your team.</p> <p>One effective way to grow your community can be via internships. Programs such as <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> and <a href="https://www.outreachy.org/">Outreachy</a> offer the chance to work with interns for 6-12 weeks, working on individual supervised projects whilst getting paid for their work.</p> <p>This webinar will cover the ins and outs of participating in internship programs like this, from the perspective of a mentoring organisation. Topics will include:</p> <p>1. Getting started with internship programs - finding mentors and defining a set of projects</p> <p>2. Time commitments for mentors, before the application period and after interns are selected.</p> <p>3. Funding for internship programs! (It&rsquo;s not as tricky as you may fear - others handle this bit!)</p> <p>4. Keeping interns engaged during the program and bringing them in as long-term contributors afterwards.</p> <p>This webinar will be run by <strong>Yo Yehudi</strong>, who has been a mentor and organisation administrator for interns in GSoC and Outreachy since 2017, supervising over 35 interns for various open source organisations, and who co-leads <a href="https://openlifesci.org/">Open Life Science</a>, an organisation dedicated to training open research community builders.</p>https://www.open-bio.org/2022/01/04/obf-membership-referendum/Tue, 04 Jan 2022 21:44:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/01/04/obf-membership-referendum/<p>During our last <a href="https://www.open-bio.org/2021/10/06/two-new-members-elected-to-obf-board/">public Board meeting</a>, the OBF announced two new initiatives that are being proposed for approval by the OBF membership in a formal votes.</p> <p>1. OBF Community Support Sponsorship: a proposed new grant programme, based on the OBF Event Fellowships but aimed at supporting grassroots projects running events in their own communities. For details see: - <a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">/2021/05/11/obf-community-support-sponsorship/</a> - <a href="https://github.com/OBF/obf-docs/issues/86">https://github.com/OBF/obf-docs/issues/86</a></p> <p>2. Code of Conduct: BOSC has a code of conduct, as part of the parent conference, but OBF does not yet have its own code of conduct. This pull request lays out a Code of Conduct for the OBF that, if approved by a membership vote, will replace the content on /code-of-conduct/. For details see: - <a href="https://github.com/OBF/obf-docs/pull/78">https://github.com/OBF/obf-docs/pull/78</a></p> <p>The deadline to vote is January 10, 2022 (NOTE: later extended to January 17.). All active OBF members should have received an email ballot on December 28 from Helios Voting with &ldquo;OBF Membership Referendum&rdquo; in the subject line. If you didn&rsquo;t receive a ballot (and you&rsquo;ve already checked your junk/spam mail folder), please contact us (board atsign open-bio.org).</p>https://www.open-bio.org/events/bosc-2022/Sun, 02 Jan 2022 19:12:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/<h1 id="bosc-2022">BOSC 2022</h1> <p>BOSC 2022 was held July 13-14, 2022, as part of the hybrid <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> (in person in Madison, Wisconsin, USA and online).</p> <p>A joint BOSC/ <a href="https://www.bio-ontologies.org.uk/ismb-annual-meeting">Bio-Ontologies</a> session included <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-keynotes">keynote speaker Melissa Haendel</a>. <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-keynotes">Jason Williams</a>&rsquo;s talk was a joint BOSC/Education COSI keynote. The <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule/">program</a> closed with a <a href="https://www.open-bio.org/events/bosc-2022/bosc-2022-panel/">panel about Building and Sustaining Inclusive Open Science Communities</a>.</p> <p>BOSC 2022 summaries:</p> <p><a href="https://f1000research.com/articles/11-1034/v1">Report at F1000Research</a> <a href="http://gigasciencejournal.com/blog/birthday-at-ismb2022/">GigaScience blog post</a> <a href="https://www.open-bio.org/2022/08/16/crowdsourced-highlights-from-bosc-2022/">Geraldine Van der Auwera&rsquo;s blog post</a> <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXYotvWZLnKd9rcNMb6r9tjf">Talk and poster videos</a></p> <p><strong><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a></strong> will be part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a> (Lyon, France / online).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/bosc-2021-closing-composite-bigger.png" alt="Screenshot from BOSC 2021"></p> <h2 id="key-dates">Key Dates</h2> <ul> <li>April 21, 2022: Abstract submission deadline</li> <li>May 19: <a href="https://www.open-bio.org/events/bosc-2022/submit/">Late poster submission</a> deadline</li> <li>June 10: Deadline for presenters to register for ISMB 2022</li> <li>July 13-14, 2022: <strong>BOSC 2022</strong>, part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> (July 10-14)</li> <li>July 15-16: <a href="https://www.open-bio.org/events/bosc-2022/obf-bosc-collaborationfest/">CollaborationFest (CoFest) 2022</a>, hybrid</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Christie-and-Jason.png" alt=""></p> <h2 id="topics">Topics</h2> <p>BOSC covers all aspects of open source bioinformatics software and open science, including (but not limited to) these topics:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Open Approaches to Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach and Training</li> <li>Open Ontologies and Tools (joint session with Bio-Ontologies)</li> </ul> <h3 id="sponsors">Sponsors</h3> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Caitlin-McHugh-BoF-1.jpeg" alt="Screenshot from BOSC 2021"></p> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some presenters. Below are the sponsors from 2022. Thanks to their generous support, we were able to grant free registration to 19 participants at BOSC 2022, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you&rsquo;re interested in sponsoring BOSC, please see our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors page</a>!</p> <h2 id="bosc-2022-platinum-sponsors">BOSC 2022 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a></p> <h2 id="bosc-2022-gold-sponsors">BOSC 2022 Gold Sponsors</h2> <p><a href="https://www.broadinstitute.org/data-sciences-platform"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/Broad-DSP-logo-1.png" alt="Broad Institute Data Science Platform"></a><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Office of Data Science Strategy"></a></p> <h2 id="bosc-2022-silver-sponsors">BOSC 2022 Silver Sponsors</h2> <p><a href="https://arvados.org"><img src="https://www.open-bio.org/wp-content/uploads/2022/05/ArvadosCurii.png" alt="Arvados, supported by Curii"></a><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="Gigascience"></a></p> <h5 id="previous-years-sponsors-are-listed-on-the-bosc-2021-sponsors-page">Previous year&rsquo;s sponsors are listed on the <a href="https://www.open-bio.org/events/bosc-2021/sponsors/">BOSC 2021 Sponsors</a> page.</h5> <h3 id="overview">Overview</h3> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, which was part of ISMB/ECCB 2021 online, took place July 29-30, 2021. The <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">BOSC 2021 talks and posters are listed here</a>, and <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">videos of all the talks are on our YouTube channel.</a></p> <p>BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <p>BOSC is usually preceded or followed by what we now call <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest (CoFest</a> for short), a two-day community development session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. All are welcome to attend CoFest, whether or not you attend BOSC!</p> <p><a href="https://www.open-bio.org/events/bosc/about/">More about BOSC&hellip;</a></p> <h2 id="registration">Registration</h2> <p>To participate in BOSC 2022, you will need to <a href="https://www.iscb.org/ismb2022">register for ISMB 2022</a>. If the registration fee is a barrier, those who submit abstracts can request a fee waiver on the submission form, and we will provide other ways for those who aren&rsquo;t submitting abstracts to request fee assistance.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Moni-GemmaTuron-JeremyYang.png" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/bosc-2022-org-committee-vert2.png" alt="BOSC 2022 Organizing Committee members"></p> <h2 id="bosc-2022-organizing-committee">BOSC 2022 Organizing Committee</h2> <p><strong>Chair: Nomi L. Harris</strong> (Lawrence Berkeley National Laboratory)</p> <ul> <li>Karsten Hokamp (Trinity College Dublin)</li> <li>Jason Williams (Cold Spring Harbor Laboratory)</li> <li>Nicole Vasilevsky (University of Colorado Anschutz Medical Campus)</li> <li>Hervé Ménager (Institut Pasteur)</li> <li>Monica Munoz-Torres (University of Colorado Anschutz Medical Campus)</li> <li>Deepak Unni (European Molecular Biology Laboratory)</li> <li><a href="http://www.scri.ac.uk/staff/petercock">Peter Cock</a> (ex officio, representing the OBF)</li> </ul> <h2 id="bosc-2022-review-committee">BOSC 2022 Review Committee</h2> <p>Melissa Black*, Scott Cain*, Seth Carbon, J. Harry Caufield*, Tyrone Chen, Christopher Fields*, Bastian Greshake Tzovaras*, Karsten Hokamp, Aziz Khan*, Hilmar Lapp, Lara Mangravite, Hande McGinty, Hervé Ménager, Steffen Möller, Monica Munoz-Torres, Kieran O&rsquo;Neill, Tazro Ohta, Konstantin Okonechnikov, Caralyn Reisle, Surya Saha*, Ian Simpson, Stian Soiland-Reyes, David Twesigomwe, Deepak Unni*, Jason Williams \* = also reviewed Late Poster abstracts</p> <h2 id="previous-boscs">Previous BOSCs</h2> <p><a href="https://www.open-bio.org/events/bosc/about#Past_BOSCs">BOSC has been held yearly since 2000.</a> <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021, which was part of</a> <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021 online</a>, took place July 29-30, 2021. The <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">BOSC 2021 talks and posters are listed here</a>, and <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">the talk videos are on our YouTube channel.</a></p> <p><a href="https://bcc2020.github.io/">BCC2020</a>, the Bioinformatics Community Conference, brought together the Galaxy Community Conference (GCC) and <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2020</a> in a joint online meeting. Participants from 62 countries joined us for sessions scheduled twice a day to accommodate both hemispheres.</p> <p><a href="https://www.open-bio.org/events/bosc-2019/">BOSC 2019</a> was part of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB 2019</a> in Basel, Switzerland. See the full <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2019 schedule</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/BOSC2021-happy-hour-28Jul-1.jpeg" alt="Screenshot from BOSC 2021 Happy Hour"></p> <h1 id="code-of-conduct">Code of Conduct</h1> <p>As part of ISMB 2022, BOSC 2022 will be covered by the <a href="https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct">ISMB/ECCB Code of Conduct.</a></p>https://www.open-bio.org/2021/12/17/riscv-summit-rgelal-2021/Fri, 17 Dec 2021 16:04:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/12/17/riscv-summit-rgelal-2021/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. <a href="https://rupeshgelal.com.np/">Rupesh Gelal</a>, a student from Nepal Engineering College, Nepal, attended the <a href="https://riscv.org/event/2021-risc-v-summit/">2021 RISC-V Summit</a>, supported by this fellowship granted to him in the second round of 2021.</em></p> <p>The pandemic has made attending conferences and events more accessible for full-time students like me, who often can’t travel internationally to attend in-person events. These days everything is possible remotely — there is no need to travel halfway across the world. Still, the cost of small hardware (headphones, webcam, speaker, and/microphone) for attending remote events can be a hindrance sometimes. Fortunately, I came across the Open Bioinformatics Foundation Event Fellowship while researching the 2021 RISC-V Summit. I applied immediately for the fellowship. After a month, I received an email notifying me about my successful application. In this post, I provide an overview of my participation at this conference.</p> <p><strong>Day 1 of RISC-V Summit</strong></p> <p>The first day of the event was really exciting. I bonded with other RISC-V community members, which helped extend my professional network. I had an opportunity to share my skills, ideas, and views with fellow participants regarding the present and future of technology and learn from them. After the initial bonding and introduction phase, I attended a lightning Talk session and enjoyed the demo session “How to Extend RISC-V to Accelerate AI/ML” given by Veronia Iskandar from TU Dresden &amp; Dr. William Jones from Embecosm. I learned the internal working of RISC-V architecture and how it can be extended to improve performance. This session was one of the reasons why I wanted to attend this year’s RISC-V summit.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/12/Screenshot-from-2021-12-06-18-10-16-1024x527.png" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2021/12/Screenshot-from-2021-12-07-19-16-13-1024x525.png" alt=""></p> <p><strong>Day 2 of RISC-V Summit</strong></p> <p>On day two, I attended a couple of sessions. First, I attended the “Efficient Issue Scheduling for Hardware Multithreaded RISC-V Pipeline” session by Dr. Shlomo Greenberg, Ben Gurion University of the Negev &amp; Sami Shamoon College Engineering, Beer-Sheva, Israel. This is where I learned about the importance of an effective scheduling algorithm as well as other multithreading techniques. Second, I listened to the talk “AI-RISC - Custom Extensions to RISC-V for Energy-efficient AI Inference at the Edge of IoT” by Vaibhav Verma from the University of Virginia. In this session, I dived deeper into the AI-RISC hardware/software co-design methodology. The session gave me better insights into the AI integration on the RISC-V-based processor.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/12/Screenshot-from-2021-12-08-17-39-18-1024x528.png" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2021/12/Screenshot-from-2021-12-08-17-41-04-1024x528.png" alt=""></p> <p><strong>Day 3 of RISC-V Summit</strong></p> <p>On the final day of the RISC-V event, I attended the “Quantitative Methods for Continuously Improving RISC-V Compilers” session by Philipp Tomsich from VRULL. Through this session, I learned how quantitative methods can be used to assess the quality of code generation and identify and prioritize potential improvements based on hot-block analysis, dynamic instruction count metrics, and instruction histograms.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/12/Screenshot-from-2021-12-09-16-38-50-1024x525.png" alt=""></p> <p>To conclude, I feel the RISC-V summit was a great learning experience. I learned a lot about the RISC-V architecture and its open-source community. The skills learned from this conference, such as collaboration, open communication, and open source best practices, will directly help me achieve my professional and academic goals. All data recordings of the conference will be available as an open source resource on YouTube on the <a href="https://www.youtube.com/c/RISCVInternational/videos">RISC-V International channel</a>.</p> <p>I would like to thank the OBF board again for selecting me for the fellowship. I will make sure to promote and advocate open-source software development and/or open science in the biological research community as well as in my community.</p>https://www.open-bio.org/2021/10/06/two-new-members-elected-to-obf-board/Wed, 06 Oct 2021 10:20:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/10/06/two-new-members-elected-to-obf-board/<p>The OBF held a public Board meeting on September 21, 2021, via Zoom. During the meeting, one Board member, Bastian Greshake Tzovaras, whose term expired, was elected to another term as Board member-at-large, and two new Board members were elected: Hilyatuz Zahroh and Caleb Kibet. Additionally, two proposals were presented (see below). The meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs">obf-docs GitHub repository</a>.</p> <p><a href="https://twitter.com/hilyatuz_zahroh">Hilyatuz (&ldquo;Hilya&rdquo;) Zahroh</a> is a bioinformatician at the Genetics Research Centre, Universitas YARSI, in Indonesia. She also works with Asia Pacific Bioinformatics Network ( <a href="https://www.apbionet.org/">APBioNet</a>) to facilitate the sharing of bioinformatics knowledge and skills through education and trainings in the Asia-Pacific region, and is involved with RINarxiv, a preprint server for Indonesia. She was a vice-chair of the 18th International Conference on Bioinformatics (InCoB) 2019, and the treasurer of the Bioinformatics and Biodiversity Conference (BBC) 2020. Hilya is committed to fast-forwarding science by promoting open access in bioinformatics and facilitating the learning of bioinformatics skills within communities.</p> <p><a href="https://twitter.com/Calkibet">Caleb Kipkurui Kibet</a> is a bioinformatics researcher at ICIPE, the International Centre of Insect Physiology and Ecology in Kenya, as well as an adjunct lecturer at Pwani University. He is the founder and project lead of <a href="https://github.com/BioinfoNet">OpenScienceKE</a>, which seeks to promote open science practices in bioinformatics. In 2019-2020, Caleb was a Mozilla Open Science Fellow; his work involved developing FAIR Genomics Data Management policy, frameworks, and infrastructure; building a community of Open Science enthusiasts; and promoting the adoption of machine learning tools in biomedical research.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/10/obf-board-meeting-Sep2021-composite.png" alt=""></p> <p>Above: Board candidates Caleb Kibet (bottom left) and Hilyatuz Zahroh (bottom right) with current Board members during the public OBF Board meeting on 21-Sept-2021.</p> <p>Two proposals were announced as pending submission to the OBF membership for a vote of approval:</p> <ol> <li> <p>The OBF is proposing a Community Support Sponsorship grant programme (see <a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">/2021/05/11/obf-community-support-sponsorship/</a>), which would give funds to grassroots communities in return for our logo appearing on their event webpages and materials, acknowledging our support. We seek community input; please add your comments to <a href="https://github.com/OBF/obf-docs/issues/86">https://github.com/OBF/obf-docs/issues/86</a>.</p> </li> <li> <p>The OBF would like to adopt a code of conduct (COC) for its activities including meetings and member projects. See pull request <a href="https://github.com/OBF/obf-docs/pull/78">https://github.com/OBF/obf-docs/pull/78</a> for the proposal, and please share your thoughts.</p> </li> </ol> <p>A membership vote on these will be held within the next 6 weeks, and the Board resolved to accept the result as binding for whether to formally implement them.</p>https://www.open-bio.org/2021/09/30/event-fellowship-deadline-extended-to-october-4-2021/Thu, 30 Sep 2021 18:37:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/30/event-fellowship-deadline-extended-to-october-4-2021/<p>The deadline for applying for an OBF Event Fellowship has just been extended to <strong>October 4, 2021</strong>! The OBF Event Fellowship program is aimed at increasing diverse participation at events relating to open source bioinformatics. You can <a href="https://www.open-bio.org/blog/">read blog posts</a> by previous Event Fellowship recipients.</p> <p>See more details on <a href="https://www.open-bio.org/event-awards/">our webpage</a>, and submit your application at <strong><a href="https://forms.gle/7ocmgvypiFHeFNfy7">https://forms.gle/7ocmgvypiFHeFNfy7</a></strong>!</p>https://www.open-bio.org/2021/09/11/obf-public-board-meeting-2021-09-21/Sat, 11 Sep 2021 16:59:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/11/obf-public-board-meeting-2021-09-21/<h2 id="date-time-and-how-to-join"><strong>Date, Time, and How to Join</strong></h2> <p>Date and time: 2021-09-21, 17:00 UTC (10am PT / 1pm ET / 18:00 UK) Participation link: <a href="https://lbnl.zoom.us/j/97312757115">https://lbnl.zoom.us/j/97312757115</a> Password: OBF2021 Meeting ID: 973 1275 7115</p> <h2 id="agenda">Agenda</h2> <p><strong>Approve minutes from the previous Public Board Meeting:</strong> <a href="https://github.com/OBF/obf-docs/pull/87">https://github.com/OBF/obf-docs/pull/87</a></p> <h3 id="term-expirations-and-elections-to-the-board-electronic-ballot">Term expirations and Elections to the Board (electronic ballot)</h3> <ul> <li>Hilyatuz Zahroh and Caleb Kibet, running for Board member at-large</li> <li>Board member Bastian Greshake Tzovaras’ term expires this year and he would like to stand for another term as member-at-large.</li> </ul> <h3 id="voting-by-obf-membership">Voting by OBF membership</h3> <ul> <li>OBF Community Support Sponsorship: a proposed new grant programme, based on the OBF Event Fellowships but aimed at supporting grassroots projects running events in their own communities. Subject to approval by the OBF membership in a formal vote. <ul> <li><a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">/2021/05/11/obf-community-support-sponsorship/</a></li> <li><a href="https://github.com/OBF/obf-docs/issues/86">https://github.com/OBF/obf-docs/issues/86</a></li> </ul> </li> <li>Code of Conduct: BOSC has a code of conduct, as part of the parent conference, but OBF does not yet have its own code of conduct. This pull request lays out a Code of Conduct for the OBF that, if approved by a membership vote, will replace the content on /code-of-conduct/. <ul> <li><a href="https://github.com/OBF/obf-docs/pull/78">https://github.com/OBF/obf-docs/pull/78</a></li> </ul> </li> </ul> <h3 id="minutes">Minutes</h3> <p>After the meeting, the meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs">obf-docs GitHub repository</a>.</p>https://www.open-bio.org/2021/09/10/iscbacademy-mad-price-ball/Fri, 10 Sep 2021 11:19:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/10/iscbacademy-mad-price-ball/<p>The ISCB, which runs the annual ISMB conference, is offering a series of webinars hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are free to ISCB members.</p> <p>The first BOSC/OBF ISCBacademy COSI webinar will take place on Tuesday, September 14, 2021, at 15:00 UTC / 11am EDT, and will feature Mad Price Ball of the Open Humans Foundation speaking about &ldquo;Open Sourcing Ourselves - Together.&rdquo; Before Dr. Ball&rsquo;s talk, BOSC 2021 Chair Nomi Harris will give a brief overview of the OBF and BOSC.</p> <p><strong><em>If you missed the webinar, you can watch the video on YouTube:</em> <a href="https://www.youtube.com/watch?v=vjMb19NxjdM"><em>https://www.youtube.com/watch?v=vjMb19NxjdM</em></a></strong></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/09/MadPriceBall-1.png" alt="Dr. Mad Price Ball"></p> <h3 id="open-sourcing-ourselves---together">Open Sourcing Ourselves - Together</h3> <p>Mad Price Ball (Open Humans Foundation)</p> <p>September 14, 2021 at 15:00 UTC / 11:00AM EDT</p> <p>ABSTRACT: &ldquo;Open source&rdquo; refers to the practice of making software freely available, re-usable, and adaptable. We might also ask: how can we apply &ldquo;open source&rdquo; to understanding ourselves as humans &ndash; our genomes, health, or behavior? While navigating concerns about privacy and consent, the principles of &ldquo;open&rdquo; should also prompt us to consider what we can do to enable others. How can we make it more &ldquo;open&rdquo; for people to research themselves? Open source communities have come to understand that it takes more than just sharing code: it requires building a community. These same principles also apply to individual and collective research about our health. Drawing on my work with the Personal Genome Project and Open Humans, I share insights and lessons I&rsquo;ve learned in efforts to collect, share, and analyze our personal data to better understand ourselves.</p> <p>BIO: Mad Price Ball is Executive Director and President of Open Humans Foundation and co-founder of Open Humans, and Affiliate Faculty at the Center for Research and Interdisciplinarity (CRI). Their work focuses on enabling people to access and use their health and personal data. They explore methods for sharing tools, ideas, and data to advance individual understanding, collective empowerment, and research. This work occurs through Open Humans and its associated nonprofit, and with the Peer Produced Research Lab at the CRI. Mad&rsquo;s past experience and research has included work in genomics and biotechnology, bioethics, digital technology and advocacy, as well as participatory and participant-centered research. <a href="http://www.madpriceball.net/">More about Mad</a></p>https://www.open-bio.org/2021/09/08/ariel-mundo-ortiz-bosc2021/Wed, 08 Sep 2021 02:43:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/08/ariel-mundo-ortiz-bosc2021/<p><em>The <a href="//www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/%E2%80%9D">BOSC-OBF 2021 Event Support Fund</a> was awarded to Ariel Mundo Ortiz, a researcher from the University of Arkansas, to participate in <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, an annual conference hosted by the <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a>. Based on the OBF Event Fellowship program, this fund aimed to facilitate the participation of diverse researchers from historically underrepresented groups at BOSC to help wider awareness and adoption of open source bioinformatics practices in the biological research community. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p>A while ago I came across a Twitter post that mentioned the Bioinformatics Open Source Conference (BOSC). A quick Google search took me to the BOSC <a href="https://www.open-bio.org/events/bosc-2021/about/">website</a>, and I was thrilled to see that one of the core concepts of the conference was to promote open science. Personally, I have been working over the last year to make my work reproducible and accessible, and the fact that BOSC provided talks and workshops focused on open science sparked my interest; I decided that although I did not have material for a presentation, I still wanted to attend the conference.</p> <p>Fortunately enough, BOSC offered this year the <a href="https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/">BOSC-OBF 2021 Event Support Fund</a>, with the aim of increasing the participation of members from groups otherwise underrepresented in BOSC. I suspected the number of applications for the Support Fund was going to be high, but nonetheless, I decided to submit my own application.</p> <p>On July 10th, I received an email notifying me about my successful application! That was excellent news, and now I was sure I would be able to attend the event. One personal challenge with the Conference this year was the time zone; all the sessions started at 5:30 am! (In my time zone).</p> <p><strong>Day 1</strong></p> <p>The challenge of time zones quickly became a minor thing after attending the first keynote session by Dr. Christie Bahlai (from Kent State University) on July 29th. Her keynote was titled “Significant heterogeneities: Ecology’s emergence as open and synthetic science” and it covered the historical background of Ecology, and how significant changes over the last two decades have moved the focus of the field, enabled Dr. Bahlai and other researchers to conduct research that is grounded in collaboration and openness.</p> <p>Her keynote resonated deeply with me; I could see how her path was similar to my own academic path. For instance, trying to analyze noisy data gathered through my research (that never looks like the “example data” from statistical books) was challenging. I was inspired by her talk, and it reinforced in me the desire to make my future work open and to continue to refine my statistical armamentarium.</p> <p><strong>Day 2</strong></p> <p>The keynote for the second day of BOSC 2021 was delivered by Dr. Thomas Hervé Mboa Nkoudou (from the African Institute of Open Science and Hardware) titled “Contribution of the maker movement to biotechnology in Africa: An open science perspective”. This keynote covered the democratization of biotechnology in Africa, and how the <em>maker</em> movement (a community-based movement that democratizes access to tools and technologies) has proven successful by promoting Biomakerspaces where African researchers can replicate existing protocols and locally produce enzymes, for example. This keynote was very interesting to me because it allowed me to appreciate a different perspective of the open science movement and the impact that reproducible research has in other parts of the world.</p> <p>That day I was also able to attend the Sessions on Visualization and Translational Bioinformatics. The talk “Robust variant interpretation in precision oncology using a graph knowledge base” by Caralyn Reisle (UBC) was a talk I enjoyed very much, as it emphasized the use of graph-based knowledge to enable the discovery of molecular pathways in cancer; this talk made me better understand the importance of the use of big data to treat and diagnose cancer, which I think will become extremely important in the future.</p> <p>Despite the challenges of 2021, and not being able to travel much, I feel BOSC 2021 was a wonderful experience. It allowed me to interact with people from around the world that believe that openness is a central theme in science, and I was able to learn about new tools, statistical analyses, and to get a better understanding of where the open science movement currently stands. I look forward to a (hopefully in person) rewarding and motivating experience for BOSC 2022!</p>https://www.open-bio.org/2021/09/07/david-twesigomwe-bosc2021/Tue, 07 Sep 2021 10:24:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/07/david-twesigomwe-bosc2021/<p><em>The <a href="%E2%80%9D/2021/06/11/bosc-obf-2021-event-support-fund/%E2%80%9D">BOSC-OBF 2021 Event Support Fund</a> was awarded to David Twesigomwe, a PhD student based at the <a href="https://www.wits.ac.za/research/sbimb">Sydney Brenner Institute for Molecular Bioscience (SBIMB)</a> - South Africa, to participate in <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, an annual conference hosted by the <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a>. Based on the OBF Event Fellowship program, this fund aimed to facilitate participation of diverse researchers from historically underrepresented groups at BOSC to help wider awareness and adoption of open source bioinformatics practices in the biological research community. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p><img src="https://lh4.googleusercontent.com/523fcIWovBbsbH4FLq-75qrPqG8Xze_CjNFQkrYg9yLszwe7lOvjzRFtKcQnmDa4oen1iUDa4E6oPLNGs-nE6wO84W5TVcAAAYrptZHEjGVVrxNrFsAJ_16vIsI5rw=s0" alt=""></p> <p>Attending the Bioinformatics Open Source Conference (BOSC) has definitely been one of my highlights for 2021 so far. I am so grateful to have received a registration fellowship as part of the global initiative supported by the <a href="https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/">BOSC-OBF 2021 Event Support Fund</a>. From the research point of view, nothing beats getting together (albeit virtually) to talk all things bioinformatics and open science with such a welcoming BOSC community as we continue adapting to new routines and work-life balance during the COVID-19 pandemic.</p> <p><strong>Pre-BOSC</strong></p> <p>The first thing that stayed with me about BOSC 2021 was the detailed critique and useful comments we received from the reviewers of our abstract. As an up-and-coming bioinformatics scientist, it was wonderful to get such actionable feedback on our pipeline ( <a href="https://github.com/SBIMB/StellarPGx">StellarPGx</a>), and suggestions on how we can promote open source contributions to the code. One of the reviewers even went the extra mile and submitted the very first issue in the GitHub repository :)</p> <p><strong>Overview of the conference</strong></p> <p><a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, which was one of the tracks of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, was really exciting despite it being a virtual event – kudos to the organising team for putting the conference together aa nd navigating all the technical issues. In particular, I enjoyed the session on workflow management systems, which included a fascinating talk by Paolo di Tommaso on the evolution of Nextflow – the workflow management system of choice for a number of students and senior scientists at the SBIMB. I also enjoyed the session on analysis tools, where I got the opportunity to present StellarPGx, and I learned a great deal from the other sessions as research reproducibility was rightly championed to all the talks.</p> <p>Furthermore, it was quite exciting to round off the days with virtual round table and happy hour group meetings with incredible role models (Chris Fields, Nomi Harris, and Geraldine Van der Auwera to mention but a few).</p> <p><strong>Welcoming community</strong></p> <p>Even though BOSC 2021 (the first BOSC for me) was held virtually, the warm welcome I received from the community – be it on the remarkably active Slack channel or in the round table meetings – was quite uplifting. Special mention to Nomi Harris and the entire organising team for dedicating a lot of time and effort in organising such an engaging conference.</p> <p><strong>Next steps</strong></p> <p>I am looking forward to incorporating the ideas and suggested open source best practices arising from BOSC 2021 in the next phase of development for <a href="https://github.com/SBIMB/StellarPGx">StellarPGx</a>. I will forever be grateful for being awarded the <a href="https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/">BOSC-OBF 2021 Event Support Fund</a> which enabled me to attend and present at #BOSC2021. I hope to be an active member of the BOSC-OBF community for years to come and to volunteer in some of the upcoming OBF activities.</p>https://www.open-bio.org/2021/08/31/gemma-turon-obf-bosc-2021/Tue, 31 Aug 2021 09:46:12 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/08/31/gemma-turon-obf-bosc-2021/<p><em>The <a href="//www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/%E2%80%9D">BOSC-OBF 2021 Event Support Fund</a> enabled awardees to register for free for <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, an annual conference hosted by the <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a>, which promotes and facilitates the open source bioinformatics development and open science.</em> <em>Based on the <a href="https://www.open-bio.org/travel-awards/">OBF Event Fellowship program</a>, the BOSC-OBF support fund aimed to facilitate participation of diverse researchers from historically underrepresented groups at BOSC, helping to spread wider awareness and adoption of open source bioinformatics practices in the biological research community.</em> <em>One of the BOSC-OBF awardees was Gemma Turon, a researcher from the <a href="//ersilia.io/%E2%80%9D">Ersilia Open Source Initiative (EOSI)</a>, who writes here about her experience at BOSC 2021.</em></p> <p><img src="https://lh4.googleusercontent.com/K9-uNNkDnFLkW_wuIMa6smlG1wakooj3LhzBtBzu90R1JHF3lzYKR8OoPONLZnLDkxCA5VC3Re1PKYrhi9BtCgJH6NcoupMU1JvYI1HkiHWWuitO3soXsUshJ24T1A=s0" alt=""></p> <p>When we started our small non-profit, the Ersilia Open Source Initiative (EOSI), to strengthen the research capacity against neglected diseases using open-source AI/ML tools, we were not aware of the large number of resources and community back-up we would encounter. I first heard of the BOSC conference in February, and quickly realized it would be a great opportunity to present our newly founded initiative and the software we were trying to develop. What interested me mostly of the BOSC was the openness and inclusion of a broad range of topics of interest, many of which are aligned with EOSI’s mission, namely Open Science and Reproducible Research, Open Biomedical Data, Open Approaches to Translational Bioinformatics and Inclusion, Outreach and Training.</p> <p>By then, we had all become used to virtual meetings, and despite there might be some  drawbacks, global reach is an advantage in these settings, enabling us to participate in international meetings from our home-made offices. Nevertheless, conference registration costs still need to be covered, and they can be unaffordable to limited-resource organizations such as ours. With delight, then, I found out about the <a href="https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/">BOSC-OBF 2021 Event Support Fund</a>, which encouraged me to continue with my application for a short talk and apply to the Support Fund to cover my registration.</p> <h2 id="overview-of-the-conference"><strong>Overview of the conference</strong></h2> <p>The three keynote speakers delivered outstanding talks on the application of open and collaborative science to a broad range of topics, from ecology (Dr. Christie Balai) to the maker movement in Africa (Dr. Thomas Hervé Mboa Nkoudou), and including a great talk on new protocols in data collection, transparency and reproducibility for data-driven biomedical research (Dr. Lara Mangravite). The last two are particularly relevant to the mission of EOSI, which is focused on implementing data-driven technologies for drug discovery research in Low and Middle Income Countries, particularly in Africa, where most of our collaborators are based.</p> <p>The short talks were organized in topic-based sessions that included short (5 min), medium (8 min) and long (16 min) talks. I would like to highlight the “Tools for Open Science” session (Day 1), which included talks about outstanding tools like the OpenCGA and the GenePattern Notebook, and the “Translational Bioinformatics” session (Day 2) where <a href="https://www.youtube.com/watch?v=yWzO8hIyf-4&amp;ab_channel=Ersilia">I introduced</a> the Ersilia Model Hub, and learned about great initiatives such as the <a href="https://www.biorxiv.org/content/10.1101/2020.12.30.424881v3">target identification in Parkinson disease</a> presented by Dr. Jeremy Yang.</p> <p>The keynote talks and different sessions were complemented by a large selection of poster presentations and community-engaging events in the form of “Birds of Feathers”.</p> <h2 id="learnings-and-thank-you"><strong>Learnings and thank you</strong></h2> <p>I first want to congratulate the BOSC organization for an incredible effort in managing such a large online event, I always received prompt answers to all my questions via email and on the conference day the set up of the meeting rooms and the availability of the staff made sure there were no technical issues and the sessions run smoothly and according to the schedule. In addition, the BOSC-OBF organisers set up the Slack channel that enabled the participants to continue on the discussions started live during the conference, a great strategy to further engage the audience and provide more feedback to the speakers and poster presenters.</p> <p>Finally, as I am writing this short blog post, I have reviewed the aims and objectives of BOSC, as stated on their <a href="https://www.open-bio.org/events/bosc-2021/about/">website</a>:</p> <ul> <li>Provide developers with a forum for displaying their work to the wider research community</li> <li>Provide a focused environment for developers and users to interact and share ideas about software development, open science, and practical techniques in bioinformatic</li> <li>Promote Open Science, with its focus on sharing data and tools, transparency, reproducibility, and data provenance</li> <li>Inform the research community of important developments in Open Source Bioinformatics.</li> </ul> <p>And I believe that they have all been accomplished in the BOSC-2021 edition. As a speaker and participant, I have had the opportunity to learn about open source tools for data sharing and research reproducibility, I have engaged in high-level discussions with other scientists and become part of the BOSC-OBF community and, moreover, I have had the opportunity to present the research we are developing at EOSI thanks to the support of the OBF Event Fellowship. I want to give my deepest thanks for the opportunity, and to encourage all readers to go to the <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">youtube channel</a> where you can find the recordings of the talks, and, if you are interested in reading more about EOSI’s mission, please check out our <a href="https://ersilia.io">page</a> and our <a href="https://medium.com/ersiliaio">Medium Blog</a>.</p>https://www.open-bio.org/2021/08/18/obf-event-fellowship-second-call-2021/Wed, 18 Aug 2021 18:45:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/08/18/obf-event-fellowship-second-call-2021/<p>The call for application for the second round of this year&rsquo;s <a href="https://www.open-bio.org">Open Bioinformatics Foundation</a> (OBF) Event Fellowship is open. Please submit your application before <strong>October 1, 2021</strong> (save a calendar reminder).</p> <p>Just announced: deadline extended to October 4, 2021!</p> <p><strong>Please apply via this Google application form: <a href="https://forms.gle/7ocmgvypiFHeFNfy7">https://forms.gle/7ocmgvypiFHeFNfy7</a>.</strong></p> <p>The OBF Event Fellowship program is aimed at increasing diverse participation at events promoting open science practices such as open source bioinformatics resource development and dissemination in the biological research community. These fellowships are available to support both in-person and remote (virtual) participation at events such as conferences, workshops, training courses or collaborative development sprints. See more details on <a href="https://www.open-bio.org/event-awards/">our webpage</a>.</p> <p>Like the previous three rounds, we are continuing to invite applications from individuals seeking financial support to attend or host virtual events.</p> <p>In the previous rounds, we have offered fellowships to participants in bioinformatics, open research and life science-related projects or conferences. This fellowship supported their participation as a speaker, poster presenter or new learners of these particular topics. You can <a href="https://www.open-bio.org/blog/">read blogposts</a> from their participation.</p> <p>If multiple members of a group are applying for this fellowship, please send your applications separately as the OBF Event Fellowship is aimed at supporting <strong>individual applicants only</strong>. For more information, please contact the OBF Event Fellowship chair by emailing: <a href="mailto:board@open-bio.org">board@open-bio.org</a>.</p>https://www.open-bio.org/2021/07/28/join-us-for-bosc-2021/Wed, 28 Jul 2021 14:28:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/07/28/join-us-for-bosc-2021/<p><a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021,</a> which is a track (COSI) of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, will take place online the 29th and 30th of July. The complete schedule is <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">here</a>.</p> <p>The event is being held in the Showcare platform &ndash; check out our <a href="https://docs.google.com/document/d/1CvVeTqwWykoaITDg0u5hikit9qNUimjxbjA_220lXas/edit">tips</a> for making the most of your online conference experience.</p> <p>We invite all attendees to join us at the pre-BOSC happy hour at the BOSC [roundtable](http://All attendees are invited to our pre-BOSC happy hour today from 17:30-18:30 UTC! Look for us at the BOSC roundtable. <a href="https://ismbeccb2021.showcare.io/roundtables/">https://ismbeccb2021.showcare.io/roundtables/</a>) on Wednesday, July 28, from 17:30-18:30 UTC!</p> <p>We encourage participants to take screenshots of the event and share them with us! Also, if you’d like to write a blog post about your experience at BOSC, we’d be happy to post it on our blog!</p> <p>Happy BOSCing!</p>https://www.open-bio.org/2021/06/23/working-on-a-cwl-toil-project-with-the-open-bioinformatics-foundation/Wed, 23 Jun 2021 08:58:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/23/working-on-a-cwl-toil-project-with-the-open-bioinformatics-foundation/<p><em>This is a guest post from Mihai Popescu, a GSoC student with CWL, which participates under the OBF umbrella. Cross-posted on the CWL forums: <a href="https://cwl.discourse.group/t/working-on-a-cwl-toil-project-with-the-open-bioinformatics-foundation/390">https://cwl.discourse.group/t/working-on-a-cwl-toil-project-with-the-open-bioinformatics-foundation/390</a></em></p> <p>I am Mihai Popescu, a second year master student at VU Amsterdam in <a href="https://vuweb.vu.nl/en/education/master/parallel-and-distributed-computer-systems">Parallel and Distributed Computer Systems</a>. I am happy that my GSoC proposal got accepted and that I have started working on the project. I attended some CWL meetings since I submitted the proposal and I got to know a small part of the community. I would like to thank my mentor Michael for introducing me to the CWL community and answering a lot of my questions about workflows.</p> <p>The objective of my <a href="https://summerofcode.withgoogle.com/projects/#6469533377757184">2021 GSoC project</a> is to implement data streaming for <code>toil-cwl-runner</code>, which is a way of running Toil using CWL. This project aims to implement data streaming to speed up the analysis by avoiding slow disk/storage IO and speeding up the start of tool execution when it isn’t required to wait for data to download. The main focus is to implement this first in AWS S3. <a href="https://toil.readthedocs.io/en/latest/">Toil</a> is an open-source pure-Python workflow engine. <a href="https://www.commonwl.org/">Common Workflow Language</a> (CWL) is an open standard for describing analysis workflows.</p> <p>Sarah Wait Zaranek from <a href="https://arvados.org/">Arvados</a> helped me get a real world CWL <a href="https://github.com/arvados/arvados-tutorial/tree/main/WGS-processing">workflow 1</a> that uses streaming. It took a while to get used to the Arvados platform and I actually ran a much bigger workflow than intended on their “playground” public instance. I ended up using a single step from the workflow to keep it simple at the start and be able to run it locally on my computer. I’ve splitted it up into two individual components ( <a href="https://github.com/mhpopescu/toil-gsoc-tests/blob/2561e007167834ca777de8e2f2a7e03fb65aab2f/bwamem.cwl">first 1</a> and <a href="https://github.com/mhpopescu/toil-gsoc-tests/blob/2561e007167834ca777de8e2f2a7e03fb65aab2f/samtools-view.cwl">second</a>) so that I could test the streaming feature.</p> <p>There are 2 runners in Toil: pure python <code>toil</code> and <code>toil-cwl-runner</code>. The <code>toil</code> runner has functionality for file streaming. The proposed solution to enable file streaming for <code>toil-cwl-runner</code> is to make use of named pipes. I tested to see if this would work by simulating the behavior. I started with a simple <a href="https://github.com/mhpopescu/toil-gsoc-tests/blob/2561e007167834ca777de8e2f2a7e03fb65aab2f/fifo-cat.py">example</a> doing a <code>cat</code> command without toil, where the input file would be streamed using a named pipe. <a href="https://github.com/mhpopescu/toil-gsoc-tests/blob/2561e007167834ca777de8e2f2a7e03fb65aab2f/fifo-sam.py">Then</a> I streamed the input for the samtools step that was in the splitted workflow. Then I streamed the input and the output for the same step, running a python toil <a href="https://github.com/mhpopescu/toil-gsoc-tests/blob/2561e007167834ca777de8e2f2a7e03fb65aab2f/samtools-view-fifo-out.py">workflow</a>.</p> <p>Streaming the output looks similar to this:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>def writeOutputToPipe(self, fin, foutStream, fileStore): </span></span><span style="display:flex;"><span> with open(fin, &#39;rb&#39;) as fi: </span></span><span style="display:flex;"><span> while True: </span></span><span style="display:flex;"><span> data = fi.read() </span></span><span style="display:flex;"><span> if not data: </span></span><span style="display:flex;"><span> break </span></span><span style="display:flex;"><span> foutStream.write(data) </span></span></code></pre></div><p>And before running the job, another thread would start to run this function. Streaming the input is similar.</p> <p>Now that I tested that using named pipes could help streaming the files, I would look at how to implement this in the source of <code>toil-cwl-runner</code> itself: <code>cwltoil.py</code>. There are a few steps for what to do next:</p> <ul> <li>Investigate the block of code that parses the CWL file</li> <li>Check if <code>streamable</code> option is set and then maybe create a new flag in internal <code>toil</code> file structures</li> <li>Investigate the block of code that downloads the file</li> <li>Add the streaming functionality when <code>streamable</code> option is set</li> </ul>https://www.open-bio.org/events/bosc-2021/bofs/Thu, 17 Jun 2021 22:40:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2021/bofs/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/OBF-BoF-2018-25.jpg" alt=""></p> <h2 id="birds-of-a-feather-bofs">Birds of a Feather (BoFs)</h2> <p>Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of shared interest.</p> <p>BoFs at ISMB/ECCB 2021 will take place each day of the meeting except the last day, at the same time as the poster session (not ideal, we know–but there are only so many viable hours in the day), from 15:20-16:20 UTC. The BoFs that are relevant to BOSC attendees will be scheduled on Thursday, July 29 (the first day of BOSC) or Wednesday, July 28 (the day before BOSC). They will be listed here after the BoF proposal deadline (June 25)</p> <p>ISMB/ECCB 2021 attendees are also welcome to organize informal BoFs as table chats in the Cafe Connect.</p>https://www.open-bio.org/2021/06/17/working-on-a-data-science-project-with-the-open-bioinformatics-foundation-wellcomeml-part-one/Thu, 17 Jun 2021 17:09:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/17/working-on-a-data-science-project-with-the-open-bioinformatics-foundation-wellcomeml-part-one/<p><em>This post is guest-posted by Federica Trevisan, an OBF GSoC student with the Wellcome Trust. Cross-posted with Federica&rsquo;s blog:</em> <a href="https://federikovi.medium.com/my-google-summer-of-code-2021-c795dd0cc794">https://federikovi.medium.com/my-google-summer-of-code-2021-c795dd0cc794</a></p> <h1 id="my-google-summer-of-code-2021">My Google Summer of Code 2021</h1> <p>Well yes, I am part of GSoC 2021 💻☀️</p> <h2 id="what-is-google-summer-of-code">What is Google Summer of Code</h2> <p>In a nutshell, <a href="https://summerofcode.withgoogle.com/">GSoC</a> is a remote program founded in 2005, in which Google connects students and organisations during the summer break from classes. In this global program the students work with an open source organization on a 10 week programming project during their break from school. In this way students can gain technical experience on real projects by “flipping bits not burgers” <em>.</em> It’s also a competitive program; this year only the 27% of students who submitted at least a proposal got accepted.¹</p> <p><img src="https://miro.medium.com/max/1200/1*VcbPjJSKRG7gBedhocLFqg.jpeg" alt="Girl selfie with GSoC shirt after attending Google Developer Days Krakow in 2017">Selfie with GSoC shirt after attending Google Developer Days Krakow in 2017</p> <p>I learned about the GSoC when I had the opportunity to participate as a Women Techmakers member at the Google Developer Days in Krakow, Poland in September 2017. It was a period in which I decided to change the path of my academic career by pursuing a masters degree in Data Science after a bachelor degree in Economics.</p> <p>Yes, that’s me wearing a GSoC shirt in 2017 without knowing that I would actually participate in summer 2021. Things happen!</p> <p>Maybe the most difficult part is choosing the right project to work for (the second one is surely writing a strong and structured proposal, that will be the topic of another post). There are many organizations, 199 this year, with various and appealing projects, the important thing is finding one (or three, the maximum number of proposals you can submit) that fits with the interests and in which you can actively contribute. I have chosen Open Bioinformatics Foundation as I’m really interested in Bioinformatics and nature-inspired computing.</p> <h2 id="open-bioinformatics-foundation">Open Bioinformatics Foundation</h2> <p>The <a href="https://www.open-bio.org/">OBF</a> is an umbrella mentoring organization that promotes the practice and philosophy of open source software development within the biological research community. Under its umbrella there are other organizations that have projects involved in GSoC. The project I am taking part of is with the global charitable foundation <strong>Wellcome Trust</strong> with my super mentor <a href="https://github.com/aCampello">Antonio Campello</a>.</p> <h2 id="developing-wellcomeml-further-for-the-visualisation-of-academic-research-data"><strong>Developing WellcomeML further for the visualisation of academic research data</strong></h2> <p>The objective for my <a href="https://summerofcode.withgoogle.com/projects/#4986101921480704">GSoC 2021</a> is to create a standard interactive visualisation tool for the results of the clustering algorithm present in the WellcomeML library. <a href="https://github.com/wellcometrust/WellcomeML">WellcomeML</a> is a python package containing a set of utility functions that use machine learning for reading, processing, embedding and classifying academic text data like publications, grants, and other documents.</p> <p>During the community bonding period in which I met the mentors, got introduced to the staff of OBF and the staff of WellcomeML I virtually met also the other students working on differents OBF projects. Me and my mentor Antonio brainstormed some ideas for the TODO list of the project by creating a <a href="https://github.com/wellcometrust/WellcomeML/projects/2">Kanban board</a>.</p> <p>Since WellcomeML is mostly developed on UNIX/UNIX-based systems, installing and running on Windows is not as straightforward as we would expect. During the talk-with-mentors period before the proposal submission I already encountered an issue when running the WellcomeML library on my Windows laptop, that has been fixed <a href="https://github.com/wellcometrust/WellcomeML/issues/257">in this issue</a> with the help of the mentors. The correct way to install WellcomeML on Windows is:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-gdscript3" data-lang="gdscript3"><span style="display:flex;"><span>pip install torch<span style="color:#f92672">==</span><span style="color:#ae81ff">1.5</span><span style="color:#f92672">.</span><span style="color:#ae81ff">1</span><span style="color:#f92672">+</span>cpu torchvision<span style="color:#f92672">==</span><span style="color:#ae81ff">0.6</span><span style="color:#f92672">.</span><span style="color:#ae81ff">1</span><span style="color:#f92672">+</span>cpu <span style="color:#f92672">-</span>f https:<span style="color:#f92672">//</span>download<span style="color:#f92672">.</span>pytorch<span style="color:#f92672">.</span>org<span style="color:#f92672">/</span>whl<span style="color:#f92672">/</span>torch_stable<span style="color:#f92672">.</span>html </span></span></code></pre></div><p><em>and then</em>:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>pip install wellcomeml[deep-learning] </span></span></code></pre></div><p>Make sure you have the correct torch version before using pip!</p> <p>After engaging with some of the mentors, other issues² have been fixed, which will make other people’s lives easier in the future for developing on Windows. Here below there are the additional steps to take for installing and testing WellcomeML on Windows.</p> <p><strong>Requirements:</strong></p> <ul> <li>Updated Windows 10</li> <li>Visual Studio Build tools 2019 with Desktop Development with C++</li> <li>Python 3.8 installed at the root of your machine (the Makefile will look for it in C://Python38)</li> <li>Administration rights</li> </ul> <p><strong>Installation:</strong></p> <ul> <li>Clone and fetch WellcomeML repository from GitHub</li> <li>Install Cygwin64</li> <li>Install make through Cygwin64 with <code>choco install make</code></li> <li>From Cygwin64 change directory <code>cd</code> to the path of the folder where the Makefile is</li> <li>Run the following Makefile <code>make virtualenv</code></li> </ul> <p><strong>Testing:</strong></p> <ul> <li><code>make test</code> running tests might take a bit of time on the first run, as you will need to download some models and build a few libraries.</li> </ul> <p>Now that I have a tested and running library in my laptop I can’t wait to start building the visualisations for the clustering algorithms. 💻☀️</p> <h2 id="notes">Notes:</h2> <ol> <li>Statistics from GSoC’21: 1292 students were selected from a total of 4795. <a href="https://opensource.googleblog.com/2021/05/google-summer-of-code-2021-students-are.html">https://opensource.googleblog.com/2021/05/google-summer-of-code-2021-students-are.html</a></li> <li>Instruction for Windows thanks to <a href="https://github.com/wellcometrust/WellcomeML/pull/302/files">https://github.com/wellcometrust/WellcomeML/pull/302/files</a></li> </ol>https://www.open-bio.org/2021/06/17/eight-incredible-gsoc-students-for-the-obf-this-year-%E2%98%80%EF%B8%8F/Thu, 17 Jun 2021 17:05:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/17/eight-incredible-gsoc-students-for-the-obf-this-year-%E2%98%80%EF%B8%8F/<p><img src="https://www.open-bio.org/wp-content/uploads/2021/06/image-8-1024x591.png" alt="sixteen grinning faces of GSoC mentors and students for the OBF.">OBF students and mentors at an OBF kickoff call</p> <p>Every year the OBF applies to participate as a mentoring organisation for <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a>, a paid work experience program where students get the chance to do paid work on an open source project and open source organisations host the students to work on their projects. This year, eight projects have participated under the OBF umbrella - read more about these fantastic students and their work below:</p> <h2 id="enabling-and-prototyping-javascript-visualization-in-qt-based-viewer-toppview">Enabling and prototyping JavaScript visualization in QT-based viewer TOPPView</h2> <p><strong>Student:</strong> Dhanmoni Nath <strong>Mentors:</strong> Julianus Pfeuffer, Timo Sachsenberg</p> <p>OpenMS’ TOPPView tool is used for mass-spectrometry data analysis. However, TOPPView is lacking some often requested high-level summary views of results that are produced by OpenMS’ other tools. Although we have other open-source libraries that provide this feature, they are written in JavaScript, and re-implementing them in C++ to integrate into TOPPView would be tedious.</p> <p>This project aims to solve this problem by enabling JavaScript visualizations in TOPPView using Qt’s QtWebEngine module.</p> <p><a href="https://summerofcode.withgoogle.com/projects/?sp-page=2#4803704407982080">https://summerofcode.withgoogle.com/projects/?sp-page=2#4803704407982080</a></p> <h2 id="gtfbase---a-curated-resource-of-multispecies-genomic-regions">GtfBase - A curated resource of multispecies genomic regions</h2> <p><strong>Student:</strong> Tanishq Gupta <strong>Mentors:</strong> Saket Choudhary, Amal Thomas</p> <p>Each genome has some common features: exons that make the mRNA, CDS, and UTRs. There are a lot of resources available that provide access to these features in the form of General Transfer Format (GTF) files. While GTF files are by themselves comprehensive, a lot of analysis is focused on individual features and these analyses often rely on a BED file, a more focused variant of GTFs. Though it is trivial to obtain a BED file from GTF, currently there are no resources that provide ready access to BED files.</p> <p>We have a collection of scripts currently available as part of gencode_regions repository: <a href="https://github.com/saketkc/gencode_regions">https://github.com/saketkc/gencode_regions</a> that tries to address this gap. For GSoC2021, our goal is to generalize these scripts into a usable tool that can be used to generate BED files for a variety of use cases and serve as a readily updated database of BED files that will keep in sync with ENSEMBL’s GTF releases.</p> <p><a href="https://summerofcode.withgoogle.com/projects/#5730763485478912">https://summerofcode.withgoogle.com/projects/#5730763485478912</a></p> <h2 id="developing-wellcomeml-further-for-the-visualisation-of-academic-research-data">Developing WellcomeML further for the visualisation of academic research data</h2> <p><strong>Student:</strong> Federica Trevisan <strong>Mentors</strong>: Jeff Uren, Elizabeth Gallagher, Antonio Campello</p> <p>WellcomeML is a python library with functions that use machine learning for reading, processing, embedding, extracting entities and classifying academic text data like publications, grants, and other documents. However, the visualisation modules of WellcomeML are scarce and the need of developing further visualisation features for the library has emerged.</p> <p>In this specific case the objective is to create a standard interactive visualisation tool for the outputs of <a href="https://github.com/wellcometrust/WellcomeML/issues/221">wellcomeml.ml.clustering</a>. The current state of the art of WellcomeML provides an ad-hoc visualisation built from scratch for each algorithm applied. In this way the codebase is very specific to the single algorithm function and doesn’t provide a standardized output for the visualisation of the results.</p> <p>The aim of this GSoC project is then to standardize the way the results are presented; an interactive dashboard, function or class for showing the clustering results for each project in a self explanatory way.</p> <p><a href="https://summerofcode.withgoogle.com/projects/#4986101921480704">https://summerofcode.withgoogle.com/projects/#4986101921480704</a></p> <h2 id="development-of-a-user-interface-to-visualise-vep-data-using-nextprot-tools">Development of a user interface to visualise VEP data using neXtProt tools</h2> <p><strong>Student:</strong> Shrey Sachdeva <strong>Mentors:</strong> Kasun Samarasinghe, Lydie Lane</p> <p>Several open source tools, such as the Ensembl Variant Effect Predictor (VEP), have been developed to predict the structural and functional effects of variants.</p> <p>The VEP tool has a number of plugins, including a neXtProt plugin that was released as a command line. The goal of this project is to develop a user interface using the neXtProt tools, to visualise the predicted variant effect output for all variants within a neXtProt entry.</p> <p><a href="https://summerofcode.withgoogle.com/projects/#5720209559650304">https://summerofcode.withgoogle.com/projects/#5720209559650304</a></p> <h2 id="implementations-of-avx-512-functions">Implementations of AVX-512 functions</h2> <p><strong>Student:</strong> Kunwar Maheep Singh <strong>Mentors:</strong> Evan Nemerson, Jun Aruga</p> <p>SIMD instruction intrinsics provide users with extreme control over vectorization of code, but the problem with using them is that they are not very portable. This is because different vendors provide their own API’s to match the instruction sets implemented in their hardware. e.g. MMX, SSE2, AVX-512, etc. on Intel x86, Altivec and VSX on PowerPC, and NEON, MVE, and SVE/SVE2 on ARM.</p> <p>SIMDe is a header only library which provides portable implementations of various SIMD APIs on unsupported hardware using instructions which are available, minimizing or even eliminating performance losses.</p> <p>AVX-512 has added many new types of instructions like conflict detection and prefetch which give more vectorizing potential to developers. A combination of these new instructions with new compilers can help vectorize code which could not be vectorized before.</p> <p>The aim of this project is to implement multiple families of AVX-512 intrinsics for SIMDe.</p> <p><a href="https://summerofcode.withgoogle.com/projects/#4790187072159744">https://summerofcode.withgoogle.com/projects/#4790187072159744</a></p> <h2 id="implementation-of-neon-functions-in-simde">Implementation of NEON functions in SIMDe</h2> <p><strong>Student:</strong> Atharva Nimbalkar <strong>Mentors:</strong> Evan Nemerson, Zhi An Ng</p> <p>SIMD stands for Single Instruction Multiple Data. It’s a class of parallel computers that performs the same instruction on multiple data points simultaneously. SIMD can be very advantageous to multimedia applications.</p> <p>SIMDe is a library that provides portable implementations of SIMD Intrinsics on hardware that don’t natively support them, while still taking advantage of SIMD when possible. It allows you to call NEON functions on x86, or SSE functions on ARM, etc.</p> <p>This project aims to add portable implementations of many more NEON functions in SIMDe. Along with native fallbacks for other popular architectures, which would allow NEON SIMD intrinsics to be used on WASM, AVX-512 etc.</p> <p><a href="https://summerofcode.withgoogle.com/projects/#4927690232037376">https://summerofcode.withgoogle.com/projects/#4927690232037376</a></p> <h2 id="design-and-implementation-of-code-is-science-front-end-using-reactjs">Design and implementation of Code is Science front-end using ReactJS</h2> <p><strong>Student</strong>: Isaac Miti <strong>Mentors</strong>: Yo Yehudi, João Paulo Tiz</p> <p>The Code is science website is currently built using vanilla HTML, CSS and JavaScript with Ruby as part of its backend. The current frontend needs to be redesigned and updated.</p> <p>This project aims to design and develop the code is science frontend using ReactJS UI library. The project development will follow frontend best practices using Google’s Material Design guidelines.</p> <p><a href="https://summerofcode.withgoogle.com/projects/#4963542471540736">https://summerofcode.withgoogle.com/projects/#4963542471540736</a></p> <h2 id="data-streaming-in-scientific-workflows-implementation-for-toil">Data streaming in scientific workflows, implementation for Toil</h2> <p><strong>Student:</strong> Mihai Popescu <strong>Mentors:</strong> Michael R. Crusoe, Lon Blauvelt</p> <p>Toil is an open-source Python workflow engine that lets people write data analysis pipelines in Python, CWL, and WDL. Toil has support for common workflow language (CWL), an open standard for describing analysis workflows.</p> <p>This project aims to implement data streaming to speed up the analysis by avoiding slow disk/storage IO and speeding up the start of tool execution when it isn’t required to wait for data to download. The main focus is to implement this first in AWS S3.</p> <p><a href="https://summerofcode.withgoogle.com/projects/6469533377757184">https://summerofcode.withgoogle.com/projects/6469533377757184</a></p>https://www.open-bio.org/2021/06/15/birds-of-a-feather-at-bosc-2021/Tue, 15 Jun 2021 19:06:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/15/birds-of-a-feather-at-bosc-2021/<p><img src="https://www.open-bio.org/wp-content/uploads/2021/06/partridge-and-pears-stamp.png" alt=""></p> <p>Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of shared interest.</p> <p><a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/bof/">BoFs at ISMB/ECCB 2021</a> will take place each day of the meeting except the last day, at the same time as the poster session (not ideal, we know&ndash;but there are only so many viable hours in the day), from 15:20-16:20 UTC. We recommend that you choose either Thursday, July 29 (the first day of BOSC) or Wednesday, July 28 (the day before BOSC).</p> <p>Any ISMB/ECCB participant is welcome to propose a BoF! All you need is a topic, a leader, and a brief description. <strong>Submit your BoF proposal at <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/bof/">https://www.iscb.org/cms_addon/conferences/ismbeccb2021/bof/</a> no later than June 25.</strong></p> <p>If you&rsquo;re organizing a BOSC-related BoF, <a href="mailto:obf-bosc@googlegroups.com">let us know</a>! We&rsquo;ll list it on our website ( <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">/events/bosc-2021/bosc-2021-schedule/</a>) and tweet about it!</p>https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/Fri, 11 Jun 2021 12:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/11/bosc-obf-2021-event-support-fund/<p>Thanks to funding from our <a href="https://www.open-bio.org/events/bosc-2021/sponsors/">sponsors</a>, we are opening a special call for applications to the <a href="https://docs.google.com/forms/d/e/1FAIpQLSefSJg9n99uZUPLxsvbm1PkV1NlH36CYFniCRxdgreefIuPgg/viewform">BOSC-OBF Event Support Fund</a>. This fund aims to increase participation of members from groups otherwise underrepresented in BOSC or in bioinformatics community events in general, including but not limited to underrepresented demographic groups (country of residence and citizenship), ethnic background (historically underrepresented and other minority groups), career stages, gender identity and expression, people with disabilities and members from low income/resource organisations.</p> <p>A limited number of qualified applicants will be chosen to receive <strong>free registration for ISMB/ECCB 2021</strong>. No other financial support (for example, for internet access or headphones) will be included.</p> <p>The <strong>application</strong> <strong>deadline is 30 June 2021</strong>, and decisions will be sent out by 8 July 2021. Apply at <a href="https://forms.gle/aDVSHpq7Gs46CNDb6">https://forms.gle/aDVSHpq7Gs46CNDb6</a>.</p> <p>We hope you’ll join us at BOSC! For more #BOSC2021 news, <a href="https://twitter.com/OBF_BOSC">follow us on Twitter</a>!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/06/2021-sponsors-horiz-1024x287.png" alt="2021 BOSC Sponsors"></p>https://www.open-bio.org/2021/06/07/sona-charles-glbio2021/Mon, 07 Jun 2021 09:16:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/07/sona-charles-glbio2021/<p><em>The</em> <a href="https://www.open-bio.org/"><em>Open Bioinformatics Foundation (OBF)</em></a> <em>Event Fellowship program supports and encourages diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. <strong>Sona Charles</strong>, a Scientist (Bioinformatics) at ICAR-Indian Institute of Spices Research, India, was supported to participate in the</em> <a href="https://www.iscb.org/glbio2021"><em>Great Lakes Bioinformatics (GLBIO) 2021 Conference</em></a> <em>by this award granted to her in the application round-1 of 2021. Find more information</em> <a href="https://www.open-bio.org/travel-awards/"><em>here.</em></a></p> <p>In this pandemic stricken world when all conferences are taking place virtually and don’t require traveling, it has become more accessible for international participants like me. However, the cost for registration, video-conferencing accessories and childcare remain the same. Luckily, I came across the Open Bioinformatics Foundation Event Fellowship, when I was hoping to attend the Great Lakes Bioinformatics (GLBIO) 2021 Conference. I had already submitted a poster entitled “ <a href="https://doi.org/10.5281/zenodo.4892737">Sequence-Based Prediction of Phytophthora- Host Interaction Using Machine Learning Methods</a>” to the conference, which was accepted. I went ahead and applied for the event fellowship at Open Bioinformatics Foundation for its first round of 2021. Two weeks later (after the application review phase), I was informed by the Chair of OBF Event Fellowship that I was awarded the fellowship.</p> <p><strong>Day 1 of GLBIO 2021</strong></p> <p>The GLBIO conference commenced on 13 May 2021 with the workshops, which is undoubtedly my favourite attraction for attending a conference. Out of all the options for workshops, I chose two: (1) Machine Learning on Microbiome Data: Theory and Practice and Introduction to Deep Learning, and (2) Creating Neural Networks in Python and R. All the code for the workshop as well as the required packages were shared much earlier so that it would be easy for us to follow. As a beginner in Machine Learning, the two workshops enabled me to gain more knowledge on the topics in which I anticipate working in the coming days.</p> <p><strong>Day 2 of GLBIO 2021</strong></p> <p>The keynote talk “Variable Selection and Interpretability in ‘Black Box’ Statistical models” took place on 14 May 2021 by Dr Lorin Crawford (screenshot of his title slide below). He introduced the various concepts in Biologically Annotated Neural Networks and their applications in Multiscale genomic inference.</p> <p><img src="https://lh4.googleusercontent.com/WeQrTCiB2bemdNwLL-5FM79AzlwyPtZCoXnminBihW6i6rhaLigy9tXqkTpHfUOkijtLEOmALm7Oqt5s3ZHYr5vGaVWW7A36Mn2q5YEyCE1_gJ56xKcSkvz69oLGEA" alt=""></p> <p>On the same day, I attended four sessions on Knowledge Guided Machine Learning (KGML) in Bio. As a beginner in this area, I really appreciated this session and wanted to learn more about the applications. The session-1 included two talks on predicting the promiscuity of enzymes and Predicting RNA Pseudouridine Sites in Nanopore Sequencing Data. The session-2 included the talks “Knowledge-based Meta-Learning for Cancer Prediction and Survival Analysis” and “Learning to align with differentiable dynamic programming” by Aidong Zhang and Michiel Stock respectively. The session-3 had three informative talks on new machine learning approaches for estimating the functional consequence of mutations in diverse human populations, for diagnostic screening of cardiovascular disease using gut microbiome data and for gut microbiome-based detection of inflammatory bowel diseases. The final session included three talks: (1) Gene signatures of COVID-19 infection severity identified using graph convolutional neural networks on single-cell RNA-Seq data, (2) Machine learning on knowledge graphs and ontologies, and (3) Supervised prediction of ageing-related genes from a weighted dynamic protein-protein interaction network. An EDI panel survey discussion was held between the sessions followed by the poster session. Day 2 of the conference was highly informative and I had a lot of take-home messages and ideas.</p> <p><strong>Day 3 of GLBIO 2021</strong></p> <p>Day 3 started with the keynote lecture titled “Methodological advancements to improve metagenomics for surveillance of antimicrobial resistance” by Dr Noelle Noyes (screenshot from her talk).</p> <p><img src="https://lh4.googleusercontent.com/y3iL0NIlPhJFqjIvLeK8x553_Zlz5_stKXGwU8pznhXzJmYmRQlq2KO5-GZzqT3z7qslQr6fQFWO2pSe_wMBZQsOpqK-Y1jsA-nGfG1w4aSbNfS0JRBagemy3sjnxg" alt=""></p> <p>Metagenomics is one of the areas of interest in my research institute and I attended the Microbiome and Multi-omics analysis sessions. I also attended two sessions on Algorithms and Machine Learning. Another keynote by Michael Osterholm attracted the attention of researchers interested in SARS-Cov2 epidemiology.</p> <p><img src="https://lh3.googleusercontent.com/E0I0-6uZ-72zSTn3dj8R7WXxKlft0krCa9_k7RDLUHhGzflmQyDjvvXQ3WUA9RqYOHurfCu_f9aEyUmkbFtu1gB8Mvv66G0OCM1YYAgm2niq3BJdqgq_x34ECmzUAA" alt=""></p> <p>It was followed by a session on SARS-CoV2 analysis and a session on proteomics and metadata. The last keynote of GLBIO2021 was on Predicting the evolution of syntenies with closing remarks by Aïda Ouangraoua.</p> <p>On Day-3, a second poster session was organised where I presented my work titled “ <a href="http://doi.org/10.5281/zenodo.4892738">Sequence-based prediction of Phytophthora-host interaction using machine learning</a>” (Sona Charles, &amp; Sreekumar J., 2021, DOI: 10.5281/zenodo.4892738). I got to interact with many researchers and receive feedback from a global audience working in the area of machine learning.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/06/image-2.png" alt="">Screenshot of the top section of my poster titled: Sequence-based prediction of Phytophthora-host interaction using machine learning, available on Zenodo under CC-BY 4.0 license, <a href="http://doi.org/10.5281/zenodo.4892738">http://doi.org/10.5281/zenodo.4892738</a></p> <p>Overall the conference was excellent and all data of the conference will be available as an open source resource on YouTube on the <a href="https://www.youtube.com/channel/UCN9kqT7pfOzZddPJHqWSuyA">ISCB TV channel</a>. I am extremely thankful to the OBF for funding my participation related cost for the conference. I will be able to cover my registration and connection related costs. Since the conference was conducted during lockdown it would have been practically impossible for me to attend the conference if the childcare grant was not awarded for the entire duration of the conference. Since the time zones were overlapping from 21:30 to 03:00 Indian Standard Time (IST), child care was the most essential resource for me for attending the conference throughout the night.</p> <p>I express my heartfelt thanks for the opportunity to present my research at a reputed international conference with the support of the OBF Event Fellowship. As part of this fellowship, I will soon be depositing my work in my GitHub repository, developed under a CC-BY license ( <a href="https://github.com/sonacharles">GitHub</a>).</p>https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/Sun, 06 Jun 2021 01:57:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/<p>The BOSC 2021 talks and poster videos are now <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">available on YouTube</a>!</p> <h4 id="bosc-2021-schedule-at-a-glance">BOSC 2021 schedule at a glance</h4> <p>(Scroll down to see the whole schedule.)</p> <h4 id="bosc-2021-talk-schedule">BOSC 2021 Talk Schedule</h4> <p>The schedule below includes keynote talks, talks from submitted abstracts, and relevant Birds of a Feather. (Scroll down to see the whole schedule.)</p> <p>For more details, including short abstracts, see the <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/tracks/bosc">ISMB/ECCB BOSC schedule</a>.</p> <p><strong>30-July-2021: The BOSC 2021 talks are now <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">available on YouTube</a> (and we will make poster videos available soon as well)!</strong></p> <p>For more details, including short abstracts, see the <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/tracks/bosc">ISMB/ECCB BOSC schedule</a>.</p> <h4 id="posters">Posters</h4> <p>Below are the posters accepted to BOSC 2021 from submitted abstracts. For more details, including short abstracts, see the <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/posters.php?track=BOSC&amp;session=E#search">ISMB/ECCB poster schedule</a>.</p>https://www.open-bio.org/2021/06/03/biopython-1-79-released/Thu, 03 Jun 2021 23:03:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/03/biopython-1-79-released/<p>Biopython 1.79 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.79">PyPI</a>.</p> <p>This is the final release supporting Python version 3.6. It also supports Python versions 3.7, 3.8, and 3.9, as well as PyPy 3.6.1 v7.1.1.</p> <p>The major changes in this version are listed below:</p> <p>- The <code>Seq</code> and <code>MutableSeq</code> classes in <code>Bio.Seq</code> now inherit from the same base class, ensuring their mutual consistency. In addition, both classes now store sequence data as <code>bytes</code> and <code>bytearray</code> objects, respectively.</p> <p>- Empty or unknown sequences can now be created directly by passing <code>None</code> to the <code>Seq</code> class, instead of using <code>UnknownSeq</code>. This latter class is now deprecated and will be removed in a future version of Biopython.</p> <p>- A new module <code>Bio.PDB.SASA</code> implements the Shrake-Rupley algorithm to calculate solvent accessible areas natively, without requiring third-party tools such as <em>DSSP</em> or <em>NACCESS</em>.</p> <p>- Other minor improvements to the <code>Bio.PDB</code> module include a new <code>center_of_mass()</code> method to calculate the center of mass or center of gravity of any Entity subclass (e.g. Structure, Chain, or Residue).</p> <p>- Changes in the KEGG <code>KGML_Pathway</code> module now produce output files compliant with KGML v0.7.2. In addition, <code>Bio.UniProt.GOA</code> now parses GPI files version 1.2.</p> <p>As in recent releases, more of our code is now explicitly available under either our original “ <em>Biopython License Agreement</em>“, or the very similar but more commonly used “ <em>3-Clause BSD License</em>“. See the <code>LICENSE.rst</code> file for more details.</p> <p>Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the <code>black</code> tool.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <p>- Damien Goutte-Gattat - Gert Hulselmans - João Rodrigues - Markus Piotrowski - Sergio Valqui - Suyash Gupta - Vini Salazar (first contribution) - Leighton Pritchard</p>https://www.open-bio.org/2021/05/28/bosc-late-poster-deadline-june-3/Fri, 28 May 2021 22:17:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/05/28/bosc-late-poster-deadline-june-3/<p><strong>There’s still a chance to</strong> <a href="https://www.open-bio.org/events/bosc-2021/submit/"><strong>submit your abstract</strong></a> <strong>in the Late Poster round, which closes June 3 at 11:59pm ET!</strong></p> <p><strong><em>What about late-breaking lightning talks?</em></strong> Unfortunately/fortunately, we got so many high-quality abstracts in the early round, we were not able to save any talk slots for the late round. Talk slots will open up only if some early-round speakers decide not to attend the conference.</p> <p><strong><em>Abstract format.</em></strong> To be considered for a poster, you only need to submit a 200-word short abstract. However, you should feel free to add a PDF (2 pages max) that better describes your work! Your PDF should include the title, author name(s), open source license, and code or project URL (even though this information is also requested on the submission form). Accepted abstracts are published on the BOSC website as-is.</p> <p><strong><em>Registration.</em></strong> This year, BOSC is a track (also called COSI) of <a href="https://www.iscb.org/ismbeccb2021/">ISMB/ECCB 2021online</a>. There is no partial registration option; BOSC participants must <a href="https://www.iscb.org/ismbeccb2021-registration">register for the full ISMB/ECCB meeting</a>.</p> <p><strong><em>Fee assistance.</em></strong> With help from our <a href="https://www.open-bio.org/events/bosc-2021/sponsors/">sponsors</a>, we are able to offer registration fee assistance to some presenters. If the cost of registration is a barrier to your participation, just check a box on the abstract submission form to request registration fee assistance!</p> <p><em><strong><a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/posters.php">How posters will work</a></strong>.</em> Authors whose poster abstracts are accepted will be able to upload content to the ISMB/ECCB virtual conference platform between July 19-23, including your full abstract, PDF of your poster (it doesn’t have to be poster-sized!), and a short (max 7 minutes) talk as a .mov or .mp4 file. Poster presenters will be able to host “video demo rooms” (with up to 15 participants) and engage in live Q&amp;A with attendees during the poster session. The BOSC poster session is from 15:20-16:20 UTC on Thursday, July 29.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> Join us on Slack! Our BOSC Slack workspace is open to the community! </span></span><span style="display:flex;"><span> Follow us on Twitter! @OBF_BOSC, #BOSC2021 </span></span></code></pre></div>https://www.open-bio.org/2021/05/12/request-for-comments-on-coc-draft/Wed, 12 May 2021 16:14:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/05/12/request-for-comments-on-coc-draft/<p>The OBF is committed to providing a harassment-free and respectful environment for all members of our community. To ensure that we are clearly describing norms, rules, and recommended practices for all our participants and members, we have provided a first draft of the OBF Code of Conduct and shared it recently in our <a href="https://github.com/OBF/newsletter/blob/master/newsletters/2021-02.md">newsletter</a>.</p> <p>You can find the draft together with our request for comments on this <a href="https://github.com/OBF/obf-docs/pull/78">pull request</a> (see a <a href="https://github.com/OBF/obf-docs/blob/malvikasharan-CoC-draft/code-of-conduct/README.md">preview here</a>). If you have not already, please take a few minutes to add your comments in this pull request by <strong>June 4th, 2021</strong>.</p> <p>The final draft of the Code of Conduct will be put up to a vote among all OBF members. With your feedback, we will ensure that it represents your voice and provides clear guidelines about how to report incidents and describes how reports will be handled.</p>https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/Tue, 11 May 2021 17:08:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/<p>The following outlines a potential new grant programme, subject to approval by the OBF membership in a formal vote, which the OBF board would hope to launch this year.</p> <h2 id="motivation">Motivation</h2> <p>In 2016, the OBF introduced a “Travel Fellowship” to help individuals attend meetings, aiming to improve diversity in the bioinformatics community. Awardees were reimbursed (with receipts) after the event in which they participated, with a standard cap of USD $1000. The Travel Fellowship was later renamed the “Event Fellowship” reflecting that with the COVID-19 pandemic (and hopefully longer-term changes in scientific conferences to promote the participation of diverse members in online events and reduce carbon emissions), attending events no longer automatically means travelling in person.</p> <p>This fellowship and some of the applications to it have drawn our attention to the fact that for similar amounts of money, we may be able to help grassroots projects running event(s) in their own communities. It would be practical if we do not have to handle itemised receipts for reimbursement, as that would be a significant time overhead for volunteer board members. Instead, the proposal is to follow the existing model of sponsoring conferences whereby the organisers of the event OBF has agreed to support to invoice us an agreed amount (e.g. USD $1000) before the event, and in return our logo appears on their event webpages and materials, acknowledging our support. Where appropriate, applicants will be encouraged to become OBF Affiliate Projects.</p> <p>This mechanism will require the event organisers to have some sort of bank account or fiscal sponsor (e.g. a university staff member’s budget, a local hackerspace) where we can transfer the funds.</p> <p>The scope explicitly excludes well-established organisations, which are able to solicit donations and sponsorships on their own. Since some of the OBF’s funds are donated to us by other organisations, we can hopefully be a useful intermediary between our supporters and smaller efforts globally.</p> <h3 id="scope">Scope</h3> <p>Single events like a scientific meeting, small conference, training workshops, hackathon, or time-limited series like monthly seminars. An organisation can receive only one financial award per calendar year, to ensure that we can offer this support to the wider community.</p> <p><em>Essential</em>:</p> <ul> <li>Strong bioinformatics component</li> <li>Strong Open Source / Open Science component</li> <li>Code of Conduct</li> </ul> <p><em>Desirable:</em></p> <ul> <li>Applying for OBF affiliate membership (need indicative time scale). If the group is already an affiliate member, rather than using this scheme, please email the board directly to discuss direct funding.</li> <li>The event that is not yet well-established or well-funded</li> <li>Promotes diversity of bioinformatics participants</li> <li>Organisers largely based in countries on the World Bank’s low or lower-middle-income list</li> <li>Meeting materials will be shared under an open licence (e.g. talk slides/videos under CC-BY)</li> </ul> <p><strong>What is not in the scope:</strong></p> <p>Well established groups able to attract their own donors and sponsors directly (e.g. ISCB, The Carpentries)</p> <h3 id="budget">Budget</h3> <p>An initial commitment of $10,000 over two years as an evaluation period, with an individual grant award cap of USD $1000 per event or $2000 for an event series.</p> <h3 id="logo-and-text">Logo and text</h3> <p>We would need a standard logo/image banner, URL, and perhaps text for the event to use.</p> <h3 id="argument-for">Argument For</h3> <p>With this scheme, OBF will be able to offer benefits to community projects that are aligned with OBF’s mission but are working on a low budget or without any organisational support. This will be an opportunity to reach the demographic and communities that are not yet served by OBF but that promote Open Source and Open Science practices. Furthermore, by encouraging new projects to become affiliated members of OBF, we will enhance the representation of diverse bioinformatics projects through the OBF platform. As a volunteer organisation that holds funds earned by volunteer labour (in particular via conference fees and Google Summer of Code), it helps to reassure OBF volunteers that funds earned through their efforts are being put to good use empowering communities that have aligned goals.</p> <h3 id="argument-against">Argument Against</h3> <p>This proposal is a deliberate expansion on where the OBF spends its income, the vast majority of which is earned through the volunteer labour of OBF community members, including those helping to organize BOSC and serving as mentors and administrators in the OBF’s Google Summer of Code participation. The OBF’s assets and income are finite, and thus funds given to projects, events, or initiatives outside of the OBF umbrella are no longer available to spend on OBF members or membership projects. In other words, for the funds committed to this program, the assumption is that frequently more meritorious recipients and/or causes can be found outside of the OBF umbrella, in the scope of this program, than within OBF’s umbrella, in the full scope of OBF’s mission. There’s little evidence supporting this assumption, and until there is, income earned through OBF volunteer labour should be disbursed within the OBF community (which, as it includes BOSC and its attendees, is already broadly defined).</p> <h2 id="process">Process</h2> <p>What happens next? This post outlines our vision; next, we will ask the OBF membership if they approve of the idea in principle. We invite feedback via this <a href="https://github.com/OBF/obf-docs/issues/86">GitHub issue</a> or emails to the board by Friday 4th June 2021. If the membership approves, the exact policy wording will be drafted as another OBF policy document on GitHub for the board to approve.</p>https://www.open-bio.org/2021/05/09/introducing-the-org-committee/Sun, 09 May 2021 21:07:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/05/09/introducing-the-org-committee/<p>BOSC is organized entirely by volunteers. We are lucky to have these amazing people on the Organizing Committee this year!</p> <hr> <p><img src="https://lh3.googleusercontent.com/MGqlLng2xb8rlZsOYSgsHdNrLBSIGtqXSon8Dsf5YuE_Ql6eUX7455qn7O7NPXofMow4jpTKxRbcHM7-0QyLyD7bwBDM_GBh03p7TOqDIGX98efpIXM6cNOgIqFFkdw7yUbO813f" alt=""></p> <p><strong>Jason Williams</strong>( <a href="https://twitter.com/JasonWilliamsNY">@JasonWilliamsNY</a>) is a new member of the BOSC Organizing Committee, though he’s been a BOSC participant and an abstract reviewer for years. Jason was a BOSC panelist in 2015 on a <a href="https://www.open-bio.org/wiki/BOSC_2015_Panel">panel about increasing diversity in open source bioinformatics</a>, and again in 2018 for a <a href="https://gccbosc2018.sched.com/event/Dup7/panel-training-and-documentation-in-bioinformatics">panel about training and documentation in open source bioinformatics</a>.</p> <p>Jason works for Cold Spring Harbor, where he’s the Assistant Director of External Collaborations for the DNA Learning Center and Lead for CyVerse Education, Outreach, and Training. Jason provides training and support to scientists and educators, as well as serving on several committees and boards for projects that advance science and science education including the Software Carpentry Foundation. In his spare time, Jason plays the cello and whips up amazing multi-course dinners. Read more about Jason and his CSHL journey <a href="https://www.cshl.edu/labdish/a-science-career-path-jason-williams/">here</a>.</p> <p><img src="https://lh5.googleusercontent.com/Vedhi40Mmwm5Iugofx4hBpAwQi5oQ_0vB46Bqd16lScHIS-iIg5wgOKQONRddZ9TSBjgyKFOncH7WSki0Hsn5bJ5etRVz6fUpMN02cBXcrSvVP2z95tOFjGFG4qh0xvw7yAdZLtY" alt=""></p> <p><strong>Malvika Sharan</strong>( <a href="https://twitter.com/MalvikaSharan">@MalvikaSharan</a>)joined the BOSC Organizing Committee in 2021. Malvika was elected to the Board of the Open Bioinformatics Foundation in 2019, where she runs the OBF’s Event Fellowship program. Malvika is the Community Manager for the Turing Way at the Alan Turing Institute, and a Co-Founder of Open Life Science, a mentoring and training program focusing on open science projects. She is also a fellow of the Software Sustainability Institute.</p> <p>Malvika is known as a community builder, open science educator and facilitator of open source projects, and is passionate about enabling collaborative culture, accessibility and inclusive practices in research. She is a frequent speaker on these topics, at BOSC and beyond. When she’s not traveling to conferences, Malvika loves to learn about food history. Read more about Malvika at her <a href="https://malvikasharan.github.io/">website</a>.</p> <p><img src="https://lh4.googleusercontent.com/QCPBRCPYGgVjKKlVc1PfurdbBa7qx8MmxPNUnVRqCiprDCMhrr0C9GmrPznHeTK8esDVS5vmgGwOUZo7T2qeZR2ncfZxvk7TycAJtYQeAfAB1lP-bTnW_No-g6oIusomJvpar-zq" alt=""></p> <p><strong>Monica Munoz-Torres</strong>( <a href="https://twitter.com/monimunozto">@monimunozto</a>) has been part of the BOSC Organizing Committee since 2017. She has also chaired several BOSC panels: <a href="https://www.open-bio.org/wiki/BOSC_2015_Panel">Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community</a> (2015), <a href="https://www.open-bio.org/wiki/BOSC_2016_Panel">Growing and sustaining open source communities</a> (2016), and <a href="https://www.open-bio.org/wiki/BOSC_2017_Panel">Open Data: Standards, Opportunities and Challenges</a> (2017).</p> <p>Moni is an Associate Research Professor at the University of Colorado School of Medicine. She is Director of Operations for NIH/NCI’s Center for Cancer Data Harmonization and Program Director for the Phenomics First Resource - an NHGRI CEGS. Moni has a strong background in biocuration; she has served as the Chair of the International Society for Biocuration (ISB) and a Steering Committee member for the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5k Initiative).</p> <p>In her spare time, Moni co-leads the Healdsburg <em>Citizens Organized to Prepare for Emergencies (COPE)</em>, a neighborhood safety organization in Sonoma County, CA, and loves to take care of her garden roses.</p> <p><img src="https://lh3.googleusercontent.com/1-JTLgF441qSon3nNb-fgqxVtCANASjT-5EQs_9mRyC7zF_YrmDlRMxua-xwuCju1qNOBx9icl5wIyR7_rMHGLVBERUjyHUBG5hKvC7Zml96ergw6rP4kE2KgEKFvOf9dKnd5dpW" alt=""></p> <p><strong>Karsten Hokamp</strong> joined the Organizing Committee for BOSC 2015, which was held in his hometown, Dublin, Ireland. In 2020, Karsten was the force behind BCC2020’s move to an online platform called Remo.co, designing every detail of the virtual conference space, down to the decorations in the online “party room”. Karsten was the Technology Chair for 2020 and is the co-chair for 2021.</p> <p>Karsten holds the role of Bioinformatics Research Officer at Trinity College Dublin, where he looks after several open source bioinformatics software packages. He likes to unwind with a swim in the sea or a vigorous game of tennis and wouldn’t refuse a freshly pulled pint of stout afterwards.</p> <p><img src="https://lh3.googleusercontent.com/Co57bDw0VbF20f7Utz55MW6dz53GjePR7eGfNZIJu_h8WG9ydtXilJC5mzCuV8lWaaXPbt-nvpPKsr0AXEs4bb2Kz1kK_z1YcIJ4aJCEu9F4fqDi7FT4m-4zuQKAHGn73JiSb8p-" alt=""></p> <p><strong>Chris Fields</strong>( <a href="https://twitter.com/cjfields">@cjfields</a>) has been on the BOSC Organizing Committee since 2011. He’s also the Secretary of the Open Bioinformatics Foundation.</p> <p>The Director of the High Performance Computing in Biology Group at the University of Illinois Champaign-Urbana, Chris is also known as one of the founders and lead architects of BioPerl, one of the earliest “Bio*” projects that formed the core of the OBF.</p> <p>Chris is also a big proponent of open science efforts in Africa through his current collaboration with H3ABioNet. His current work focuses on day-to-day tasks with a bioinformatics core, keeping up with current sequencing technologies, and generally just trying to stay sane in an ever-changing research and analysis landscape.  He looks forward to having a pulled pint of stout with Karsten and others at some future point.</p> <p><img src="https://lh3.googleusercontent.com/fnSNnx2SMlQpFBxtOL_yyIF7iQ5P_tElmtKpcxrS3DYo6p-joqi_oWI7b6OrBgXvmcQq39kZu_K7yIPBEUx-Jbpay4_yBjonTZ176GBT_K18Eu_X2yv2d8D4i7rLA0lt4amrub_z" alt=""></p> <p><strong>Peter Cock</strong>( <a href="https://twitter.com/pjacock">@pjacock</a>) has been involved in BOSC organization since 2011, and co-chaired the conference from 2014-2016. He is currently the President of the OBF, having previously served as Secretary and Treasurer.</p> <p>Peter is a senior bioinformatician at the James Hutton Institute in Scotland, and one of the core developers of Biopython since getting his PhD. He moved to Scotland in part to be closer to the mountains, but since starting a family has not been able to visit as often as before.</p> <p><img src="https://lh5.googleusercontent.com/Dsc2srrZqEndfO8tgDqnuBSnCVclgmFJsdZzwIBUOBu-YfRWcZijyomADwRIws9zTIrw43hts_5lSgjaTBU4cfFAiziLeCHicPHfl-qrSSQ5sy-3cxhc2VC1s-V2XmK2aphw6pI6" alt=""></p> <p><strong>Nomi Harris</strong>( <a href="https://twitter.com/NomiHarris">@nomiharris</a>) helped to plan the very first BOSC in 2000, and has chaired or co-chaired the meeting since 2011. She also serves on the Board of the OBF.</p> <p>Nomi is a Program Manager at Lawrence Berkeley National Laboratory, where she helps to coordinate a number of large open source bioinformatics projects. Previously, she was a bioinformatics software developer.</p> <p>Nomi loves music, and organizes both a Renaissance vocal quintet and a folk music circle. During the pandemic, she has been volunteering for <a href="https://www.welcome.helpberkeley.org/">Help Berkeley</a> and fostering kittens for the <a href="https://berkeleyhumane.org/get-involved/">Berkeley Humane Society</a>.</p>https://www.open-bio.org/2021/04/09/bosc-abstract-parties/Fri, 09 Apr 2021 16:58:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/04/09/bosc-abstract-parties/<p>Are you thinking of writing an abstract for BOSC? We&rsquo;re here to help! The BOSC Organizing Committee is holding two &ldquo;abstract parties&rdquo; that will be fun collaborative work sessions. We&rsquo;ll start by giving some tips for writing a great BOSC abstract, and then open the floor to questions and &ldquo;workshopping&rdquo;: show us your in-progress abstract, and we&rsquo;ll give you helpful suggestions. Or you can just attend and work on your abstract in silent solidarity with others!</p> <p>We&rsquo;ve chosen two different times for worldwide coverage:</p> <ul> <li>Thursday, April 15, 22:00 UTC (3pm PT / 6pm ET / 8am (Friday) AEST): <a href="https://lbnl.zoom.us/j/95136477143?pwd=MHVtQUZ2V3VLY1V5SnRXLytxSkRpQT09">Zoom link</a></li> <li>Thursday, April 22, 14:00 UTC (7am PT / 10am ET / 15:00 BST): <a href="https://cshl-dnalc.zoom.us/j/96052351236?pwd=bnU5ZVNkSFpSNUNUemhHZnlPRi9ldz09">Zoom link</a></li> </ul> <p>We hope you&rsquo;ll put on your writing hat and meet us there! (And join us on our <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">Slack channel</a> as well!) If you can&rsquo;t make it to either of the parties, you can look at <a href="https://docs.google.com/presentation/d/1nflJhmwkFe5yaE3tBbrAgBJOAiw9rE4WwuJkGvKCiUQ/edit">these slides</a>, which explain what you need to know to put together a good BOSC abstract!</p>https://www.open-bio.org/2021/03/24/join-us-at-bosc-2021/Wed, 24 Mar 2021 21:21:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/03/24/join-us-at-bosc-2021/<p><img src="https://www.open-bio.org/wp-content/uploads/2021/03/Colour-Horizontal-Full-Name.png" alt=""></p> <h4 id="bosc-2021-will-take-place-july-29-30-as-part-of-ismbeccb-2021-online">BOSC 2021 will take place July 29-30, as part of <a href="https://www.iscb.org/ismbeccb2021/">ISMB/ECCB 2021 Online</a>.</h4> <h4 id="key-dates">Key Dates</h4> <p><strong>May 6, 2021 (11:59pm EDT): Deadline for</strong> <a href="https://www.open-bio.org/events/bosc/submit/"><strong>submitting one-page talk/poster abstracts</strong></a> May 27: Talk/poster acceptance notifications June 3: Late poster (and Late-Breaking Lightning Talk) submission deadline June 10: Late poster / LBLT acceptance notifications <strong>July 29-30:</strong> <a href="https://www.open-bio.org/events/bosc/"><strong>BOSC 2021</strong></a> <strong>Online (part of ISMB/ECCB 2021 Online)</strong> July 31-Aug 1: <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest (CoFest)</a></p> <h5 id="about-bosc-2021">About BOSC 2021</h5> <p>BOSC is returning to ISMB in 2021, after a successful partnership with Galaxy for the first Bioinformatics Community Conference last year (BCC2020 online). Originally slated to take place in Lyon, France, <a href="https://www.iscb.org/ismbeccb2021/">ISMB/ECCB 2021</a> will be held online, and features over a dozen tracks, including BOSC. As usual, <a href="https://www.open-bio.org/events/bosc/">BOSC</a> will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more!</p> <h5 id="timing">Timing</h5> <p><strong>BOSC 2021 will take place the last two days of ISMB/ECCB: July 29-30.</strong> Our usual free collaborative work event, <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CoFest,</a> will be held July 31 - August 1.</p> <p>The complete ISMB/ECCB schedule is available <a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2021/schedule/schedule.php">here</a>. The core hours for talks will be <strong>11:00-15:30 UTC</strong>, with poster sessions and ISMB keynotes from 15:30-17:30 UTC. The core hours correspond to:</p> <p>13:00-17:30 CEST (Europe) 12:00-16:30 BST (UK/Ireland) 7:00-11:30am EDT (East coast of North America) 4:00-8:30am PDT (West coast of North America) 9:00pm-1:30am AEST (East coast of Australia)</p> <h5 id="abstract-submission">Abstract submission</h5> <p>We encourage you to <a href="https://www.open-bio.org/events/bosc/submit/"><strong>submit abstracts</strong></a> on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, or posters. The deadline for abstract submission is <strong>May 6th (11:59pm EDT / 03:59 (May 7th) UTC)!</strong></p> <p><strong>BOSC session topics include</strong> (but are not limited to):</p> <p>Open Science and Reproducible Research Open Biomedical Data Citizen/Participatory Science Standards and Interoperability Data Science Workflows Open Approaches to Translational Bioinformatics Open Science for Global Health Developer Tools and Libraries Inclusion, Outreach and Training Bioinformatics Open Source Project Reports (about new or existing projects)</p> <h4 id="requesting-registration-fee-assistance">Requesting registration fee assistance</h4> <p>We realize that the cost of ISMB/ECCB may be prohibitive for some. If you are <a href="https://www.open-bio.org/events/bosc-2021/submit/">submitting an abstract to BOSC</a> and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests &ndash; the abstract reviewers will not.) We regret that we will not be able to offer registration fee assistance for those who are not submitting abstracts. (But you should consider submitting an abstract! Even if your work is preliminary, it may qualify for a poster.)</p> <h4 id="stay-in-touch">Stay in touch!</h4> <p>Learn more about BOSC: <a href="https://www.open-bio.org/events/bosc/">/events/bosc/</a> Join our BOSC announcements mailing list: <a href="https://groups.google.com/forum/#!forum/bosc-announce">https://groups.google.com/forum/#!forum/bosc-announce</a> Chat with us on Slack: <a href="https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew">https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew</a> Find us on Twitter at <a href="http://twitter.com/OBF_BOSC">@OBF_BOSC</a> and use #BOSC2021 for this year’s conference.</p> <p>We hope to see you online at <a href="https://www.open-bio.org/events/bosc/">BOSC 2021</a>! Please share this announcement with people or groups who might be interested. We are particularly interested in reaching out to diverse communities who may not yet be aware of BOSC!</p>https://www.open-bio.org/events/bosc-2021/bosc-2021-keynotes/Tue, 23 Mar 2021 17:18:19 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2021/bosc-2021-keynotes/<p><img src="https://www.open-bio.org/wp-content/uploads/2021/03/christie-bahlai-scaled.jpeg" alt="Dr. Christie Bahlai"></p> <h3 id="christie-bahlai--kent-state-university">Christie Bahlai ( <a href="https://www.kent.edu/biology/christie-bahlai">Kent State University</a>)</h3> <p><em>Significant heterogeneities: Ecology&rsquo;s emergence as open and synthetic science</em></p> <p>ABSTRACT: Ecology has undergone several major cultural shifts in the past century. Eager to define the field as a ‘hard’ science distinct from natural history, early 20th century ecologists rigorously tested theory through intensive, controlled experiments, often working in relative isolation. The environmental movement of the latter 20th century again redefined the science of ecology in terms of connectivity and an appreciation of scale, fostering collaborations and infrastructure. Now, the open data revolution is changing how scientists approach explaining and predicting the behavior of ecological systems. Furthermore, these open and synthetic approaches create opportunities to incorporate diverse perspectives, data, and engagement in data-intensive ecology. However, simply sharing data cannot overcome a century of ecologists working in siloes. Not only are data collected in different places and across time subject to environmental variability, differences in how observations are made as a result of human choices of how to measure, how to record, and how (and if!) to share information can dramatically impact our ability to understand ecological patterns. In this talk, I will explore how ecology has shifted from a ‘lone wolf’ science to a distributed, collectivist endeavor, and how technology and culture intersect to shape both scientific approaches and career paths.</p> <p>Christie Bahlai, PhD, is a computational ecologist in the Department of Biological Sciences at Kent State University and a former Mozilla Fellow. She uses approaches from data science to help solve problems in conservation, sustainability, and ecosystem management, partnering with conservation and tech nonprofits. Her current research focuses on developing tools to support information synthesis in temporal ecology. Dr. Bahlai has strong interests in social justice in science, and believes that directly addressing diversity issues through technology and culture change benefits both scientists and science.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/04/Thomas-Mboa.jpg" alt="Dr. Thomas Hervé Mboa Nkoudou "></p> <h3 id="thomas-hervé-mboa-nkoudou--mboalab-and-open-air">Thomas Hervé Mboa Nkoudou ( <a href="https://www.mboalab.africa/">Mboalab</a> and <a href="https://openair.africa/">Open AIR</a>)</h3> <p><em>Contribution du mouvement maker dans le domaine de la biotechnologie en Afrique: Une perspective de la science ouverte  (Contribution of the maker movement to biotechnology in Africa: An open science perspective)</em> _ Note: This talk will be delivered in French with English subtitles._ ABSTRACT: The maker movement is a community-based movement driven by a common understanding that democratizing access to tools and technologies will revolutionize the distribution of material goods and disrupt existing socio-economic systems. With the Internet, the maker movement is reinforced by trends of openness, better, open science. Indeed, nowadays, information circulates instantaneously from one end of the world to the other, offering the possibility to exchange, share and contribute to the enrichment of knowledge with implications in the fields of health, environment, education, etc. In this presentation, I will show evidence of the contribution of the maker movement to the democratisation of biotechnology in Africa. I will also discuss the local realities that need to be considered in order to ensure the success of such an undertaking. To do this, I will address the following points:</p> <ul> <li> <p>The dynamics of the circulation of biotechnology knowledge (protocols, data, design, etc.) in makerspaces;</p> </li> <li> <p>The presentation of concrete initiatives of Biomakerspaces in Africa, as well as the impact that these innovation spaces have in their immediate environment;</p> </li> <li> <p>Obstacles to the implementation of such initiatives and possible solutions to overcome them.</p> </li> </ul> <p><a href="https://orcid.org/0000-0001-9678-7765">Thomas Hervé Mboa Nkoudou, PhD</a>, is a researcher in Open Science and Science Communication. With a background in biochemistry, he works to promote DIYbio and democratize biotechnology in Africa, and aims to help create a more inclusive, data-driven research community. He founded the <a href="https://www.mboalab.africa/">Mboalab</a> innovation lab in Cameroon, and co-leads the African Institute of Open Science and Hardware. Dr. Mboa is also the International President of APSOHA, the Association for the Promotion of Open Science in Haiti and Africa. He is currently a postdoc at the University of Ottawa in Canada, working with the <a href="https://openair.africa/">Open African Innovation Research Partnership</a>. Dr. Mboa was featured in a <a href="https://www.nature.com/articles/d41586-021-00956-6?fbclid=IwAR2D7MxjuOKCUU7sEwqYVQx6m30kdh8se9fwKxC0-GMTuuZYzyFp8bjkxxI">recent article in Nature</a> about early-career researchers who are leaders.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/04/Lara-Mangravite.jpeg" alt="Dr. Lara Mangravite"></p> <h3 id="lara-mangravite--sage-bionetworks">Lara Mangravite ( <a href="https://sagebionetworks.org/">Sage Bionetworks</a>)</h3> <p>(Talk co-hosted with <a href="https://www.biofunctionprediction.org/meetings/">Function-COSI</a>)</p> <p><em>Open approaches to advance data-intensive biomedicine</em></p> <p>ABSTRACT: Data for health research is all around us. In the last decade, we have moved from a paradigm where research data is collected in a research clinic to a paradigm where research data may stem from anywhere – including our visits to the doctor and our daily interactions with technology. These information streams offer tremendous opportunity to advance research in areas from public health to precision medicine. They can also be extremely intrusive - requiring us to evolve the ways in which we collect, manage, and analyze research data. As always, the translation of science into medicine requires robust and reproducible outcomes with clear actionable consequence. Here, we will discuss approaches to apply open science principles – transparency, reproducibility, and independent contribution – to meet the evolving needs of data-intensive biomedical research.</p> <p>Lara Mangravite, PhD, is president of Sage Bionetworks, a non-profit research organization that focuses on open practices to advance biomedicine through data-driven science and digital research. Recognizing that all research is limited by restrictions placed on the distribution of information, Sage works closely with institutes, foundations, and research communities to redefine how complex biological data is gathered, shared and used. By improving information flow and research practices, Sage seeks to enable research outcomes of sufficient confidence to support translation. Dr. Mangravite obtained a PhD in pharmaceutical chemistry from the University of California, San Francisco, and completed a postdoctoral fellowship in cardiovascular pharmacogenomics at the Children’s Hospital Oakland Research Institute.</p>https://www.open-bio.org/2021/02/19/obf-event-fellowship-round-1-2021/Fri, 19 Feb 2021 10:36:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/19/obf-event-fellowship-round-1-2021/<p>The call for applications for the OBF Event Fellowship 2021, round 1 is now open. <strong>The deadline for this round is 1 April 2021.</strong> Applications should be submitted via <a href="https://forms.gle/ppExEeJpx8UDMWQB6">this Google Form</a>.</p> <p>We invite applications from candidates who are seeking financial support to attend or host virtual events in 2021. The selected awardees can use the OBF Event Fellowship to cover conference registration fees and potentially additional expenses associated with attending or hosting the event, such as small hardware (microphone, speaker, webcam), childcare for the duration of the event and high-speed internet. Like last year, in this round, we will consider applications to attend or host virtual events only. This decision has been made due to the ongoing Coronavirus pandemic induced lockdown and restricted travels. Expenses that will be incurred by remote participation have to be justified in the application and will be evaluated on a case-by-case basis.</p> <p><strong>Group applications are not in scope, but:</strong> if multiple members of the same group would like to attend the same event, each member should send their application separately. If members of an organising committee would like to apply for support for hosting an event, the application should be sent by one person (preferably the lead organiser).</p> <p><strong>Planning to attend</strong> <a href="https://www.open-bio.org/events/bosc-2021/"><strong>BOSC 2021</strong></a> <strong>?</strong> You can request a registration fee waiver/reduction when submitting your abstract for a talk or poster directly via the <a href="https://easychair.org/conferences/?conf=ismbeccb2021abstracts">BOSC abstract submission form</a>. If you would like to participate without a talk or poster, please fill the OBF Event Fellowship <a href="https://forms.gle/ppExEeJpx8UDMWQB6">application form</a> providing your motivation and expected outcomes from attending BOSC 2021.</p> <p>More details regarding the fellowship application, review, and reimbursement process can be foundon our website: <a href="https://www.open-bio.org/event-awards/">/event-awards/</a>. If you have questions, please contact the OBF board by emailing <a href="mailto:board@open-bio.org">board@open-bio.org</a>.</p> <p><strong>Learn about the OBF Event Fellowship Awardees from 2020!</strong></p> <p><strong>Round 1 (1 April 2020)</strong></p> <p>As part of the fellowship process, all OBF Event Fellowship awardees write blog posts that are posted on the OBF website ( <a href="https://www.open-bio.org/category/travel-fellowship/">see here</a>). Below are the blog posts by the awardees from 2020 application rounds.</p> <p>Using his OBF Event Fellowship Award, Armando Blondel Djiyou Djeuda hosted the H3ABioNet‘s Introduction to Bioinformatics course (IBT) in Cameroon for the first time. Read his report in <a href="https://www.open-bio.org/2020/09/24/h3abionet-course-2020-armando-blondel/">this blog post</a>.</p> <p>Gigi Kenneth and Edidiong Etuk attended the Bioinformatics Open Source Conference (BOSC) track at the Bioinformatics Community Conference 2020. It was a first-time opportunity for them to attend bioinformatics and open science workshops at an international conference. Read their posts: <a href="https://www.open-bio.org/2020/08/16/bcc2020-edidiong-etuk/">A Software Engineer’s Experience at BCC 2020</a> (by Edidiong) and <a href="https://www.open-bio.org/2020/08/19/bcc-2020-gigi-kenneth/">Getting introduced to Bioinformatics and Open Science through BCC 2020</a>(by Gigi).</p> <p>Pengfei Fan from Queen’s May College in London attended the Conference on Lasers and Electro-Optics 2020 and shared his experience in this blog post: <a href="https://www.open-bio.org/2020/08/25/cleo2020-pengfei-fan/">Smart computational imaging</a>.</p> <p><strong>Round 2 (1 October 2020)</strong></p> <p>Siddhant Sharma, an undergraduate student from India, received the OBF Event Fellowship to participate in the <a href="https://isc.embs.org/2020silesian/">International Student Conference 2020</a> (IEEE, EMBS). A post will be shared soon.</p>https://www.open-bio.org/2021/02/15/seeking-volunteers-for-obf-2021/Mon, 15 Feb 2021 19:02:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/15/seeking-volunteers-for-obf-2021/<p><em>TL;DR: Nominate candidates or yourself for the OBF board via this <a href="https://forms.gle/PJZLoPXGqKQsEYGJA">form</a> or work with OBF in other volunteer capacities.</em></p> <p><strong>Nominations are welcome for the OBF Board</strong> <strong>election</strong></p> <p>OBF is committed to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The roles and functions of OBF have evolved over the last 20 years, and currently include:</p> <p>- hosting and sponsoring the annual events, Bioinformatics Open Source Conference - running open source events like CodeFests and Google Summer of Code (GSoC) - offering Event fellowships to promote diversity of underrepresented community members at open source events - onboarding and supporting OBF member projects by providing financial management support (e.g., reimbursements and payments and advertising) - maintaining OBF website, social media and newsletter for information dissemination - advocating through policy and public statements</p> <p>OBF board members are elected through public nomination and voting. As board member Yo Yehudi (see <a href="https://www.open-bio.org/2021/02/12/title-would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/">this post</a>) reaches the end of her term, we are reflecting on the need to recruit new and more diverse board members.</p> <p>In particular, we would like to invite members from low-tech/low-income communities or historically marginalised groups to bring new perspectives to the OBF community and highlight new areas of interest. Elected members of the OBF Board will be instrumental in steering OBF’s work to address urgent challenges and needs in open source bioinformatics communities that we might not have yet recognized.</p> <p>If the OBF’s goals and values resonate with you, we encourage you to nominate yourself or someone else (please check with them first!) who would be a good addition to the OBF board. Please fill out this form by 1 April 2021: <a href="https://forms.gle/PJZLoPXGqKQsEYGJA">https://forms.gle/PJZLoPXGqKQsEYGJA</a>.</p> <p>An election for new board members will be held at the next public board meeting (around May or June 2021 - exact data will be announced soon).</p> <p><strong>Working with OBF in other volunteer capacity</strong></p> <p>In addition to the projects mentioned earlier, we are grateful to the members of the OBF community who participate in other community initiatives including (but not limited to) organising BOSC annually, handling GSoC mentorship activities and building capacity (skill development and training) and advocacy around open source in bioinformatics.</p> <p>These tasks could not have been accomplished without the support of our community members. If you would like to be involved in OBF but don’t want to nominate yourself for a position on the Board, we would be delighted talk to you about how you could get involved with these or other projects:</p> <p>- <a href="https://github.com/obf/newsletter">Curate and edit our quarterly (approximately) newsletter</a>, time commitment approximately 4 hours per issue - Help maintain and update our website: <a href="https://www.open-bio.org">https://www.open-bio.org</a> (WordPress, HTML, CSS skills) - Help manage our social channels (such as <a href="https://twitter.com/obf_news">Twitter</a>) - <a href="https://www.open-bio.org/events/gsoc/">Become a GSoC</a> mentor or organisation admin - Volunteer at the Bioinformatics Open Source Conference</p> <p>We appreciate that many of these roles may be new to you and we would offer mentorship and support if it is your first time occupying this type of position - please don’t feel that inexperience should stop you from applying!</p> <p>OBF also offers support for individuals and groups to promote open source practices and build bioinformatics skills. Here are a few opportunities that you can benefit from:</p> <p>- <a href="https://www.open-bio.org/event-awards">Apply for the OBF Event fellowship</a>, 2 deadlines on 1 April and 1 October 2021 - <a href="https://www.open-bio.org/membership">Become an OBF member to participate in the community</a> - Apply to become an affiliate project by discussing with the board ( <a href="https://www.open-bio.org/projects/#affiliated-projects">see currently affiliated projects</a>) - Apply for the OBF Grassroots Event Sponsorship (will be announced soon)</p> <p>We would also love to hear your ideas for how you could help boost OBF’s commitments to:</p> <p>- representing interests of bioinformatics and open source communities from developing countries - onboarding member projects from low and middle-income backgrounds - supporting individuals and communities who are contributing to policy development - boosting grassroots projects that can benefit from OBF’s support - spreading awareness of OBF Event Fellowship and affiliation programs</p> <p>Sound interesting? If so, please get in touch with the board by emailing <a href="mailto:board@open-bio.org">board@open-bio.org</a>. If you want more information, or want to talk to one of us about being on the board or in the OBF community in general, see the <a href="https://www.open-bio.org/board/">OBF Board page</a> for contact information.</p>https://www.open-bio.org/2021/02/13/google-summer-of-code-2021-we-need-your-project-ideas/Sat, 13 Feb 2021 13:55:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/13/google-summer-of-code-2021-we-need-your-project-ideas/<p>It&rsquo;s <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> (GSoC) application time again - I&rsquo;ll be leading the OBF GSoC application and org admin process this year alongside Sarthak Sehgal, Michael Crusoe, and Kai Blin. The OBF typically works as an umbrella organisation for other sub-projects - if you have an open + bio related code project that you think could use a student intern this year, please read on.</p> <p>TL;DR: Please send ideas for half-sized projects (1.5 months, not 3 months) <strong>by Thursday 18 feb</strong>, New mailing list, Code of Conduct.</p> <p>Longer version:</p> <p><strong>New mailing list: please subscribe!</strong> A few notes for this year: from here on we&rsquo;ll be using Google Groups rather than the old OBF GSoC lists or direct to private mailing address. This will make moderation easier.</p> <p>If you&rsquo;re interested in mentoring this year, I&rsquo;d recommend signing up to these two lists for now - we&rsquo;ll mostly use the mentors list until (if) we&rsquo;re accepted as an organisation, and the general list will become more active once (if) we have any students.</p> <p><a href="https://groups.google.com/g/obf-gsoc-general">https://groups.google.com/g/obf-gsoc-general</a> <a href="https://groups.google.com/g/obf-gsoc-mentors">https://groups.google.com/g/obf-gsoc-mentors</a> <strong>No further emails will be sent to the old OBF GSoC mailing lists or to individual email addresses.</strong></p> <p><strong>Code of Conduct</strong>: The OBF is in the process of drafting a code of conduct, which will soon be presented to the OBF membership to (hopefully) vote to adopt it. Please take a few minutes to preview it here: <a href="https://github.com/OBF/obf-docs/pull/78/files">https://github.com/OBF/obf-docs/pull/78/files</a> - while it&rsquo;s not officially ratified yet, it would be good to run this year&rsquo;s GSoC with this CoC&rsquo;s intent behind our behaviour.</p> <p><strong>Project ideas</strong>: Things are a little different from previous GSoCs. Projects should be 175 hours long - that&rsquo;s about 1.5 months of work compared to the 3 months we&rsquo;re used to, although students can choose to do this work part-time over the whole GSoC period or full-time over a shorter period. This also means all stipends are halved for interns.</p> <p>Please add your project ideas to this list by THURSDAY 18 FEBRUARY (using suggest mode). <a href="https://docs.google.com/document/d/1kPf-fLDmjoVGf7TvbOB6H12pC_s_y_5TUGiKAxre64M/edit?usp=sharing">https://docs.google.com/document/d/1kPf-fLDmjoVGf7TvbOB6H12pC_s_y_5TUGiKAxre64M/edit?usp=sharing</a> - you can add ideas after this if needed, but we need as many fully fleshed ideas as possible already online for the organisation review phase.</p> <p>These are the project ideas from last year for inspiration: <a href="https://www.open-bio.org/events/gsoc/gsoc-project-ideas/">/events/gsoc/gsoc-project-ideas/</a> <strong>We&rsquo;re all pretty tired</strong></p> <ul> <li>Make sure you have 2-3 mentors for every project idea to cover in case of something coming up (such as covid related downtime, whether illness, caring, or anything else).</li> <li>If you&rsquo;re interested in helping us with org admin duties, we&rsquo;d love to have you on board and are willing to provide you support and mentoring while you learn how to do it. Email <a href="mailto:obf-gsoc-admins@googlegroups.com">obf-gsoc-admins@googlegroups.com</a> to discuss it.</li> </ul> <p>**Finally - any questions? ** If you have any questions please email either the mentor group ( <a href="mailto:obf-gsoc-mentors@googlegroups.com">obf-gsoc-mentors@googlegroups.com</a>) or the admin group ( <a href="mailto:obf-gsoc-admins@googlegroups.com">obf-gsoc-admins@googlegroups.com</a>). You can also book a quick chat with me if that&rsquo;s easier: <a href="https://calendly.com/yo-yehudi-manchester/gsoc-chat?month=2021-02">https://calendly.com/yo-yehudi-manchester/gsoc-chat?month=2021-02</a></p>https://www.open-bio.org/2021/02/12/would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/Fri, 12 Feb 2021 15:46:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/12/would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/<p>About three years ago I nervously responded to a <a href="https://www.open-bio.org/2017/11/14/obf-visioning-2017/">blog post from the OBF looking for board member applications</a> from people who were interested in leading open science related initiatives. This went as well as I possibly could have hoped - both myself and the other applicant, Bastian Greshake Tzovaras, <a href="https://www.open-bio.org/2018/03/20/welcome-to-our-new-board-members/">officially joined the board in March of 2018</a> for a three-year term.</p> <p>Over the last (nearly) three years, I’ve learned a lot and have participated in many OBF activities I can be proud of. We launched <a href="https://www.open-bio.org/2018/11/05/new-obf-logo/">a new community-designed OBF logo</a> (special thanks to Aleix Lafita-Masip and all the others who contributed!), I mentored the fabulous Deepashree Deshmukh, an <a href="https://www.outreachy.org/">Outreachy</a> intern, to migrate the OBF website from its old mediawiki-based format onto <a href="https://www.open-bio.org/2019/04/08/goodbye-mediawiki-hello-new-website/">a shiny new Wordpress site</a>, I joined the OBF GSoC org admin team alongside Sarthak Sehgal, and we launched <a href="https://github.com/obf/newsletter">an OBF newsletter</a>. We’re still working on preparing an OBF Code of Conduct, which hopefully will be launched soon.</p> <p>As I will step down from the board at the end of my term, I’d like to imagine that my replacement(s?) on the board will achieve even more significant impact. I’d also like to see the OBF leadership become more representative of bioinformatics as a whole, and all the different places and walks of life that bioinformaticians, open source coders, community managers, documentation writers, program managers, and other open science enthusiasts come from.</p> <p>As such, I am excited to announce that the OBF is seeking applications for new board members. If you would like to apply to join the leadership for an organisation that can make a difference in our community, that runs a fantastic yearly conference (BOSC), and has a budget to support fellowships and member projects - <a href="https://www.open-bio.org/2021/02/15/seeking-volunteers-for-obf-2021/">please do apply</a>. I’d especially like to encourage applications from people outside who were born and/or live outside Europe or the United States - we haven’t had enough of your voices in the OBF leadership team to date and I’m certain you would add significant value to the team. I’m also very happy to answer informal queries at a personal level if it helps - feel free to ping me at yochannah [at] gmail dot com.</p>https://www.open-bio.org/2021/02/12/bosc-2021-will-be-part-of-ismb-eccb-2021-online/Fri, 12 Feb 2021 06:22:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/12/bosc-2021-will-be-part-of-ismb-eccb-2021-online/<p>BOSC is returning to ISMB in 2021, after a successful partnership with Galaxy for the first Bioinformatics Community Conference last year ( <a href="https://bcc2020.github.io/">BCC2020 online</a>). Originally slated to take place in Lyon, France, <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a> announced today that the conference will be virtual. This news may be disappointing to some, but for others it offers an opportunity to participate in a conference that they would not have been able to travel to attend.</p> <p><a href="https://www.iscb.org/ismbeccb2021-registration">Registration for the ISMB/ECCB 2021 virtual conference</a> is for the full conference only &ndash; there will not be an option to register for only some of the days, as there has been in the past. Registration fees are based on your status as a working professional, postdoc, or student, as well as what country you work in (or your home country for students).</p> <h3 id="requesting-registration-fee-assistance">Requesting registration fee assistance</h3> <p>We realize that the cost of ISMB/ECCB may be prohibitive for some. If you are <a href="https://www.open-bio.org/events/bosc-2021/submit/">submitting an abstract to BOSC</a> and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests &ndash; the abstract reviewers will not.) We regret that we will not be able to offer registration fee assistance for those who are not submitting abstracts. (But you should consider submitting an abstract! Even if your work is preliminary, it may qualify for a poster.)</p> <p>We hope to see you online at BOSC 2021!</p>https://www.open-bio.org/events/bosc-2020/bosc-2020-collaborationfest/Thu, 11 Feb 2021 18:20:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/bosc-2020-collaborationfest/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/attendees_stairs.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h1 id="collaborationfest-2020">CollaborationFest 2020</h1> <p>As part of <a href="https://bcc2020.github.io/">BCC2020</a>, the first Bioinformatics Community Conference, the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) co-sponsored an online <a href="https://bcc2020.github.io/cofest/">CollaborationFest</a>, a 2 (or 4) day collaborative work event where our community gathered virtually to contribute code, documentation, training materials, and challenging analysis problems and use cases.</p> <p>For more information please see the <a href="https://bcc2020.github.io/cofest/">BCC2020 CollaborationFest page</a> for this virtual event.</p> <h2 id="history">History</h2> <p>BCC2020 CollaborationFest was be the 11th annual pre- or post-BOSC collaboration fest. Previous fun and successful events were <a href="https://www.open-bio.org/wiki/Codefest_2010">Codefest 2010</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> in Vienna, <a href="https://www.open-bio.org/wiki/Codefest_2012">Codefest 2012</a> in Los Angeles, <a href="https://www.open-bio.org/wiki/Codefest_2013">Codefest 2013</a> in Berlin, <a href="https://www.open-bio.org/wiki/Codefest_2014">Codefest 2014</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2015">Codefest 2015</a> in Dublin, <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a> in Orlando, <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> in Prague, <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC Collaboration Fest 2018</a> in Portland, and <a href="https://www.open-bio.org/events/bosc/bosc-2019-collaborationfest">Collaboration Fest 2019</a> in Basel.</p>https://www.open-bio.org/2021/01/28/domain-names-available-for-adoption/Thu, 28 Jan 2021 09:26:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/01/28/domain-names-available-for-adoption/<p>The OBF has two sets of domain names available for adoption by a non-profit or open source project: biows.org, biows.com, biows.net and biocpp.org, biocpp.com, biocpp.net</p> <p>These domains were registered and donated to us with bio-web-services (biows) and bio-c-plus-plus (BioC++ or BioCPP) in mind, but we&rsquo;ve failed to find a good home for them.</p> <p>Please note that this is like adopting a free puppy - we&rsquo;ll transfer them at no cost, but domain names come with annual renewal charges which the recipient organisation would be responsible for paying.</p> <p>Serious enquiries to the OBF board by email by the end of February 2020 please.</p>https://www.open-bio.org/2021/01/13/metadocencia-2020-laura-acion/Wed, 13 Jan 2021 18:26:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/01/13/metadocencia-2020-laura-acion/<p><em>The</em> <a href="https://www.open-bio.org/travel-awards"><em>Open Bioinformatics Foundation (OBF) Event Fellowship program</em></a> <em>aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community.</em> <a href="http://lacion.rbind.io"><em>Dr. Laura Ación</em></a> <em>, a researcher at the</em> <a href="http://www.ic.fcen.uba.ar/en/"><em>Instituto de Cálculo, University of Buenos Aires, Argentina</em></a> <em>. She is also one of the co-founders of</em> <a href="https://www.metadocencia.org/en/"><em>MetaDocencia</em></a> <em>, which she could partly support with the OBF Event fellowship granted to her in the December 2019 application round.</em></p> <p><strong>What was supposed to happen</strong></p> <p>I applied to OBF Event Fellowship to attend <a href="https://2020.carpentrycon.org/">CarpentryCon 2020</a> (June 29 – July 1 in Madison, WI) and <a href="https://user2020.r-project.org/">useR! 2020</a> (July 7-10 in St. Louis, MO). Plans were going perfectly because shortly after receiving the fellowship, CarpentryCon 2020 organizers invited me to give a keynote talk. It was a once in a lifetime event alignment! My first international keynote talk for a beloved community with extensive ties to Bioinformatics education. Plus, useR!, the primary academic conference about R, a language widely used in open-source bioinformatics projects. Traveling from Buenos Aires to North America to participate in international meetings is usually unaffordable. I was ecstatic. However, as you know, <em>nothing happened as expected in 2020!</em></p> <p><strong>What happened</strong></p> <p>Having the <a href="https://www.open-bio.org/2020/03/13/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19-%ef%bb%bf/">OBF fellowship award repurposed</a> to host or attend online events was one of the 2020 silver linings because it enormously facilitated my work towards the advancement of MetaDocencia.</p> <p>On March 16th, 2020, all in-person classes and training opportunities were canceled in Argentina due to the pandemic, with no clear indication of when they will resume. That afternoon, it was already clear that we all had to stay home for a while (thus my WhatsApp avatar “Yo me quedo en casa,” meaning, “I stay at home”). That afternoon I sent two audio messages to a group of friends.</p> <p><img src="https://lh3.googleusercontent.com/xivJ7lanRnTpFzn0kxeUV4BsUlQNiXLAEIKNsgk54mlrnlsh5PfOJNCodoX6PQkgw_rg_YS73E-1Suc9Gw1Ub_qbVyXdaklbjpOfIkn8YKsgPRY-i933uEibSfX-79tPyEUMezZ3" alt="">The two audio messages with the idea that sparked MetaDocencia</p> <p>These audios said:</p> <blockquote> <p>“Girrrrrrrrrlsssssss, how are you? I hope you are fine! I think I just found my way of helping in the midst of all that is going on! (&hellip;) I just got the idea of using all we know on how to teach online to help train teachers that will be having to take their classes online immediately.</p> <p>I am all ears about your thoughts. To me, this seems like THE opportunity [to put out there all we know about active teaching].</p> <p>These past days, I had no idea what my role could be amid this pandemic. (…) Today, when I saw the Ministry of Education press conference, I realized it is a crucial moment. Everyone will be switching their content to online delivery mode. Maybe we need to teach one workshop very fast; one, two, three, as many as needed. What do you think?”</p> <p>First time I shared my idea for MetaDocencia project with my colleagues and friends</p> </blockquote> <p>The answers of this group of academics, researchers, and teachers with deep ties to the Latin American research and teaching community were immediate. That is how the MetaDocencia ride started.</p> <p>MetaDocencia is &lsquo;meta teaching&rsquo; in Spanish. Our mission is to nurture a community of Spanish-speaking educators by teaching concrete, evidence-based, and student-centred educational methods. We collaboratively develop open, reusable, and accessible resources to foster effective training practices.</p> <p><strong>THE opportunity</strong></p> <p>You may wonder why in March 2020 I thought we had ‘THE’ opportunity and how MetaDocencia connects to Open Bioinformatics. Despite open educational communities exist worldwide, most of them speak in English and hence, language is an enormous barrier in Latin America. Translations of contents are necessary but not enough for culturally-responsive teaching. Furthermore, “meeting our learners where they are” in Latin America means not making assumptions about the knowledge of technologies such as Zoom, Slack, or Google docs and being conscious about internet access and accessibility inequalities.</p> <p><img src="https://lh3.googleusercontent.com/2QEg6VTLLSP_SB-fArIDmobOcLOD-yeaJgxv5w9M7HWljj_TIrzmy1ohPGiGjc3OPujDh-e2e_SwwvT6Cy_ZcPXyZIDD2tw8YfEDCoGSGLWfML9EC5_dUwl4ljhLUqtlGIC_dQPA" alt=""></p> <p>A lot of terrain levelling work is needed before meaningful international integration is feasible. ‘Communities of Practice’ are still a new concept in our region. Tools like active classrooms powered by minimal technology such as peer-instructions, shared note-taking, or a Code of Conduct are far from being standard in (online) classrooms and events, even among the most tech-savvy professionals in our region.</p> <p>MetaDocencia helps bridge this gap by empowering Spanish-speaking educators from countries that are under-served in the area of Open Science. Several participants of MetaDocencia are bioinformaticians. Hence, advancing bioinformatics knowledge in Latin America is included in our overall goals, which also require the teaching of open source practices. The coronavirus pandemic forced all classes and events to run online, which meant that all bioinformatics educators, among others, needed to learn how to teach online effectively.</p> <p>Consequently, MetaDocencia has focused mainly on the 3-hour workshop <a href="https://www.metadocencia.org/cursos/abc-online/intro-abc/">”Introduction to Online Teaching Essentials.”</a> This hands-on workshop builds on open educational resources to teach how to run synchronous events. It includes practical, evidence-based tips for delivering an engaging online workshop, class, tutorial, panel, or another event type. We learned these techniques mostly from <a href="https://carpentries.org/">The Carpentries</a> and <a href="https://education.rstudio.com/trainers/">RStudio Education</a>. In these workshops, we introduce our teaching philosophy (e.g., Code of Conduct, open licensing, community building, active teaching). Participants experience each of our tips and advice starting at <a href="https://docs.google.com/forms/d/e/1FAIpQLSddnptIAMdRgJYH0Vm6cNrk63x5f969Rd4pbuoGKmDgN02xFw/viewform">pre-registration</a> and staying in touch afterward through our <a href="https://join.slack.com/t/metadocencia/shared_invite/zt-ek8a0rup-MQB_5qUKhr9zIGKQAUImXA">Slack</a>.</p> <p>Since March 27th, 2020, we taught this workshop 41 times (yes, a lot more than my initial thoughts of “one, two, three”! 😍) to more than half of the 1,300 Spanish-speaking educators from 20 countries who registered their interest (as of January 2021). Despite unstable internet connections and many other staying-at-home circumstances, more than 90% of workshop attendants stayed engaged throughout the workshop and completed our end-of-workshop survey. Among these educators and researchers, there are bioinformaticians, biologists, school teachers and professors.</p> <p><img src="https://lh5.googleusercontent.com/-mIXgExEqQfuVu8pTnzl4sPxFlrESQKEdwznnsAmIAROBzOBTknMZ4KOZ2t4-GjQJgpitAHG9tFrOrttoDlYtqi78dgRepvXhz88HnQW9uf_v9LPNR9FBS22CjN-CwmSDETx80gS" alt="">Ana Julia Velez Rueda, a bioinformatician who is also a part of the leadership team of the <a href="https://womenbioinfodatascla.github.io/index.html">First Congress of Women in Bioinformatics and Data Science Latin America</a>. She attended one of our first workshops, recommends MetaDocencia <a href="https://twitter.com/AnaJuliaVelezR1/status/1249183711532285952">in this tweet</a>.</p> <p><strong>Community stewardship and outreach</strong></p> <p>MetaDocencia also fosters a community through a 100% Spanish-speaking <a href="https://join.slack.com/t/metadocencia/shared_invite/zt-ek8a0rup-MQB_5qUKhr9zIGKQAUImXA">Slack workspace</a>, where everyone is welcome and must follow our Code of Conduct. It currently hosts almost 400 members encouraged to share material, resources, and experiences. In MetaDocencia, we believe that the best support for teaching during this pandemic comes from others who also experienced teaching online during these challenging times. We are also active <a href="https://twitter.com/metadocencia">tweeps</a> and <a href="https://www.metadocencia.org/">asynchronous content creators</a>.</p> <p>In 2020, we also presented MetaDocencia in Spanish and English in over a dozen communities and events. We spearheaded the first <a href="https://blog.rladies.org/post/spanishmetameetup/">R-Ladies Global event in Spanish</a>, <a href="https://twitter.com/metadocencia/status/1326540189020254208">taught at LatinR Conference</a>, and presented our experience in different formats at <a href="https://twitter.com/metadocencia/status/1329073374962868225">Open Life Science</a>, <a href="https://twitter.com/metadocencia/status/1326180815643025408">Carpentry Con</a>, <a href="https://twitter.com/metadocencia/status/1329416637171298304">Open Education Conference</a>, <a href="https://twitter.com/metadocencia/status/1327264959059824645">IEEE International Conference on Imaging Processing</a>, <a href="https://twitter.com/metadocencia/status/1328660907065425920">PyCon Argentina</a>, and <a href="https://twitter.com/metadocencia/status/1327627850321686531">Open Source Community Call</a>, among several other events related to Open Science and Open Education. We also collaborated with PyLadies El Alto (Bolivia) and <a href="https://twitter.com/metadocencia/status/1330885062611456002">nedear.la</a>.</p> <p>Everything MetaDocencia achieved in 2020 is detailed in our bilingual <a href="https://www.metadocencia.org/en/post/reporte-2020/">end-of-year report</a>.</p> <p><strong>Team effort</strong></p> <p>From my initial WhatsApp audios in March 2020, MetaDocencia has come a long, long way. Since its very inception, MetaDocencia was not a one-woman effort. Indeed, all MetaDocencia´s accomplishments took the deeds of a fast-growing <a href="https://www.metadocencia.org/en/#equipo">group of volunteers</a> with experience in teaching technical skills, delivering online classes, and working remotely, locally, regionally, and globally. Our team is geographically-spread, including eleven collaborators in Argentina, France, and the United Kingdom. In Argentina, we make MetaDocencia from six different cities (i.e., Buenos Aires, Rosario, Resistencia, Corrientes, Balcarce, and La Pampa). We are Carpentries-certified instructors and instructor trainers, RStudio certified instructors or regionally-knowledgeable accessibility experts. An international advisory team of education experts also guides us in our vision of thinking globally while acting locally.</p> <p>All of <a href="https://github.com/MetaDocencia">our activities at MetaDocencia</a> are free, open, and executed through 100% volunteer work. Thus, the fellowship award offered to me by the Open Bioinformatics Foundation helped me pay for tools (such as Zoom and Calendly subscriptions and a desk microphone) were crucial for MetaDocencia´s infrastructure. As per the OBF board members, email discussions with me about repurposing my fellowship allowed them to improve their fellowship plans during the pandemic in 2020. Indeed, the OBF Event Fellowship was previously called OBF &lsquo;Travel&rsquo; Fellowship.</p> <p><strong>More silver linings coming in 2021</strong></p> <p>I did not dare to envision in 2020 anything about 2021. However, 2021 looks bright for MetaDocencia as it will continue expanding its training activities to incorporate technical skills relevant to open and reproducible research computing, bioinformatics, and data science. With the support of other funding opportunities offered to MetaDocencia’s sustainability, we also seek to build capacity to further our reach to more under-served Latin American regions. We envision generating more accessible materials (e.g., free, in Spanish, welcoming, and safe for everyone) to lower as many barriers as possible for as many people as possible. To achieve this, in addition to pursuing further funding, we will work on furthering or creating partnerships with alike-spirited communities and organizations.</p> <p>Would you like to join us on this beautiful and exciting ride? You (yes, you!) are welcome! Please check out <a href="https://www.metadocencia.org/post/como-colaborar/">ways to participate</a> in MetaDocencia. You can also join our <a href="https://join.slack.com/t/metadocencia/shared_invite/zt-ek8a0rup-MQB_5qUKhr9zIGKQAUImXA">Slack workspace</a> or <a href="https://twitter.com/metadocencia">follow us</a> on Twitter.</p> <p><strong>Endlessly thankful</strong></p> <p>Endless thanks to the Open Bioinformatics Foundation for being part of the MetaDocencia journey and helping me realize my most impactful vision yet, while I have the chance to add my two cents to open bioinformatics education!✨🌈</p>https://www.open-bio.org/events/bosc-2021/Sun, 03 Jan 2021 19:52:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2021/<p><img src="https://www.open-bio.org/wp-content/uploads/2020/08/nomi-abby-chris-karsten-peter-yo-1-1.jpeg" alt="Screenshot from Bioinformatics Community Conference 2020 July 19-21, 2020"></p> <h1 id="bosc-2021">BOSC 2021</h1> <p>BOSC 2021 is over! Part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021 online</a>, BOSC took place July 29-30, 2021, with <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CoFest</a> following on July 31 - Aug 1. We thank all the participants and our <a href="https://www.open-bio.org/events/bosc2021/sponsors/">sponsors</a>, who enabled us to grant free registration to 20 participants around the world!</p> <p>Check out the complete <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">BOSC 2021 talk schedule</a>, and <a href="https://www.youtube.com/playlist?list=PLir-OOQiOhXZ6jV_cld3Hp-C_0m4aCznk">videos of all the talks!</a></p> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. In July 2020, <a href="https://bcc2020.github.io/">BCC2020</a>, the first Bioinformatics Community Conference, brought together the Galaxy Community Conference (GCC) and <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2020</a> in a joint online meeting that attracted over 600 participants from 62 countries.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/05/keynotes-horizontal.png" alt="2021 Keynote Speakers"></p> <h3 id="keynotes">Keynotes</h3> <p><a href="https://www.open-bio.org/bosc2021/bosc-2021-keynotes/">Keynote speakers</a> at BOSC 2021:</p> <ul> <li>Christie Bahlai</li> <li>Thomas Hervé Mboa Nkoudou</li> <li>Lara Mangravite</li> </ul> <h2 id="key-dates">Key Dates</h2> <ul> <li>May 6, 2021: <a href="events/bosc-2021/submit/">Abstract submission</a> deadline</li> <li>June 3: Late poster submission deadline</li> <li>June 20: Deadline for presenters to r <a href="https://www.iscb.org/ismbeccb2021-registration">register for ISMB/ECCB 2021</a></li> <li>June: Deadline to <a href="https://www.open-bio.org/2021/06/15/birds-of-a-feather-at-bosc-2021/">suggest a Birds of a Feather</a></li> <li>June 30: Recorded talks due</li> <li>July 29-30: <strong>BOSC 2021</strong>, part of <a href="https:=">ISMB/ECCB 2021</a> (online)</li> <li><a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CoFest</a>: July 31-Aug 1 (online)</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/01/emmy-moni.png" alt=""></p> <h2 id="topics">Topics</h2> <p>BOSC covers all aspects of open source bioinformatics software and open science, including (but not limited to) these topics:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Open Approaches to Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach and Training</li> </ul> <p><a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">Check out the full BOSC 2021 schedule!</a></p> <h4 id="platinum-sponsors">Platinum Sponsors</h4> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="https://www.alzheimersdata.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/ADDI_Logo_FullColor_Vert_RGB.png" alt="Alzheimer’s Disease Data Initiative"></a></p> <h4 id="gold-sponsors">Gold sponsors</h4> <p><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a><a href="https://www.broadinstitute.org/"><img src="https://www.broadinstitute.org/files/news/media-images/logos//BroadInstLogoforDigitalRGB.png" alt="Broad Institute Logo"></a></p> <h4 id="silver-sponsors">Silver sponsors</h4> <p><a href="https://elifesciences.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/04/image.png" alt="eLife"></a><a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a><a href="https://oup.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/OUP_logo_navy.png" alt="Oxford University Press"></a><a href="https://bioteam.net"><img src="https://www.open-bio.org/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png" alt=""></a></p> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some presenters. If you&rsquo;re interested in sponsoring BOSC, please see our <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsorships page</a>!</p> <h3 id="overview">Overview</h3> <p>BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <p>BOSC is usually preceded or followed by what we now call <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest (CoFest</a> for short), a two-day community development session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. All are welcome to attend CoFest, whether or not you attend BOSC!</p> <p><a href="https://www.open-bio.org/events/bosc/about/">More about BOSC&hellip;</a></p> <h2 id="registration">Registration</h2> <p>Registration for BOSC 2021 is through <a href="https://www.iscb.org/ismbeccb2021-registration">ISMB/ECCB 2021</a>. If the registration fee is a barrier, those who <a href="https://www.open-bio.org/events/bosc/submit">submit abstracts</a> can request fee assistance on the submission form.</p> <p>The post-BOSC <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CoFest</a> will be free, but will require registration.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/01/nomi-dave-deepak-hilmar-joby-karsten-moni-nicole-1.jpeg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/05/bosc-2021-org-committee-vertical-1.png" alt=""></p> <h2 id="organizing-committee">Organizing Committee</h2> <p><strong>Chair: Nomi L. Harris</strong> (Lawrence Berkeley National Laboratory)</p> <p>Co-chair: Karsten Hokamp (Trinity College Dublin) Chris Fields ( <a href="http://bioperl.org/">Bioperl developer</a>; <a href="https://hpcbio.illinois.edu/">HPCBio</a>, University of Illinois) Jason Williams (Cold Spring Harbor Laboratory) Jessica Maia (BD) <a href="https://malvikasharan.github.io/">Malvika Sharan</a> (The Alan Turing Institute) Monica Munoz-Torres (University of Colorado, Denver) <a href="http://www.scri.ac.uk/staff/petercock">Peter Cock</a> ( <a href="http://biopython.org/">Biopython developer</a>; <a href="http://www.hutton.ac.uk/">James Hutton Institute</a>)</p> <h2 id="review-committee">Review Committee</h2> <p>Kai Blin*, Christian Brueffer, Scott Cain*, J. Harry Caufield*, Tyrone Chen, Luis Pedro Coelho*, Gianluca Della Vedova, Scott Edmunds, Christopher Fields*, Bastian Greshake Tzovaras*, Nomi L. Harris, Janna Hastings, Michael Heuer, Karsten Hokamp, Matúš Kalaš*, Aziz Khan, Radhika Khetani, Aleix Lafita-Masip, Hilmar Lapp, Hervé Ménager, Kieran O&rsquo;Neill, Tazro Ohta, Konstantin Okonechnikov, Lorena Pantano, Surya Saha*, Sonika Tyagi, Deepak Unni, Jason Williams, Yo Yehudi \* = also reviewed Late Poster abstracts</p> <h2 id="previous-boscs">Previous BOSCs</h2> <p>BOSC has been held yearly since 2000. See <a href="https://www.open-bio.org/events/bosc/about#Past_BOSCs">information about the first 21 BOSC conferences.</a></p> <p><a href="https://bcc2020.github.io/">BCC2020</a>, the first Bioinformatics Community Conference, brought together the Galaxy Community Conference (GCC) and BOSC in a joint online meeting in July 2020. Participants from 62 countries joined us for sessions scheduled twice a day to accommodate both hemispheres. The complete BOSC 2020 schedule is <a href="https://www.open-bio.org/events/bosc/schedule/">here</a>.</p> <p><a href="https://www.open-bio.org/events/bosc-2019/">BOSC 2019</a> was part of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB 2019</a> in Basel, Switzerland. See the full <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2019 schedule</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image1-1-e1610331040457.png" alt=""></p> <h1 id="code-of-conduct">Code of Conduct</h1> <p>As part of ISMB/ECCB, BOSC 2021 will be covered by the <a href="https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct">ISMB/ECCB Code of Conduct.</a></p>https://www.open-bio.org/2020/11/04/google-summer-of-code-2020-wrap-up/Wed, 04 Nov 2020 10:06:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/11/04/google-summer-of-code-2020-wrap-up/<p>OBF was accepted as a mentoring organisation for Google Summer of Code this year. It was another good year for OBF, with Kai Blin, Michael R. Crusoe, Sarthak Sehgal, and Yo Yehudi as administrators. We hosted eight students all of which successfully completed their work:</p> <ol> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/4898360579850240/">Srijan Verma</a> (mentors: Dmitry Petrov, Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/6576740249370624/">Himanshi Mathur</a> (mentors: Jun Aruga, Evan Nemerson, Michael R. Crusoe) - Implementation of SVML in SIMDe ( <a href="https://medium.com/@himanshi18037/final-work-product-gsoc-2020-5fba8744cbcf">final report</a>, <a href="https://medium.com/@himanshi18037">other blogs</a>, <a href="https://simd-everywhere.github.io/blog/">SIMD Everywhere</a>)</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/6238152676605952/">Boshen Yan</a> (mentors: Amal Thomas, Marius Beek, Saket) - Implementing user-friendly search features in PysraDB ( <a href="https://bscrow.github.io/gsoc2020.html">final report</a>, <a href="https://github.com/bscrow/pysradb/blob/basic-search-feature/WEEKLY_WRITEUP.md">weekly writeup</a>, <a href="https://bscrow.github.io/gsoc2020.html">work summary</a>)</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/5403269754519552/">Shekhar Shukla</a> (mentors: Oliver Alka, Hannes Röst, Timo Sachsenberg) - OpenMS R Package ( <a href="https://gist.github.com/24sharkS/7cb791091a8301f7c8460f15c04b97a0">final report</a>, <a href="https://24sharks.github.io/">blogs</a>, <a href="https://github.com/OpenMS/OpenMS/projects/31">OpenMS</a>)</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/5109120027328512/">Francesco Porto</a> (mentors: George Githinji, Erik Garrison, Pjotr Prins) - Parallel Graph Traversal for Variation Graphs</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/6302555174338560/">Eliza Martin</a> (mentors: Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Protein sequence and structural analysis CWL pipeline for comparative biology</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/4905563541995520/">Hidayat Ullah Khan</a> (mentors: Jun Aruga, Evan Nemerson, Michael R. Crusoe) - SIMDe: Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extension ( <a href="https://masterchef2209.wordpress.com/2020/08/26/final-work-product-submission-report-google-summer-of-code-2020/">final report</a>, <a href="https://masterchef2209.wordpress.com/2020/06/17/guide-to-intel-sse4-2-crc-intrinisics-implementation-for-simde/">mentee blogposts</a>, <a href="https://simd-everywhere.github.io/blog/">SIMD Everywhere</a>)</li> <li><a href="https://summerofcode.withgoogle.com/archive/2020/projects/5225514815455232/">T. Waschischeck</a> (mentors: Chris Bielow, Julianus Pfeuffer) - Using DeNovo Sequencing to Predict Protein Database Suitability ( <a href="https://openmsgsoc2020.blogspot.com/2020/08/gsoc-final-report.html">final report</a>, <a href="https://openmsgsoc2020.blogspot.com/">student blog</a>, <a href="https://github.com/OpenMS/OpenMS/projects/30">OpenMS</a>)</li> </ol> <p>This year, OBF received 5000 USD from Google for being a mentoring organisation. The funds from GSoC go into the general OBF Fund that is primarily used to sponsor <a href="https://www.open-bio.org/event-awards/">OBF Event Fellowships</a> which is a program aimed at increasing diverse participation at events promoting open science practices such as resource development and dissemination in the bioinformatics and biological research community.</p> <p>Thank you to all our volunteer GSoC administrators and mentors - and of course thank you to the students - we hope you&rsquo;ll continue to work in bioinformatics and/or open source.</p>https://www.open-bio.org/2020/09/24/h3abionet-course-2020-armando-blondel/Thu, 24 Sep 2020 08:06:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/09/24/h3abionet-course-2020-armando-blondel/<p><em>The <a href="https://www.open-bio.org/travel-awards">Open Bioinformatics Foundation (OBF) Event Fellowship program</a> aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Armando Blondel DJIYOU DJEUDA, a researcher from University of Douala, Cameroon, set up and host <a href="https://www.h3abionet.org/categories/training/introduction-to-bioinformatics-training-2020">H3ABioNet‘s Introduction to Bioinformatics course (IBT)</a>, supported by this fellowship granted to him in application round 1 of 2020.</em></p> <p>Due to the rich biodiversity of sub-Saharan African countries, bioinformatics and data management are crucial in helping to advance biomedical research. While many African countries are emerging in those specific fields, Cameroon and Central African countries in general, are still lagging behind. Based on this observation, in 2019, we created Bioinformatics and Biostatistics Hub (B2Hub) at the Biotechnology Center of the <a href="https://uy1.uninet.cm/">University of Yaounde I</a>. Our aim through this platform is to promote bioinformatics and biostatistics among graduate students and young researchers from Central Africa.</p> <p>After successfully organizing a <a href="https://lapher-biotech.net/2020/02/13/b2hub-bioinformatics-and-biostatistics/">first Bioinformatics workshop in 2019</a>, this year I set up a virtual classroom for the <a href="https://www.h3abionet.org/categories/training/introduction-to-bioinformatics-training-2020">H3ABioNet‘s Introduction to Bioinformatics course (IBT)</a> at the <a href="https://lapher-biotech.net/">Laboratory for Public Health Research Biotechnologies</a>, Biotechnology Center, <a href="https://uy1.uninet.cm/">University of Yaounde I</a>. I decided to host this event because no other host was selected in Cameroon (even in Central Africa) last year and as a result, I and most likely many other interested Central African candidates were unable to attend this course.</p> <p>The workshop ran from May to August 2020 (see <a href="https://www.h3abionet.org/categories/training/introduction-to-bioinformatics-training-2020">full curriculum</a>). In this blog post, I have provided a monthly summary of how this workshop was conducted. I have also provided the demographic distribution of our attendees, their learning process, personal and COVID-19 related challenges experienced by them, and the overall impact of this event.</p> <h3 id="training-format"><strong>Training Format</strong></h3> <p>The training was carried out using a distance-based learning model where classrooms were set up at different sites (a total of 47 sites with more than 1000 participants this year) and linked to the trainer via Zoom conferencing software during biweekly contact sessions. The trainers used a combination of theoretical and practical sessions for participants to gain practical experience in using various tools and resources. Initially, the course was supposed to run from 10:30 am to 2:30 pm every Tuesday and Thursday for 3 months (12th May 2020 to the 27th August 2020) at the Biotechnology Center, University of Yaounde I, Cameroon. However, due to the current Covid-19 pandemic, it was no longer possible to have contact sessions and the training was then shifted entirely online. In our classroom, we decided to keep in contact with our participants through online meetings every week and we created a WhatsApp group to allow participants to ask questions directly to our teaching assistants and exchange each other.</p> <p>As a consequence, the course was highly demanding particularly in terms of internet connection and other basic equipment to conduct online meetings (such as webcam, headsets, small hardware needs, or a TV screen for practicals), especially in our context where it is not yet widely accessible. Thanks to the support of the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation (OBF)</a> through the OBF (travel) fellowship, I was able to get those equipment and successfully host our first IBT course.</p> <h3 id="may-introduction-to-bioinformatics-resources"><strong>May: Introduction to Bioinformatics Resources</strong></h3> <p>We started our journey in May with a short introduction about Bioinformatics and its relevance in biomedical research, before moving to module 1: Introduction to databases and resources. In this module, we learned with Dr Shaun Aron how to navigate through biological databases and resources (like <a href="https://www.ncbi.nlm.nih.gov/">NCBI</a> or <a href="https://www.ebi.ac.uk/">EBI</a>), perform basic protein and DNA analysis (sequence features, start sites, restrictions sites and so on), and conduct a more efficient search using <a href="https://pubmed.ncbi.nlm.nih.gov/">PubMed</a>.</p> <h3 id="june-unix-command-line-and-sequence-alignment-theory"><strong>June: Unix Command-line and Sequence Alignment Theory</strong></h3> <p>After a promising first month, we covered two exciting modules in June. We started with an introductory workshop to the Linux/UNIX command-line, which was delivered by Dr. Amel Ghouila. Using an emulator called <a href="https://www.cygwin.com/">Cygwin</a> (for Microsoft users) or Ubuntu (for MAC OS users), we got useful commands and tips to manipulate files and directories. Most of the participants were afraid because it was their first time working on Linux and its command-line environment. However, Dr. Ghouila was able to ease the learning process of beginners to command line computing. We then moved to the third module: Sequence alignment theory and application. In this module, after describing the most popular algorithms used for both global and local alignment, Dr. Jonathan Kayondo then taught us how to use <a href="https://blast.ncbi.nlm.nih.gov/">BLAST</a> and other pairwise sequence alignment tools (such as <a href="blank">EMBOSS water</a> and <a href="blank">EMBOSS needle</a>) to answer some biological questions.</p> <h3 id="july-multiple-sequence-alignment-and-genomics"><strong>July: Multiple Sequence Alignment and Genomics</strong></h3> <p>In July, we deepened our knowledge and skills in sequence alignment, especially using multiple sequence alignment (MSA) tools and software. We learned the main characteristics of the most popular programs for building MSA and how to select the appropriate one to use. Indeed, we saw the differences between Cobalt, ClustalW, MUSCLE, and Tcoffee, and we used mainly online tools during our practical sessions. Besides, we had an initiation to <a href="https://www.jalview.org/">Jalview</a>, an exceptional multiple sequence alignment viewer, editor, and analysis tool. Dr. Ahmed M. Alzohairy showed us how to use Jalview for editing and analyzing MSAs produced with the most popular MSA programs we saw before.</p> <p>We then continued during the same month with one of the most attractive modules in my opinion: Genomics. We started with a short overview of sequencing technologies and NGS and further proceeded with more complex topics such as genome annotation, comparative genomics, and human variation. During this module, we used the <a href="https://www.ensembl.org/index.html">Ensembl genome browser</a>, an amazing platform that allows access to publicly available reference genomic data such as genes (through tools and a visual interface), variation data, and annotation of your variants through the <a href="https://www.ensembl.org/vep#:~:text=VEP%20determines%20the%20effect%20of,as%20well%20as%20regulatory%20regions.&amp;text=SIFT%20and%20PolyPhen%2D2%20scores,...">Variant Effect Predictor (VEP) tool</a>. We closed this module by applying some basic Linux command-lines we learned in module 2, to visualize our data and retrieve some basic information from our sample sequences.</p> <h3 id="august-molecular-evolution-and-phylogenetics"><strong>August: Molecular Evolution and Phylogenetics</strong></h3> <p>Finally, we entered into our last month (August) with the last module: Molecular evolution and phylogenetics. This module, entirely taught by Dr. Anna Zhukova, was full of new skills, tools, and resources. Briefly, we were introduced to the components of a phylogenetic tree, discussed the basic principles of building a tree, different types of methods (Distance method, max parsimony, and Max likelihood), and how to interpret a phylogenetic tree. During practical sessions, we build our trees using both an online tool ( <a href="https://ngphylogeny.fr/tools/">NGPhylogeny</a>) and a downloadable software tool ( <a href="http://doua.prabi.fr/software/seaview">Seaview</a>). We also used <a href="https://itol.embl.de/upload.cgi">iTOL</a> for tree visualization and manipulation tools and <a href="http://www.atgc-montpellier.fr/sms/">SMS</a> for the selection of the best evolutionary model. We end up training with tree dating and phylogeography. During this session, we used <a href="http://tree.bio.ed.ac.uk/software/tempest/">TempEst</a>, a downloadable software tool to check for temporal signals in the tree, <a href="https://lsdating.pasteur.fr">LSD/LSD2</a>, an online tree dating and rooting tool, and <a href="https://pastml.pasteur.fr/">PastML</a> for ancestral character reconstruction.</p> <h3 id="demographic-distribution-of-workshop-attendees"><strong>Demographic Distribution of Workshop Attendees</strong></h3> <p>A total of 44 participants were selected in our classroom (41% were female), mainly coming from Cameroon. We also enrolled 3 participants coming from neighboring countries, especially Chad. They were mostly MSc and PhD students (87.5%) but also post-doc or young researchers (10%). At the end of the training, we build a <a href="https://docs.google.com/forms/d/1WqH5i9xr83P4KC0HhgEOAyhnvWUe63nB0siwTyLRzms/edit#question=803302123&amp;field=1644277189">post-training evaluation form using a Google forms questionnaire</a> to obtain feedback from participants. The majority (82%) of our participants found the information and/or skills gained during this training highly relevant and useful in their daily activities, 86% of them were satisfied with the course design and methodology and will therefore highly recommend this training course to their classmates and/or colleagues. The dark point of our training was the low completion rate.</p> <p>Indeed, only 15 participants out of 44 have completed the entire training and obtained a certificate. The most evocated reason among those who did not complete the course was the lack of internet connection at home to complete their assignments and they had not enough time to complete the training. However, even those who did not complete the training admitted having improved their bioinformatics skills and will be happy to complete the training during the next edition as long as we maintain contact sessions as initially planned.</p> <h3 id="positive-feedback"><strong>Positive Feedback</strong></h3> <p>I would also like to end up by sharing with you some general comments and appreciation by our participants:</p> <blockquote> <p>“ <strong><em>This training was as I expected. This allowed me to use many tools and computer software to analyze and annotate different types of biological data as well as to retrieve information from databases and more&hellip; This gave me the level I needed to start my own analyzes related to my PhD research.</em></strong>” Brice Fonkou NATCHEMA SOH, PhD candidate, Faculty of Sciences, University of Yaoundé I, Cameroon.</p> </blockquote> <blockquote> <p>“ <strong><em>The training was great and understandable for a beginner like me. Haven&rsquo;t done that before, it was really challenging but finally relevant.</em></strong>” Nelly Ornelle ONANA ATEBA, PhD candidate, Faculty of Sciences, University of Yaoundé I, Cameroon.</p> </blockquote> <blockquote> <p>“ <strong><em>It was a good experience. I loved being part of it. I will do it again if the opportunity comes to me.</em></strong>” Pacome Valery TCHUENKAM KOM, PhD candidate at the Dschang School of science and technology, University of Dschang, Cameroon.</p> </blockquote> <blockquote> <p>“ <strong><em>The course was very enlightening and instructive, with great insights that will definitely be helpful in my current and future research avenues.</em></strong>” Willy Leroi TOGNA PABO, PhD candidate at the University of Buea, Cameroon.</p> </blockquote> <p>To conclude, I would like to acknowledge the OBF for providing a fellowship to host an IBT classroom here in Cameroon. Thanks to this fellowship, we will now be able to offer an Introduction to Bioinformatics course to interested students and young graduates every year. This is a great step in the process of expanding bioinformatics skills and knowledge in an underrepresented region like Central Africa. Encouraged by the success of this year’s workshop, we are now considering hosting intermediate courses and building an open learning circle in our classroom. Feel free to get in touch if you would like to stay updated on this activity (email: armando_djiyou@yahoo.fr).</p>https://www.open-bio.org/2020/09/04/biopython-1-78-released/Fri, 04 Sep 2020 12:11:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/09/04/biopython-1-78-released/<p>Biopython 1.78 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.78">PyPI</a>.</p> <p>The main change is that <code>Bio.Alphabet</code> is no longer used. In some cases you will now have to specify expected letters, molecule type (DNA, RNA, protein), or gap character explicitly. Please consult the updated <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Tutorial</a> and <a href="https://biopython.org/docs/1.78/api/">API documentation</a> for guidance. This simplification has sped up many <code>Seq</code> object methods. See <a href="https://biopython.org/wiki/Alphabet">https://biopython.org/wiki/Alphabet</a> for more information.</p> <p><code>Bio.SeqIO.parse()</code> is faster with &ldquo;fastq&rdquo; format due to small improvements in the <code>Bio.SeqIO.QualityIO</code> module.</p> <p>The <code>SeqFeature</code> object&rsquo;s <code>.extract()</code> method can now be used for trans-spliced locations via an optional dictionary of references.</p> <p>As in recent releases, more of our code is now explicitly available under either our original &quot; <em>Biopython License Agreement</em>&quot;, or the very similar but more commonly used &quot; <em>3-Clause BSD License</em>&quot;. See the <code>LICENSE.rst</code> file for more details.</p> <p>Additionally, a number of small bugs and typos have been fixed with additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and all of the tests have been reformatted with the <code>black</code> tool to match the main code base.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Adam Sjøgren (first contribution)</li> <li>Carlos Pena</li> <li>Chris Daley</li> <li>Chris Rands</li> <li>Christian Brueffer</li> <li>Damien Goutte-Gattat</li> <li>João Rodrigues</li> <li>João Vitor F Cavalcante (first contribution)</li> <li>Marie Crane</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Sergio Valqui</li> <li>Yogesh Kulkarni (first contribution)</li> <li>Zheng Ruan</li> </ul>https://www.open-bio.org/2020/09/01/planning-an-online-conference-is-hard/Tue, 01 Sep 2020 04:10:19 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/09/01/planning-an-online-conference-is-hard/<h3 id="online-by-at-least-a-factor-of-two">Online. By at least a factor of two.</h3> <p><strong>Our recent article entitled <a href="https://bcc2020.github.io/blog/lessons-learnt">Lessons learnt from organizing a virtual conference</a> discusses some of our technology choices and how we leveraged them to put on a successful online meeting.</strong> That article touches briefly on some of the challenges we faced, but it doesn’t fully convey how much work it was&ndash;both in advance and during the event.</p> <p><em><strong>Before we go any further, who are you?</strong></em> This post was written by Nomi Harris, the long-time (co-)chair of BOSC, and the co-chair (along with Dave Clements) of <a href="https://bcc2020.github.io/">BCC2020</a> (the Bioinformatics Community Conference, a collaboration between the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference (GCC)). The perspective expressed in this post is mine alone, and does not necessarily reflect the views of others on the BCC2020 organizing committee. Also, although BCC2020 was an equal partnership between BOSC and GCC and the planning was done jointly (except for abstract reviews), my perspective is naturally BOSC-centric.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image3.jpg" alt="Nomi Harris, with a fake bookshelf backdrop and a pear facemask. "><em>Me, with a fake bookshelf backdrop and a pear facemask. (The BCC2020 sign only appeared backwards to me, not to the viewers.)</em></p> <p><strong><em>What was the original plan for BCC2020, and wha</em> t changed?</strong> BCC2020 was originally going to take place in Toronto. The organizing committee made the decision in March to move it online, and it became increasingly clear with every day that passed that there was no way we could have held the conference in person in Toronto as originally planned.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image4.png" alt=""><em>The original BCC home page showed the Toronto skyline at night.</em></p> <p><strong><em>Who runs these meetings, anyw</em> ay?</strong> One thing to understand about BCC2020 is that aside from a few Galaxy people for whom planning conferences is part (a small part) of their job, all the organizers are volunteers. We have regular jobs, and we work on conference organization during our evenings and weekends.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image2-1024x576.jpg" alt=""><em>The BCC2020 organizing committee</em></p> <p>Many of us on the BCC2020 organizing committee have been involved in BOSC or GCC organization for years. (I, for example, was involved in planning the very first BOSC in 2000, started co-chairing it in 2010, and have chaired or co-chaired it every year since then.) So we are pretty used to doing the huge amount of work involved in planning an in-person BOSC. None of us had ever organized a large online meeting before, so there was a big learning curve. <strong>Our recent article entitled <a href="https://bcc2020.github.io/blog/lessons-learnt">Lessons learnt from organizing a virtual conference</a> discusses some of our technology choices and how we leveraged them to put on a successful online meeting.</strong> That article touches briefly on some of the challenges we faced, but it doesn’t fully convey how much work it was&ndash;both in advance and during the event.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image6-1024x434.jpg" alt=""><em>The organizing committee met almost every week during the spring and summer.</em></p> <p><strong><em>There must be things that are easier with an online m</em> eeting <em>, right?</em></strong> Yes, a few, but not a lot. There’s no travel required for an online meeting, so there’s no need to book plane tickets or research hotels&ndash;but that’s true for everyone who participates in a meeting, not just the organizers. As meeting organizers, we don’t plan travel for anyone other than ourselves, so that doesn’t really count towards lightening our organization duties. We didn’t have to worry about handing out name tags or T-shirts, but those tasks are also not the direct responsibility of the organizing committee. An online meeting doesn’t involve food or coffee&ndash;but the volunteer organizing committee doesn’t generally have to do any planning for those; they are handled by the venue. So are the projector, wifi, air conditioning, the chairs in the conference rooms, etc. Basically, only if we for some reason decided to hold our conference in an empty warehouse would the organizational overhead come close to the difficulty level of planning an online meeting.</p> <h2 id="why-was-organizing-an-online-meeting-so-hard"><strong>Why was organizing an online meeting so hard?</strong></h2> <p><strong><em>This was our first online meeting.</em></strong> We’d never done this before, so we had to figure out a lot of things. It almost certainly wouldn’t be quite this hard to organize another online meeting next year, particularly if we stick with the same technology choices. Karsten postulates that online conferences probably have a higher “reusability factor” than in-person ones, from a planning perspective.</p> <p><strong><em>More options to consider.</em></strong> For an in-person meeting, many of the choices and the responsibility for supporting those choices fall on the venue. For example, there are many different kinds of video projectors. Some are better than others. Some are more expensive than others. Which one should we choose for our meeting? Fortunately, we never had to make that choice: the venue has whatever projectors they have. With an online meeting, we not only had to (metaphorically) choose a projector, we had to set it up and run it ourselves. And the projector was only part of the story: we had to make choices and configure and support a variety of tech platforms that would not be required at an in-person meeting (such as a chat app).</p> <p><strong><em>We were early adopters.</em></strong> Admittedly, we made our job harder by choosing a video conferencing platform (Remo.co) that was new to us and to our attendees. Some things would have been simpler if we’d just run the meeting as a bunch of separate Zoom rooms. We wouldn’t have had to do as much training (of the organizers, the workshop leaders, the speakers, and the many volunteers), nor would we have had to write as much documentation. We wouldn’t have had to design floor plans for each of our virtual “buildings” (though actually Karsten Hokamp, who is a total hero, did all of that, as well as preparing most of the documentation and leading most of the training sessions. Seriously, he deserves to be knighted or something.)</p> <p>The fact that Remo was new and still in active development led to some issues (for example, shortly before the conference, their system for registering attendees broke; at another point, private messaging stopped working). But overall, despite the challenges, we felt (and most of the participants agreed) that Remo offered an online conference experience that was more fun and more reminiscent of an in-person meeting. The reasons why we chose Remo, and the challenges and opportunities it presented, are covered in more detail in the article mentioned earlier ( <a href="https://bcc2020.github.io/blog/lessons-learnt">Lessons learnt from organizing a virtual conference</a>),</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image5-1024x667.png" alt=""><em>Chatting at one of the “tables” in Remo.</em></p> <p><strong><em>Tangent: serendipity at online meetings&ndash;it happens.</em></strong> While I’m on that subject, let me share an anecdote that didn’t make it into the “lessons learnt” post. One evening during the conference, I needed to talk to Dave Clements, but I wasn’t sure where he was. He wasn’t answering email or responding in Discord. But as I wandered through our virtual buildings, I happened to spot him in the poster building. He was at one of the sponsor tables, chatting with someone there (I could tell that they were talking because of the little microphone icons on their photos). I could choose to approach the table and break in on their conversation, or wait until they were done. It was uncannily similar to wandering through a conference center and serendipitously seeing someone you knew.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image9-1024x815.png" alt=""><em>I ran into some old friends at the pre-meeting open house.</em></p> <p><em><strong>How do you walk and talk at a virtual meeting?</strong></em> That story might give you a sense of one reason running an online conference is hard: you have to come up with substitutes for things that you get for free in real life, like walking around a conference center and using your voice to talk to people. We couldn’t find a single technology platform that supported threaded, persistent chat in addition to video conferencing, so we ended up using Discord as well as Remo.</p> <p><strong><em>Online talks: what could possibly go wro</em> ng?</strong> Another big challenge was how to present the talks. At an in-person meeting, the speakers just show up and talk. We realized pretty quickly that it would be way too risky to have all the speakers give their talks live during our online meeting. So many things could go wrong. They could get confused about the time zone and fail to show up. Their internet connection could be spotty, or could fail completely. Their computer could decide to reboot in the middle of their talk. Their toddler could toddle into the room and yank their headset off their head (this happens regularly to one of our organizing committee members). Things can and do go wrong at in-person talks, too (the video projector not working is a popular one), but online talks present a whole new array of possible fails.</p> <p>We decided to have presenters pre-record their talks and share the videos with us. Actually, I have to admit that I was pretty sure that at least a few presenters would fail to get their videos done on time (or at all), but we had amazingly high compliance, and only a few speakers who brazenly went over their allotted time. We had to check all the videos to make sure the volume was ok (sometimes it wasn’t) and that the beginning and end of the video wasn’t truncated (sometimes it was). We then had to upload all the videos to a site from which they could be streamed&ndash;we chose Vimeo rather than YouTube because YouTube’s terms of service don’t allow you to stream videos for an audience. That was a lot of work, but once again, Karsten did it. (Is he a saint or WHAT?) We also added the video links to the online schedule, so that attendees could watch them asynchronously if they wanted to, which was a nice thing to do but again involved more work.</p> <p>During the talk sessions, the session techs had to start each talk video at the appropriate time. We discovered as the meeting proceeded that different latencies in attendees’ internet connections meant that for some people, the video took longer to play, and therefore when the next talk started, they hadn’t yet finished watching the last one. This was one of a number of challenges we faced with the talk video presentations.</p> <p><strong><em>Working harder for inclusivity.</em></strong> In some cases, we made choices that created more work for the organizers but which helped to make our meeting more inclusive and accessible. For example, we decided to run the sessions twice each day, once at a time convenient for people in the Western hemisphere, and again 12 hours later at a time convenient for people in Asia and Australia.</p> <p>Another thing we did to increase accessibility was to pay for (with the help of a sponsor donation) closed-captioning all the talks, including the live keynotes as well as the pre-recorded talks. This was a cool feature, but it also took time to set up. We paid a company to do the actual captioning, but we had to provide the pre-recorded videos to them and get back the captioned videos, as well as coordinating the captioning of the live talks. Was it worth the expense and effort? I think so. 25% of the respondents to our post-conference survey said that they’d made use of the CC, and there were many positive comments about it (for example, “Fantastic, very helpful. I have good hearing, but it helped me digest more effectively anyway.”).</p> <p><strong><em>Time zones are hard.</em></strong> One of the things that makes online conferences complicated to organize is time zones. At an in-person conference, there is only one time zone to deal with. We had participants joining us from all over the world, representing an array of time zones that included some that are, unbelievably, off by half an hour. Every schedule we dealt with had to list multiple time zones. That would have been hard enough, but since we ran the whole conference in two hemispheres, we had to list the times for every event in two hemispheres, translated into multiple time zones.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image7-1024x481.png" alt=""><em>A portion of one of the spreadsheets we used to deal with multiple time zones.</em></p> <p><strong><em>Many volunteers were needed.</em></strong> To successfully run our online conference, we required the help of dozens of additional volunteers in addition to the people on the organizing committee. Volunteers (for whom we are extremely grateful!) were needed to help staff the Help Desk, to stream the videos during the parallel sessions, to monitor the various chat forums, and to help visitors to the poster building figure out how to find the posters they wanted to see. All of the volunteers had to be trained, and we had to assemble huge spreadsheets to organize who was volunteering when (with multiple time zones listed, of course).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image8-1024x355.png" alt=""><em>Karsten explaining the BCC2020 setup in Remo during one of the many volunteer training sessions.</em></p> <p><strong><em>Stress displacement: during the conference vs. in adva</em> nce.</strong> When I plan an in-person meeting, most of the planning happens ahead of time. The meeting itself is somewhat stressful and exhausting, but also a lot of fun (last year, for example, I got to float down the Rhein with a bunch of other conference attendees). There is some pressure on the session chairs, who have to manage the Q&amp;A and make sure speakers don’t go on too long. But the “on-the-ground” stress at an online meeting is so much higher. The session techs (who were responsible for starting each video at the appropriate time) had a particularly nail-biting time of it. (Conversely, the speakers, who had already done the hard work of preparing their talk videos in advance, found the online meeting relatively unstressful.)</p> <p><strong><em>Did I mention that planning an online meeting is a lot of work?</em></strong> All in all, I would say that I personally spent about 2x as much time on BCC2020 organizational activities as I do organizing an in-person BOSC&ndash;and that’s a substantial amount of time. And that’s just me. Karsten alone probably spent more time on BCC2020 preparation than there are actual hours in the days leading up to the meeting. (But his job in particular would be easier next time if we chose to run another online conference in Remo.)</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image10-1024x1002.png" alt=""><em>One of many organizational spreadsheets we created to help us keep track of everything. This one (which listed details for each session, including session chair, session tech, talk titles, presenters, talk lengths, video URLs, Q&amp;A times, and more) was nicknamed “the colorful spreadsheet”</em></p> <p>Why am I going on about how haaaaard it is to plan an online meeting? It’s not because I want praise or sympathy (though those are always appreciated), but because we want to manage expectations for next year’s conference. We know that many people would like us to offer an online conference even if next year’s meeting is physical. Here are a few such comments from the post-conference survey:</p> <p>“Please make next year’s meeting virtual/hybrid not F2F only.”</p> <p>“Please keep some aspect of this virtual if it goes back to face-to-face. I may only be able to attend virtually for the foreseeable future. Having this inexpensive option makes this community more accessible and more inclusive.”</p> <p>“Would really appreciate keeping this conference virtually accessible in the future, at least a hybrid approach maybe!”</p> <p><strong><em>So will we make the next BOSC both virtual and in-person?</em></strong> We’ll see what we can do&ndash;we sincerely do want to make the conference as accessible and inclusive as possible. But at the same time, there are only so many hours in the day, and all of the organizing committee members have other jobs that pay the rent. If putting on an online conference is 2x the work of an in-person one, running a hybrid event would be 3x as hard, which is simply not feasible. We don’t yet know whether BOSC 2021 will be online or in-person, but whichever it is, we will not be able to support both a full in-person and a full online experience. We hope you understand, and we hope you will join us if you can.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/image1-1-1024x576.png" alt=""><em>Some of the attendees at the online BOSC party&ndash;the next best thing to being there!</em></p>https://www.open-bio.org/2020/08/25/cleo2020-pengfei-fan/Tue, 25 Aug 2020 12:23:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/08/25/cleo2020-pengfei-fan/<p><em>The <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Pengfei Fan, a researcher from Queen Mary University of London, was supported to participate in <a href="https://www.cleoconference.org/">CLEO 2020</a> by this fellowship granted to him in the application round-1 of 2020. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p>During the last two decades, we are witnessing a fascinating growth of computational imaging (CI) methods, e.g. tomography, compressive sensing and 3D/super-resolved/lensless microscopy, and artificial intelligence (AI) algorithms, mainly machine learning and deep learning, both from the theoretical (mathematical) and practical (experimental) point of view. New computational capabilities in terms of, e.g., big data, large scale optimisation, neural networks and highly parallel computing, are facilitating further improvements in numerically enhanced imaging surpassing the limitations imposed by &lsquo;classical&rsquo; all-optical information processing systems. It is joyful to observe how CI and AI merge to innovatively address challenging tasks fuelled by wide-spreading applications in 3D imaging, biomedicine, microscopy and general physics of light propagation in scattering media, to name just a few. When designing a computational imaging technique, one needs to originally link the applicable data acquisition scheme with the capable image reconstruction algorithm, often aided by learning-based frameworks employed not only for image classification and interpretation but also for image formation and final outcome restoration. As the AI stimulatory development continues to flourish, open-source tools and software, especially deep learning framework and platform, have become a key ingredient of modern science. Hundreds of software packages, libraries, and applications have become essential tools.</p> <p>We count on open-source software and tools in almost every research project, and it is also our responsibility to maintain and develop them. I have been engaging in a research project on deep learning for optical imaging and sensing, and our group at Queen Mary University of London are developing a robust ultrathin multimode fibre based endoscope. Progress in bioinformatics relies on new techniques for investigating the complex dynamics of biological systems. This research theme will develop the crucial role for Data Science and Artificial Intelligence in answering many fundamental questions in genomics and biology regarding the structure and function of genomes, the molecular interplay within cells and organs, the role, shape and functions of proteins as well as advancing imaging techniques.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/08/pengfei-1024x684.png" alt=""><em>An All-virtual Presentation of CLEO 2020 Technical Conference</em> (Screenshot from the event, shared with permission)</p> <p>CLEO is the world&rsquo;s premier international forum to learn about innovative advances, research and new technologies from the optical science industry. Biomedical imaging and sensing is always an essential part of CLEO every year. The <a href="https://www.cleoconference.org/">CLEO 2020</a> Technical Conference was held as scheduled in a first-ever, all-virtual format. The conference reached almost 20,000 registrants from 75 countries. By the end of the conference, 33,322 minutes of programming was presented. 248 Technical, Poster and Dynamic ePoster Sessions equated to more than 2,000 scientific presentations — all delivered in a combination of live and pre-recorded sessions and demonstrating a wide breadth of advancements and discoveries. The session recordings are now available on the conference website for individuals who registered for CLEO.</p> <p>The first day of the conference started with an exciting symposium on Integrated Photonics for Neural Networks and Deep Learning, which was presided by Ozdal Boyraz from University of California Irvine. After the symposium, participants started travelling to different virtual ‘rooms’ to attend their favourite sessions. I presented our current research results at <a href="https://event.crowdcompass.com/cleo20/activity/PsIbmnSv8L">Fiber Based Imaging</a> session, and our software, code and datasets have been published and were highlighted again. We were happy to share the datasets at the conference to catalyse the impact of data science and AI across the world. Specifically, these interesting datasets could be made the focus of a data study event or an impactful long-term project. As data owners, we have been given an opportunity and support to form a data science and bioinformatics community around our data and kick-start interdisciplinary or translational project collaborations.</p> <p>The second day of the conference was kicked off with ‘Meet the OSA Editors’ talk, which was followed by two content-rich plenary sessions. The first one is on Intelligent Optical Synthesizer by Professor Kaoru Minoshima from University of Electro-Communications. Another is on Silicon Photonics by John Bowers, Director of the Institute for Energy Efficiency and Professor, University of California Santa Barbara. On the third day, there was also one plenary session on Advanced Resources for Optical Quantum Information Processing by Paul Kwiat from University of Illinois at Urbana-Champaign. I also participated in one Special Symposium on Artificial Intelligence for Photonics Imaging and Sensing, where Lei Tian, from Boston University, gave an invited talk about Deep learning-based computational biomedical microscopy with uncertainty quantification. On the fourth day and fifth day, I went through the fantastic Joint Poster Sessions: Micro- and Nano-Photonic Devices, and Photonic Innovations for Biological Sciences respectively.</p> <p>To conclude, I would like to thank the OBF for providing me with the OBF Event Fellowship to cover the presentation fee to participate in CLEO 2020. This fellowship was an excellent opportunity to connect with open source and open science enthusiasts, and I firmly believe that this community will ideally promote open-source software development and advocate diversify in the years to come.</p>https://www.open-bio.org/2020/08/22/obf-event-fellowship-round-2-2020/Sat, 22 Aug 2020 15:46:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/08/22/obf-event-fellowship-round-2-2020/<p>We are glad to announce that the call for applications for the <a href="https://www.open-bio.org/wp/event-awards">OBF Event Fellowship</a> is now open. <strong>The deadline for this round is 1 October 2020.</strong> Applications should be submitted via <a href="https://forms.gle/aDZbZGcDWKWe3ocy7">this Google Form</a>.</p> <h3 id="renaming-from-obf-travel-fellowship-to-obf-event-fellowship"><strong>Renaming from “OBF Travel Fellowship” to “OBF Event Fellowship”</strong></h3> <p>One of the goals of the OBF fellowship is to increase the participation of members from traditionally underrepresented groups at events or communities that promote Open Source software development and/or open science practices in the biological sciences. Since so many scientific meetings have been or are now run online, and we wish to explicitly support remote participation for this year, we are renaming ‘OBF Travel Fellowship’ to ‘OBF Event Fellowship’.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/08/distributed-event-1.jpg" alt="">The OBF Event fellowship now supports participation in virtual events. Image reference: The Turing Way Community, &amp; Scriberia. <a href="http://doi.org/10.5281/zenodo.3695300">http://doi.org/10.5281/zenodo.3695300</a></p> <p>This year, the COVID-19 pandemic has compelled research communities to move all in-person meetings to online. Although this situation has limited our ability to freely travel and meet each other in person, we have seen more diverse participants than ever attend and benefit from scientific conferences and training events. Financial burden, visa issues, and general lack of equitable support prevent many of our community members from participating in conferences that often take place far from their home countries. Therefore, virtual events have proven to be more accessible by allowing researchers to attend conferences for a small fee or for free, listen and learn from the experts from their fields, share their work with others and represent their communities. Taking this aspect into account, OBF will continue to offer OBF Event Fellowships for our community members to attend both in-person events and virtual events after the COVID-19 pandemic is over.</p> <h3 id="inviting-applications-to-attend-virtual-events"><strong>Inviting applications to attend virtual events</strong></h3> <p>For the OBF Event Fellowship Round 2 of 2020, we are inviting applications from candidates who are seeking financial support to attend virtual events. At the time of launching this call, we don’t foresee any scientific event taking place in person in 2020 or the first half of 2021. We encourage our community members to follow the <a href="https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance">guidelines provided by WHO</a> and as recommended by their local authorities, and plan their participation in online scientific events accordingly.</p> <p>The selected awardees can use the OBF Event Fellowship to cover conference registration fees and the costs of small hardware (such as a microphone, speaker, and webcam), childcare for the duration of the event, and other supporting materials.</p> <p>Reimbursement for expenses incurred by remote participation will be evaluated on a case-by-case basis. For example, we are aware that due to the load-shedding issues in many developing countries, our applicants might need to pay for the fuel for a generator to keep their electricity running for the duration of the event. Similarly, the cost of high-speed internet may vary across countries and may also be requested by applicants from some developing countries.</p> <p>More details regarding the fellowship application, review, and reimbursement can be found <a href="https://github.com/OBF/obf-docs/blob/Fellowship-for-remote-events/Travel_fellowships.md">on GitHub</a> (current draft in <a href="https://github.com/OBF/obf-docs/pull/79">pull request 79</a> on OBF’s GitHub repository).</p> <p>Since we are in the process of finalizing the guidelines for this fellowship, we invite feedback and suggestions on the draft <a href="https://github.com/OBF/obf-docs/">on GitHub</a> from our community members to help us make the OBF Event Fellowship truly beneficial. For additional information, please contact OBF board members by emailing <a href="mailto:board@open-bio.org">board@open-bio.org</a>.</p>https://www.open-bio.org/2020/08/19/bcc-2020-gigi-kenneth/Wed, 19 Aug 2020 18:56:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/08/19/bcc-2020-gigi-kenneth/<p><em>The <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Gigi Kenneth, a biochemistry undergrad and a bioinformatics enthusiast from Nigeria, was supported to participate in <a href="https://www.open-bio.org/events/bosc/about/">Bioinformatics Community Conference</a> 2020 by this fellowship granted to her in the application round-1 of 2020. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p>I’m a biochemistry undergraduate, in my final year from the <a href="https://www.uniport.edu.ng/">University of Port Harcourt</a>, Nigeria. I started learning about artificial intelligence and machine learning last year (2019), which I found really interesting and was really amazed by its applications in various fields. I found myself wondering about how these related to my graduate program, so I did some digging and was awed by the incredible work being done in this field.</p> <p>A couple of months into my tech journey, I realized there are several buzz words in the computational field that I am not completely aware of. One of them that stood out the most was Open Source. I did some googling and barely understood what I read and hoped that I would learn about it along the way. Bioinformatics was another new word I came across a couple of times. I must admit that it intrigued me as I went through the list of organizations in <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> (GSoC 2020), several of which had listed interesting bioinformatics projects.</p> <p><a href="https://bcc2020.github.io/">Bioinformatics Community Conference</a> (BCC) 2020 opened my eyes to the amazing ongoing work in both Bioinformatics and Open Source, and I’m really grateful that I got to be a part of this conference through the OBF Event Fellowship.</p> <p>When I found out my application got accepted and that my registration fee for BCC 2020’s virtual conference had been waived, I happily signed up for a lot of sessions. I attended the pre-conference sessions about <a href="https://www.nextflow.io/">Nextflow</a>, <a href="http://intermine.org/">Intermine</a>, <a href="http://openlifesci.org/">Open Life Science</a> and <a href="https://usegalaxy.org/">Galaxy</a>. I missed out on the sessions on introduction to machine learning but it was interesting going through the shared notes that were shared with everyone. The session I enjoyed the most was about handling biological data using <a href="https://www.python.org/">Python</a>, <a href="https://jupyter.org/">Jupyter</a> and Intermine that Yo Yehudi hosted. I’ve since taken a deeper look into Intermine, explored <a href="https://www.humanmine.org/humanmine/begin.do">HumanMine</a> a bit more, and shared what I was able to grasp with some friends. It was a lot of fun trying to get the hang of the online platforms like <a href="https://bcc2020.sched.com/event/d0uh/pre-bcc-open-house">Shed</a>(for schedule), <a href="https://discord.com/">Discord</a>(for chat) and <a href="https://remo.co/">Remo</a>(for virtual participation) as the conference progressed.</p> <p>There were several interesting talks during the conference about research and a variety of open source tools. It was also fun switching between the Galaxy and BOSC sessions (the two parallel community tracks) when topics got a little complicated in one of the sessions.</p> <p>Abigail Cabunoc Mayes’ keynote was really amazing where she talked about understanding bias and discrimination in research data and code, and how to combat them in our work. Lincoln Stein’s keynote about how open source has changed the world was also really insightful and I got to understand a bit about the processes involved in the research. The keynote about how open minds bring open collaborations by Prashanth Suravajhala was also very interesting.</p> <p>In between sessions, I enjoyed joining different virtual tables and going to different virtual floors on Remo where I got to interact with really cool people during the conference.</p> <p>I learned a lot, and also realized that there’s a lot more out there that I don’t know. I’m encouraged to continue pursuing my goals in bioinformatics and soon enough, be able to contribute to open source as well.</p>https://www.open-bio.org/2020/08/16/bcc2020-edidiong-etuk/Sun, 16 Aug 2020 11:55:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/08/16/bcc2020-edidiong-etuk/<p><em>The <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Edidiong Etuk (Eddie), an open-source lover and a software engineer from Nigeria, was supported to take part in <a href="https://www.open-bio.org/events/bosc/about/">Bioinformatics Open Source Conference</a> 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p><strong>TL;DR</strong> This post is about my experience at Bioinformatics Community Conference 2020.</p> <p>Before attending the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference</a> (BCC) 2020, I had zero experience with Bioinformatics. But, after the conference, I am more confident in my ability to tackle bioinformatics-related tasks, challenges and discussions. I enjoyed every moment of BCC2020 virtual conference, hung out with a lot of cool folks through the <a href="http://remo.co/">Remo conference platform</a>, and got introduced to new concepts in bioinformatics through workshops, keynotes, short talks, poster sessions and community interactions. In this post, I am summarising my experiences and lessons learned from this conference.</p> <h2 id="bcc-pre-conference-workshops">BCC Pre-Conference Workshops</h2> <p>I registered for two workshops: <a href="https://docs.dockstore.org/en/develop/getting-started/getting-started.html"><em>Dockstore Fundamentals: Introduction to Docker and Descriptors for Reproducible Analysis</em></a> and I must say I found them easy to understand as a beginner. I had an idea of what <a href="https://www.docker.com/">Docker</a> was but the tutors made working with Docker so easy. They also switched up and explained Descriptors (focus was on <a href="https://openwdl.org/">Workflow Description Language</a>). It was a good introduction to Dockstore.</p> <p>Next, I attended Reproducible Analysis in the Cloud with <a href="https://dockstore.org/">Dockstore</a> and <a href="http://terra.bio/">Terra</a>, where I got introduced to Terra, <a href="https://anvilproject.org/">Anvil</a>, and learned more about Dockstore. The ability to access data, run analysis, and use the cloud all from Terra while fostering collaboration is what this training was about. All experiments I toyed with, worked and results could be seen easily and tracking bugs or experiment failure was seamless.</p> <p>One regret I had during the workshops is the number of sessions I missed. All the sessions were so interesting that I wished I could attend all training and workshops. All the training materials and notes were made available, so I guess I’d have enough resources to start with when learning them on my own.</p> <h2 id="main-conference">Main Conference</h2> <p>I attended the West sessions of the 3-day main conference as this favored my timezone. As a volunteer for BOSC, I spent a lot of my time in the BOSC building (yes a virtual building). There were several interesting talks during the conference about research and a variety of open-source tools which I can’t point to, but some of those I describe below.</p> <p><strong>Day 1</strong></p> <p>Day 1 started with a keynote from Lincoln Stein who showed us how Open-Source has improved the biomedical world.</p> <p>The presentations were all short and precise and though some were very technical, I got a thing or two from them. The most memorable presentation was <a href="https://bcc2020.sched.com/event/coKR/streamlining-accessibility-and-computability-of-large-scale-genomic-datasets-with-the-nhgri-genome-data-science-analysis-visualization-and-informatics-lab-space-anvil"><em>Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL)</em></a>.</p> <p>It was very relatable and I applaud the creativity behind the presentation, bravo Michael!!</p> <p>Poster sessions were cool and were held in a different virtual building from Galaxy and BOSC tracks. This was a good opportunity for me to see innovative work by the researchers in various bioinformatics communities. I also had a chance to chat with the representatives of the sponsors at the sponsor tables.</p> <p><strong>Day 2</strong></p> <p>On Day 2, Prashanth N Suravajhala gave the keynote on the importance of mentoring students. It was sad to hear that the building he was delivering his keynote from had some emergency situation during the presentation, but kudos to him for delivering an excellent keynote.</p> <p>Another memorable session was <em>Building open source communities and empowering new contributors</em> by Yo Yehudi. This talk was important as without Yo’s mentorship from Outreachy, I wouldn’t be here (Thanks Yo!). Although that session clashed with a Galaxy session, luckily the recordings were made available so I got to watch <em>The cloud-native Galaxy: Galaxy on Kubernetes</em>. I’m interested in everything Kubernetes so the session, of course, interested me.</p> <p><strong>Day 3</strong></p> <p>Day 3 hit closer to home due to my work at <a href="https://github.com/getpopper/popper">Popper</a>, everything about workflow management seemed understandable. Although I gotta add, there are a lot of workflow engines out there for reproducibility in research.</p> <p>It would make a lot of sense if they all came together to do a conference to ensure we’re all going in the same direction and not competing with each other. Of course, there were a lot of interesting posters which I got to check out.</p> <h2 id="welcoming-community">Welcoming Community</h2> <p>Everyone at BCC 2020 was very welcoming, Birds of a Feather session at the virtual-bar was a great addition to the event. I had my drink with me, and of course, we all drank responsibly (lol!). I enjoyed switching tables and going to different floors on Remo where I got to interact with warm and friendly people during the conference.</p> <p>The Bioinformatics community is the most welcoming out there! Special shout out to everyone who made me feel welcome, Michael R. Crusoe, Dave Clements, Emmy Tsang (who pronounced my name very well), Nomi Harris, and others! You were all fun to hang with and I hope next year I can meet y’all in person!</p> <p>BCC exemplified diversity in tech and I loved it. BOSC Happy Hour West was thrilling as we had 18 people on the stage (please don’t try this on Remo! 😬).</p> <h2 id="next-steps">Next Steps</h2> <p>Due to my interest in Bioinformatics, I am working to dockerize <a href="http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl">DoBlastzChainNet</a> and <a href="https://github.com/getpopper/popper">popperize</a> it to make it reproducible. This is going great and I’ll appreciate any help.</p> <p>Thanks to OBF for this amazing opportunity! Till next time!</p>https://www.open-bio.org/2020/08/13/lessons-learned/Thu, 13 Aug 2020 19:28:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/08/13/lessons-learned/<p><a href="http://bcc2020.github.io/">BCC2020</a> (the collaborative BOSC + GCC meeting) was held online, with over 800 people registered for some part of the meeting. We used <a href="http://remo.co/">Remo.co</a> as the technology platform, along with Discord for chat. Read about why we chose those, how it worked out, and our tips for others who are organizing virtual conferences <a href="https://bcc2020.github.io/blog/lessons-learnt">here</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/08/abby-chris-yo-greenroom-whole-room-1024x638.png" alt="">&ldquo;Table view&rdquo; in Remo during BCC2020</p>https://www.open-bio.org/2020/07/08/bcc2020-pre-conference-open-house/Wed, 08 Jul 2020 04:06:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/07/08/bcc2020-pre-conference-open-house/<p><img src="https://www.open-bio.org/wp-content/uploads/2020/07/Screen-Shot-2020-07-07-at-9.53.48-PM.png" alt="virtual open house"></p> <p>After much discussion, the <a href="https://bcc2020.github.io/">BCC2020</a> organizing committee has decided to hold the meeting on <a href="https://remo.co/remo-101/">Remo.co</a>, which is similar to Zoom but offers a more conference-like experience, with &ldquo;floors&rdquo; and &ldquo;tables&rdquo; where you can mingle with other attendees. It has great small group and presentation support, including for posters and demos. It&rsquo;s also more fun than most online conference platforms.</p> <p>Because Remo is not familiar to most BCC participants, we are holding two open houses, one in each hemisphere, the day before BCC training starts. These walk-throughs will introduce participants to Remo&rsquo;s features and demonstrate how to navigate between sessions, poster/demos, BoFs, training and everything else.</p> <p>All <a href="https://bcc2020.github.io/Registration/">registered participants</a> will receive invites by email the day before the open houses. If you&rsquo;re not already registered, remember that the early registration discount ends on July 10, and registration will close on July 15.</p> <p>The events below show up in the Eastern US timezone (ET) but you can follow the instructions to switch to your local timezone.</p> <ul> <li><a href="https://bcc2020.sched.com/event/d0ub/pre-bcc-open-house">Western hemisphere open house</a> (Thursday, July 16)</li> <li><a href="https://bcc2020.sched.com/event/d0uh/pre-bcc-open-house%22">Eastern hemisphere open house</a> (Friday, July 17)</li> </ul> <p>We are looking forward to showing you the BCC venue. (But you&rsquo;ll have to bring your own snacks.)</p>https://www.open-bio.org/events/bosc-2020/schedule/Wed, 17 Jun 2020 03:38:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/schedule/<h2 id="this-is-the-schedule-for-2020-the-2021-schedule-is-here">(This is the schedule for 2020. The 2021 schedule is <a href="https://www.open-bio.org/events/bosc-2021/bosc-2021-schedule/">here</a>.)</h2> <h4 id="bcc2020-overview-complete-bcc2020-schedule-here">BCC2020 overview (complete BCC2020 schedule <a href="https://bcc2020.sched.com/">here</a>)</h4> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/06/Screen-Shot-2020-06-20-at-5.40.19-PM.png" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/06/Screen-Shot-2020-06-23-at-4.41.27-PM.png" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/06/Screen-Shot-2020-06-20-at-5.41.09-PM.png" alt=""></p> <h4 id="bosc-2020-talk-schedule">BOSC 2020 Talk Schedule</h4> <p>Below are the talks accepted to BOSC 2020 from submitted abstracts. The full schedule of BOSC and Galaxy talks (in both hemispheres) is available on the <a href="https://bcc2020.sched.com/">sched page</a>. You can filter that schedule by Eastern or Western hemisphere (and also choose your time zone).</p> <h4 id="postersdemos">Posters/Demos</h4> <p><a href="https://bcc2020.sched.com/overview/subject/Poster-Demo">Posters and demos are now included in the BCC schedule</a>! There is one poster session per day per hemisphere. Each poster presenter is assigned to one poster session, but you can visit and comment on posters any time during the conference.</p> <h4 id="birds-of-a-feather-bofs">Birds of a Feather (BoFs)</h4> <p>Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.</p> <p>The <a href="https://bcc2020.sched.com/overview/subject/BoF">BCC2020 BoF schedule is here</a>. BoFs are held just before and after each day of the main conference. BCC2020 attendees are also welcome to organize informal BoFs as table chats.</p> <h3 id="collaborationfest">CollaborationFest</h3> <p>BOSC runs a collaborative work event (formerly called CodeFest, and now called <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest, or CoFest</a> for short) before or after the conference. At these events, participants work together to contribute to bioinformatics software, documentation, training materials, and use cases. <a href="https://www.open-bio.org/events/bosc/collaborationfest/">This year&rsquo;s CoFest and CoFest Encore</a> will take place online the four days after BCC2020. <a href="https://bcc2020.github.io/Registration/">Registration</a> is required, but there is no charge.</p>https://www.open-bio.org/2020/05/25/biopython-1-77-released/Mon, 25 May 2020 14:34:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/05/25/biopython-1-77-released/<p>Biopython 1.77 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.77">PyPI</a>.</p> <p>This is the first release since we dropped support for Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.</p> <p>This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been tested on PyPy3.6.1 v7.1.1.</p> <p><code>pairwise2</code> now allows the input of parameters with keywords and returns the alignments as a list of <code>namedtuples</code>.</p> <p>The codon tables have been updated to NCBI genetic code table version 4.5, which adds <em>Cephalodiscidae</em> mitochondrial as table 33.</p> <p><code>Bio.Restriction</code> has been updated to the January 2020 release of REBASE.</p> <p>A major contribution by Rob Miller to <code>Bio.PDB</code> provides new methods to handle protein structure transformations using dihedral angles (internal coordinates). The new framework supports lossless interconversion between internal and cartesian coordinates, which, among other uses, simplifies the analysis and manipulation of coordinates of protein structures.</p> <p>As in recent releases, more of our code is now explicitly available under either our original &quot; <em>Biopython License Agreement</em>&quot;, or the very similar but more commonly used &quot; <em>3-Clause BSD License</em>&quot;. See the <code>LICENSE.rst</code> file for more details.</p> <p>Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the <code>black</code> tool.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alexander Decurnou (first contribution)</li> <li>Andrei Istrate (first contribution)</li> <li>Andrey Raspopov</li> <li>Austin Varela (first contribution)</li> <li>Chris Daley</li> <li>Chris Rands</li> <li>Deepak Khatri</li> <li>Hielke Walinga (first contribution)</li> <li>Kai Blin</li> <li>Karthikeyan Singaravelan (first contribution)</li> <li>Markus Piotrowski</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Rob Miller</li> <li>Sergio Valqui</li> <li>Steve Bond</li> <li>Sujan Dulal (first contribution)</li> <li>Tianyi Shi (first contribution)</li> </ul> <p><em>Update</em>: And the following two whom we had initially wrongly listed under the previous release:</p> <ul> <li>Artemi Bendandi (first contribution)</li> <li>Konstantinos Zisis (first contribution)</li> </ul>https://www.open-bio.org/2020/05/22/help-us-make-bcc2020/Fri, 22 May 2020 18:31:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/05/22/help-us-make-bcc2020/<p>We&rsquo;re old hands at organizing in-person <a href="https://www.open-bio.org/events/bosc/about/">BOSC</a> s (some of us were involved in planning the very first BOSC, in 2000), but this is the first time we&rsquo;re attempting an online conference, and we want your help to make <a href="https://bcc2020.github.io/">BCC2020</a> a rewarding experience for all.</p> <p>We know many of you have attended other virtual conferences recently, and we&rsquo;re interested in hearing what worked well and what didn&rsquo;t. In particular, we are trying to figure out how to make virtual posters work, and how to run Q&amp;A (with audio, or just typed? live, right after the talks, or asynchronous?). We&rsquo;re also interested in ideas for adding fun social elements to what could otherwise be a pretty dull extended videoconference.</p> <p>To share your ideas with us, we invite you to join one or both of our public gitter chat rooms: BOSC: <a href="https://gitter.im/OBF/BOSC_community">https://gitter.im/OBF/BOSC_community</a> BCC: <a href="https://gitter.im/bcc2020/community">https://gitter.im/bcc2020/community</a></p> <p>Or, if you prefer, you can email us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>.</p> <p>We look forward to your suggestions, and hope to see you at <a href="https://bcc2020.github.io/">BCC2020</a>!</p>https://www.open-bio.org/2020/05/08/obf-travel-fellow-2020-1/Fri, 08 May 2020 14:20:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/05/08/obf-travel-fellow-2020-1/<p><strong><em>on behalf of the OBF Board members</em></strong></p> <p>We are delighted to announce that four awardees have been selected to receive the OBF travel fellowship for 2020 round 1, to support their participation in virtual events.</p> <p>The OBF travel fellowship is now offered 2 times a year to multiple awardees towards supporting their participation in scientific workshops, conference and training events. The selection of individuals is made based on their applications, which state how their participation in the chosen event helps them promote open science practices in bioinformatics and/or enhance representation of minority groups in their communities.</p> <p>In response to the current COVID-19 outbreak, as most conferences have moved online, this fellowship will support our awardees in attending virtual conferences ( <a href="https://www.open-bio.org/2020/03/13/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19-%ef%bb%bf/">see our last blog</a>) by helping them pay any costs related to their participation such as registration fees, headset, internet and other small hardware needs. With this step, we also want to urge our community members to consider ways that minimise the impact of global health emergencies being caused by this pandemic.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/05/OBF-fellow-2020-1-1024x683.jpeg" alt="A person attending an online call/course and taking down notes. There is a cup coffee, reading glasses, diary and books on next to their laptop.">Image on Unsplash by @thoughtcatalog: <a href="https://unsplash.com/photos/505eectW54k">https://unsplash.com/photos/505eectW54k</a></p> <p>Read more about our awardees below:</p> <p><strong>Gigi Kenneth</strong> is a biochemistry undergrad and a bioinformatics enthusiast who has been learning ways to combine biochemistry and deep learning through open-source tools and tutorials. As a young researcher from Nigeria, Gigi has had very little opportunity to learn about bioinformatics events during her university courses. Therefore, she would like to attend the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC) 2020</a> from 19 to 21 July 2020. This event combines the Bioinformatics Open Source Conference and Galaxy Community Conference, 2020. This opportunity will expose Gigi to the current practices in bioinformatics that she can bring back to her community.</p> <p><strong>Armando Blondel Djiyou Djeuda</strong> is from Cameroon and will be hosting a virtual classroom for the <a href="https://h3abionet.org/categories/training/introduction-to-bioinformatics-training-2020">H3ABioNet‘s Introduction to Bioinformatics course (IBT)</a> at the Biotechnology Center, University of Yaounde I. This year, Armando decided to host this event because no other host was selected in Central Africa last year, and as a result, he was unable to attend this course. Over a period of 3 months, IBT provides an introduction to the field of bioinformatics using a distance-based learning model, where classrooms are set up at different sites and trainers are supported via the conferencing system in biweekly sessions. Armando has found that compared to other African countries, skills in Bioinformatics and genomics are lacking in Cameroon and Central Africa in general and this opportunity will help expand bioinformatics skills and knowledge in an underrepresented region.</p> <p><strong>Edidiong Etuk</strong> became interested in bioinformatics after contributing to <a href="http://intermine.org/">InterMine</a>, an open-source biological resource, during the <a href="https://www.outreachy.org/">Outreachy</a> contribution period. This was a unique opportunity for Edidiong as he could participate in the open source community online while still living in Nigeria. Edidiong will be attending BCC 2020 to enhance his knowledge of bioinformatics. He also hopes that his participation will help him represent his community of Ibibo people, an ethnic group that is widely underrepresented in the Open Science community.</p> <p><strong>Pengfei Fan</strong>’sresearch project on optical imaging and sensing integrates deep learning approaches to develop a robust ultrathin multimode fibre based endoscope. This research theme relates to both Data Science and Artificial Intelligence and aims to answer many fundamental questions in genomics and biology. Pengfei will be presenting his current research results at <a href="https://www.cleoconference.org/home/">CLEO 2020</a> taking place online from 11 to 15 May 2020. In this talk, Pengfei will highlight the open source software, code and datasets published by their research team and invite interdisciplinary or translational project collaborations from young researchers.</p> <p>Congratulations once again to our newest awardees!</p>https://www.open-bio.org/2020/05/03/bcc2020-inc-bosc-2020-abstracts-due-this-week/Sun, 03 May 2020 12:28:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/05/03/bcc2020-inc-bosc-2020-abstracts-due-this-week/<p>We look forward to receiving lots of abstracts by the end of this week from people interested in presenting at the online <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>, which combines the Galaxy Community Conference, and our own Bioinformatics Open Source Conference (BOSC). The <a href="https://bcc2020.github.io/submit/">BCC2020 abstract submission</a> deadline is Friday 8 May 2020.</p> <p>Some of the recent round of the <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowships</a> will be supporting BCC2020 attendees with video conferencing costs (headsets, web-cameras, etc), full announcement coming soon.</p>https://www.open-bio.org/events/bosc-2019/bosc-2019-collaborationfest/Tue, 28 Apr 2020 13:47:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2019/bosc-2019-collaborationfest/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/attendees_stairs.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h1 id="collaborationfest-2019">CollaborationFest 2019</h1> <p>In conjunction with our annual meeting BOSC, the OBF runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute to bioinformatics software, documentation, training materials, and use cases.</p> <p>CoFest 2019 took place the two days after BOSC, July 26-27, 2019, at <a href="https://www.dayone.swiss/dayone.html">The Swiss Innovation Hub for Personalized Medicine</a> in Basel, Switzerland. <a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit#gid=0">Registration</a> is free; <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsorships</a> offset the cost of venue, coffee and snacks.</p> <p><a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit#gid=0">Sign up</a> now to attend in person or partipate remotely!</p> <h2 id="objectives">Objectives</h2> <p>CoFest is an opportunity for anyone interested in open science, biology and programming to meet, discuss and work collaboratively. Everyone is welcome to attend. We will have a mix of experienced developers, users, trainers, and researchers, newcomers to bioinformatics, and everything in between.</p> <p>The goal of many collaborative work events is to produce code, period. CoFest&rsquo;s goals are much wider:</p> <ul> <li>Grow and foster the contributor community for open source bioinformatics projects.</li> <li>Extend, enhance, and otherwise improve open source bioinformatics code.</li> <li>Create, extend, and otherwise improve non-code artifacts, such as documentation and training materials</li> </ul> <h2 id="what-to-expect">What to expect</h2> <p>The BOSC CollaborationFest is a collaborative two-day working session. The only requirement for attendance is that you have an interest in open source software and solving scientific problems. We will have contributors to open source bioinformatics tools present to collaboratively work with, and we welcome new attendees who want to learn and contribute to open source code or documentation.</p> <p>The rough structure of the two days is:</p> <ul> <li>Start about 9am with introductions from everyone attending about their goals and plans for the two days.</li> <li>Assemble into working groups based on shared interests like programming languages, open source projects or biological questions. We use the <a href="https://docs.google.com/document/d/1UaScEaOchWPCTdBei8PLCIcKLEqVdhDimOj4zFydhnk/edit?usp=sharing">collaboratively brainstormed Google document</a> as the basis for setting up groups. Attendees determine the goals for the two days. If you have an idea for a project, please add it before the event. Any and all suggestions are welcome.</li> <li>Work and discuss. Enjoy a productive time.</li> <li>We&rsquo;ll have regular breaks where each group can deliver short reports on their progress, with a daily wrap up session from about 6pm.</li> <li>We have informal lunches, dinners, and drinks as a way for everyone to get to know each other better.</li> <li>At the end of the two days, we summarize contributions and work accomplished in a meeting report.</li> </ul> <h2 id="attending">Attending</h2> <p>You are very welcome to attend. There is no cost; we only ask you to register to help organize numbers. Please add yourself if you are interested to <a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit?usp=sharing">this Google spreadsheet</a>. We&rsquo;ll coordinate through the <a href="https://gitter.im/chapmanb/obf-codefest">CoFest Gitter chat room</a> and <a href="https://gitter.im/OBF/BOSC_community">BOSC Gitter chat room</a>, so please sign up and introduce yourself there.</p> <p>If you&rsquo;re not able to physically attend, we&rsquo;re still more than happy to have you participate in CoFest. Please sign up on the <a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit?usp=sharing">the Google spreadsheet</a> and list yourself as remote only. Our <a href="https://gitter.im/chapmanb/obf-codefest">CoFest Gitter chat room</a> will be used to coordinate and discuss in real time and we&rsquo;ll have an open Google Hangout to make it easier to be part of CoFest remotely.</p> <p>Add your <a href="https://docs.google.com/document/d/1UaScEaOchWPCTdBei8PLCIcKLEqVdhDimOj4zFydhnk/edit?usp=sharing">project ideas to the shared google document</a>. The ideas can include smaller focused projects and larger work. We want suggestions from everyone and will organize into groups around these during CoFest.</p> <h2 id="code-of-conduct">Code of Conduct</h2> <p>The CoFest will be covered by <a href="https://www.iscb.org/ismbeccb2019-codeofconduct">ISMB’s Code of Conduct</a> (our preceding meeting BOSC 2019 is part of the ISCB organised ISMB/ECCB 2019 conference).</p> <h2 id="logistics">Logistics</h2> <p><a href="https://www.dayone.swiss/dayone.html"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/dayone_logo.png" alt="DayOne logo"></a></p> <p>The host venue for CoFest will be:</p> <p><a href="https://www.dayone.swiss/dayone.html">DayOne - The Swiss Innovation Hub for Personalized Medicine</a> Hochbergerstrasse 60C, 4057 Basel, Switzerland.</p> <p><a href="https://goo.gl/maps/AvZkyjvsm1DQrGmL6">https://goo.gl/maps/AvZkyjvsm1DQrGmL6</a> <a href="https://osm.org/go/0CdsbPozF?node=3215472544">https://osm.org/go/0CdsbPozF?node=3215472544</a></p> <p>More details like building access arrangements will be forthcoming.</p> <h2 id="history">History</h2> <p>This will be the 10th annual pre- or post-BOSC collaboration fest. Previous fun and successful events were <a href="https://www.open-bio.org/wiki/Codefest_2010">Codefest 2010</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> in Vienna, <a href="https://www.open-bio.org/wiki/Codefest_2012">Codefest 2012</a> in Los Angeles, <a href="https://www.open-bio.org/wiki/Codefest_2013">Codefest 2013</a> in Berlin, <a href="https://www.open-bio.org/wiki/Codefest_2014">Codefest 2014</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2015">Codefest 2015</a> in Dublin, <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a> in Orlando, <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> in Prague, and <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC Collaboration Fest 2018</a> in Portland.</p> <h2 id="sponsors">Sponsors</h2> <p>We welcome <a href="https://www.open-bio.org/events/bosc/sponsors/">sponsors</a> who want to be involved with the open source community. Sponsorship money will cover venue costs, help provide food and drink for the CoFest, and any surplus can help other activities like our <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation Travel Fellowships</a>. If interested, please get in touch with any of the CoFest organizers or the <a href="mailto:bosc@open-bio.org">BOSC committee</a> (general).</p> <h2 id="organizers">Organizers</h2> <p>CoFest 2019 organizers: <a href="https://github.com/apeltzer/">Alexander Peltzer</a>, <a href="https://github.com/heuermh">Michael Heuer</a>, <a href="https://github.com/peterjc">Peter Cock</a>, <a href="https://github.com/Pseudomanifold">Bastian Rieck</a>.</p>https://www.open-bio.org/2020/04/14/galaxy-admin-2020/Tue, 14 Apr 2020 16:15:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/04/14/galaxy-admin-2020/<p><em>The <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting Open Source bioinformatics software development and open science in the biological research community. Michael Thompson&rsquo;s participation at the</em> <a href="https://galaxyproject.org/events/2020-03-admin/">Galaxy Admin Training 2020</a> <em>workshop in Barcelona was supported by this fellowship. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p>I had the opportunity to visit the <a href="https://www.bsc.es/">Barcelona Supercomputing Center (B.S.C)</a> in Spain from 2nd - 6th March 2020 to participate in the <a href="https://galaxyproject.org/events/2020-03-admin/">Galaxy Admin Training 2020</a>, organized by <a href="https://galaxyproject.eu/">Galaxy Europe</a> and in partnership with <a href="https://www.bsc.es/">B.S.C</a>, <a href="https://elixir-europe.org/">Elixir</a>, and <a href="https://www.denbi.de/">de.NBI</a>.</p> <h3 id="purpose"><strong>Purpose</strong></h3> <p>The reason for attending was to gain the skill-set required to deploy and administer Galaxy within my university ( <a href="https://www.knust.edu.gh/">Kwame Nkrumah University of Science and Technology</a>) which currently has a small group of students and researchers involved in Bioinformatics. I have had previous experience with HPC applications although this was my first for Galaxy. Our university’s deployment of Galaxy is also intended to be open to any researcher within my country, Ghana.</p> <h3 id="the-event"><strong>The Event</strong></h3> <p>The event was very well organized with training provided by Helena Rasche  (Galaxy Europe), Nate Coraor (Galaxy Project, Penn State University, U.S.A), Marius van den Beek (Galaxy Project, Penn State University, Europe), Saskia Hiltemann (Erasmus Medical Center, the Netherlands), and Nicola Soranzo (Earlham Institute).</p> <p>The training materials are available <a href="https://github.com/galaxyproject/admin-training">here</a>.</p> <p>On the first day, after registration, we dived straight into the setup/installation using Ansible. It was followed by a talk on the advanced setup of the system and configuration of tool-sheds. Later that day, we had a tour of the Barcelona Supercomputing Center to see <a href="https://www.bsc.es/marenostrum/marenostrum"><em>MareNostrum</em></a> – a supercomputer with a peak performance of 11.15 Petaflops.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/03/20200302_GalaxyAdminTraining_MN4_2-1024x576.jpeg" alt="">Participants receiving a lecture on the architecture of MareNostrum.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/03/20200302_GalaxyAdminTraining_MN4_3-1024x576.jpeg" alt="">A guided tour of MareNostrum.</p> <p>The second day of the training hosted talks on deploying scientific tools using <em>Ephemeris</em>, configuring and using authentication methods, access to reference data for scientific analysis, configuring job scheduling, and connecting Galaxy to your existing HPC cluster.</p> <p>On day three, we continued with more about job scheduling and connecting to compute clusters, connecting to remote clusters using Pulsar, storage management, making queries with <em>Gxadmin,</em> and monitoring with <em>Telegraf</em>, <em>InfluxDB</em> and <em>Grafana</em>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/03/20200302_GalaxyAdminTraining_room-1024x576.jpeg" alt="">The training session.</p> <p>The fifth day was about using interactive tools, development (deploying your own tools), build automation and advanced customization of the software (user interface). There was a session on Training As A Service (TiaaS) – a feature that allows you to create small groups of dedicated resources within Galaxy for running training sessions in a manner that isolates itself from the production work on the same platform.</p> <p>On the last day, we had talks on how to deal with issues when they arise, management of different python versions, developing tools using <em>Planemo.</em> I had to leave before the very last talk about creating tutorials from the training resources provided.</p> <h3 id="takeaways"><strong>Takeaways</strong></h3> <p>Every part of the event had hands-on training exercises. During these exercises, the trainers did a very good job of sharing their experiences. These experiences – what I call ‘street wisdom ‘– were useful in situating the exercises in real-life scenarios.</p> <p>Particularly, I found the sessions on tool development, generating queries and monitoring very useful. The ability to integrate existing tools would enable the platform to support the different needs of the user community.  The monitoring and reporting utilities also provide an evidence-based and transparent approach to evaluating the usage of resources. This is important to demonstrate to our funders (the university in this case) how the facility is used and, when necessary, to make a case for upgrades or expansion.</p> <p>Everything about Galaxy is Ansible! It is an example of very extensive use of automation without which management and maintenance would far more tedious. It enforces the DRY (Don’t Repeat Yourself) philosophy; the packaging and documentation of the entire software platform is an encouragement to use configuration management software extensively (and in all types of large software deployments).</p> <p>Although a large number of the tools available on Galaxy are for use within the field of Bioinformatics, the platform has been designed to enable it to run almost any kind of tool. This means that one deployment of the platform can serve different scientific user groups if the available tools can be developed and integrated into the platform. To facilitate this, there is extensive tool development documentation. I find this particularly important in scenarios where there may not be a lot of resources (infrastructure, human, funding) to run different types of HPC platforms – some HPC/HTC installations out there are very limited, especially in developing countries. In my opinion, Galaxy alone, with a bit of effort in tool development, can be used to support a wide range of disciplines.</p> <h3 id="what-next"><strong>What Next</strong></h3> <p>The next few months will involve planning and organizing to deploy Galaxy for use locally. I am confident we would have some success stories and, hopefully, interesting use cases of the platform to share in another blog post later.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/03/e2-1024x611.jpg" alt="">Workshop participants at BSC.</p> <h3 id="thanks-to-obf"><strong>Thanks to OBF!</strong></h3> <p>The opportunity to participate in the Galaxy Admin 2020 Training in Barcelona would not have been possible without the travel fellowship from OBF. I have had the opportunity to connect with different Galaxy Admins and to join a community of people enthusiastic about providing support to the scientific community. Many thanks to OBF!</p> <p><strong>Me</strong></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/03/Me.jpg" alt=""></p> <p>I am an IT Manager at the University Information Technology Services (U.I.T.S) of the Kwame Nkrumah University of Science and Technology (K.N.U.S.T). I am also a member of the H3ABioNet project.</p>https://www.open-bio.org/2020/04/03/james-taylor-in-memoriam/Fri, 03 Apr 2020 23:08:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/04/03/james-taylor-in-memoriam/<p>The Open Bioinformatics Foundation was shocked and saddened to learn that our colleague and collaborator <a href="https://bio.jhu.edu/2020/04/03/in-memoriam-professor-james-taylor/">James Taylor, a professor of biology and computer science at Johns Hopkins University, died on April 2, 2020</a>. James was one of the creators and PIs of the Galaxy Project, which is among the most widely used platforms in open bioinformatics. The Galaxy community has created a <a href="https://galaxyproject.org/news/2020-04-james-taylor/">tribute page</a> for James.</p> <p>We have close ties to James and the Galaxy project via our flagship conference. <a href="https://www.open-bio.org/events/bosc/">BOSC</a>, which was first held in partnership with the Galaxy Community Conference (GCC) in 2018, will again be co-hosted with GCC at the online Bioinformatics Community Conference (BCC2020) this July.</p> <p>OBF joins many others in mourning the loss of a pillar of the bioinformatics community.</p>https://www.open-bio.org/2020/03/24/bosc-2020-will-be-online/Tue, 24 Mar 2020 16:29:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/03/24/bosc-2020-will-be-online/<p><a href="https://bcc2020.github.io/">The 2020 Bioinformatics Community Conference (BCC2020)</a>, which brings together the BOSC and Galaxy communities, will take place online&ndash;more info <a href="https://bcc2020.github.io/blog/going-virtual">here</a>.</p> <p>The online meeting will still be held July 18-21. Registration will open in a few weeks, and fees will be lower than for an in-person meeting. <a href="https://www.open-bio.org/events/bosc/submit/">Abstract submission</a> will open soon and will close April 30th. We will follow the usual submission and review processes.</p> <p>We are discussing how to arrange the schedule to allow for participation across the globe. We welcome your input on how to make our first Virtual Bioinformatics Community Conference a success.</p>https://www.open-bio.org/2020/03/13/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19-%EF%BB%BF/Fri, 13 Mar 2020 22:16:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/03/13/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19-%EF%BB%BF/<p>In light of the current outbreak, we urge everyone to avoid travelling if possible, in order to slow the rate at which the virus spreads to vulnerable people. You may have read that the <a href="https://bcc2020.github.io/blog/postponement">BCC (BOSC+Galaxy) committee is delaying registration whilst considering the best options</a>.</p> <p>With the next <a href="https://www.open-bio.org/travel-awards/">travel fellowship deadline</a> approaching on April 1st, we are issuing slightly different advice regarding the types of applications we’d like to see, compared to previous years.</p> <h2 id="lets-go-remote">Let’s go remote</h2> <p>Given how many conferences are (quite sensibly) being cancelled at the moment, we would like to help facilitate remote conferences where possible. We are open to creative ideas for ways to increase diversity and representation for remote conferences. </p> <p>As an example, this might mean that instead of spending your fellowship on a hotel and travel, your fellowship budget might cover a headset, webcam, remote conference fee, and access to high-speed internet for the duration of the conference. This is not an exhaustive list of things we are willing to consider covering - you may have better ideas for ways to manage safe virus-free conference participation and we’d love to hear them and/or see your application for a fellowship. Like before, fellowships are open to people anywhere in the world, so long as they’re for open+bio related events. </p> <h2 id="still-planning-to-attend-something-in-person">Still planning to attend something in person?</h2> <p>We have the following tips if you do wish to request an in-person conference related fellowship: </p> <ul> <li>Please make sure to budget for travel insurance. This is a requirement for any fellowships to be granted - but be aware that many travel insurance policies may not cover cancellations due to events such as pandemics.</li> <li>Applications to attend conferences with dates a long time in the future, e.g. late 2020 or early 2021, may be better candidates for travel fellowships than conferences that are scheduled in the near future, though of course we don’t know when the outbreak will be contained and travel will become safe.</li> </ul>https://www.open-bio.org/2020/03/02/obf-accepted-for-gsoc-2020/Mon, 02 Mar 2020 03:47:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/03/02/obf-accepted-for-gsoc-2020/<p>OBF has been selected as a Google Summer of Code <a href="https://summerofcode.withgoogle.com/organizations/4996161846378496/">mentor organisation</a> for the 5th consecutive time! We are proud to be hosting over <a href="http://open-bio.org/events/gsoc/project-ideas/">13 projects</a> from various sub-organisations that aim to promote open science. This year OBF&rsquo;s application was led by Sarthak Sehgal, Kai Blin, Yo Yehudi, and Michael Crusoe. Last year, <a href="https://summerofcode.withgoogle.com/archive/2019/organizations/5294944380518400/">GSoC 2019</a>, was another good year with five students successfully completing their projects.</p> <h2 id="call-to-students-to-apply-for-gsoc">Call to students to apply for GSoC</h2> <p>OBF is welcoming students across the globe with a passion for open science to apply for GSoC. You can view the eligibility criteria <a href="https://developers.google.com/open-source/gsoc/faq">here</a> and the whole timeline <a href="https://developers.google.com/open-source/gsoc/timeline">here</a>. The application portal opens on March 16 but feel free to contact the mentors of projects you are interested in already. It’s a fantastic opportunity to write code, learn about open source development, and be a part of a welcoming and diverse community, while earning a stipend! All information about OBF&rsquo;s GSoC participation can be found <a href="http://open-bio.org/gsoc/">here.</a></p> <h3 id="looking-forward-to-another-successful-google-summer-of-code">Looking forward to another successful Google Summer of Code!</h3>https://www.open-bio.org/2020/02/17/travel-fellowship20-round1/Mon, 17 Feb 2020 09:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/02/17/travel-fellowship20-round1/<p>We are currently accepting applications for the <strong>first application round for the <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> 2020</strong>. This fellowship aims to promote the conference/event participation of attendees who advocate and present their work related to open-source bioinformatics software development and open science in the biological research community. In 2019, a total of 9 applicants received OBF travel fellowships to attend various conferences across the globe to present their work, gain new skills and promote Open Science practices in their respective areas of life science.</p> <p><strong>Apply for <a href="https://docs.google.com/forms/d/e/1FAIpQLScCYMt_Id9FSKzHtOxyBgiOIXa61CLiveqh5JLx5rQsFoW8fA/viewform">round 1 of 2020 here</a>.</strong></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/02/open-1-1-3.jpeg" alt=""></p> <p>(Image on <a href="https://unsplash.com/photos/ZYBl6VnUd_0">Unsplash by @timmossholder</a>)</p> <p>If you are unsure of your eligibility for this fellowship or want to understand the fellowship process better, check the details on our <a href="https://www.open-bio.org/travel-awards/">website</a> and read <a href="https://www.open-bio.org/category/travel-fellowship/">blog posts of past recipients</a>.</p> <p>The <a href="https://www.open-bio.org/events/bosc/">Bioinformatics Open Source Conference (BOSC)</a> will be joining the Galaxy Community Conference at <a href="https://bcc2020.github.io/">BCC2020</a> - the Bioinformatics Community Conference. The main conference will take place from 19 to 21 July 2020 at <a href="https://bcc2020.github.io/location/">Victoria University in Toronto, Canada</a>. The optional pre-conference training day will be 18 July and the CoFest and CoFest Encore days will span from 22 to 25 July. Registration for BCC2020 will open in March 2020 ( <a href="https://bcc2020.github.io/Registration/">see details</a>).</p> <p>The fellowship application deadline for this round is <strong><a href="https://www.timeanddate.com/countdown/to?iso=20200401T23&amp;p0=63&amp;font=cursive&amp;csz=1">1 April 2020, midnight in any part of the world</a></strong>. Those who plan to attend BCC2020 or other conferences related to open source / open science, and whose presence would promote diverse skills and perspectives, are encouraged to <a href="https://www.open-bio.org/travel-awards/">apply</a>.</p>https://www.open-bio.org/2020/01/14/obf-board-elections-december-2019/Tue, 14 Jan 2020 16:47:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/01/14/obf-board-elections-december-2019/<p>During the <a href="https://github.com/OBF/obf-docs/pull/71">public OBF Board Meeting held on December 17, 2019</a>, elections were held for five <a href="https://www.open-bio.org/board/">Board members</a> whose terms were about to expire. All five stood for re-election to the Board, though with some changes of officers:</p> <ul> <li>Hilmar Lapp: stepped down after 8 years as President of the Board; elected to At-Large seat.</li> <li>Peter Cock: elected as President of the Board.</li> <li>Heather Wiencko: elected as Treasurer, replacing previous Treasurer Peter Cock.</li> <li>Chris Fields: re-elected as Secretary.</li> <li>Nomi Harris: re-elected as At-Large Board member.</li> </ul> <p>In accordance with the <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">OBF Bylaws</a>, the newly elected Board members and officers will serve a three-year term.</p> <p>The Board thanked Hilmar for his many years as President. Hilmar oversaw or supported many major changes including moving to SPI as a fiscal sponsor, introduction of the Travel Fellowships, and our ongoing work to introduce a code of conduct and formalise our affiliate project policy. We are grateful that Hilmar will continue to contribute to the Board as a member at large.</p>https://www.open-bio.org/events/gsoc/gsoc-contact/Sun, 05 Jan 2020 15:55:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/gsoc/gsoc-contact/<h1 id="contact">Contact</h1> <p>Before applying, please read our <a href="https://www.open-bio.org/wp/events/gsoc/gsoc-guide">documentation on information that GSoC contributors should know and guidelines we expect you to follow</a>. We also require that you include certain information, listed below, under “ <a href="https://www.open-bio.org/wp/events/gsoc/gsoc-guide#when-you-apply">When you apply.</a>”</p> <p>Also, it would be a good idea to CC the organization administrator group email below, so they can make sure that you are properly taken care of!</p> <p>If you are not quite sure which project you would like to contribute to, you can email to the organization administrator for help. However, do not worry overly much about picking the right OBF project at the outset. If you are unsure, simply make your best guess, and other members of the email list will help you to find the best organization to suit your idea.</p> <h2 id="general-queries">General queries</h2> <p>If a question needs to be answered by a specific mentor, please email that mentor, or an org admin if your mentor is not responding. For more general GSoC OBF queries, please use <a href="https://groups.google.com/g/obf-gsoc-general">https://groups.google.com/g/obf-gsoc-general</a>. Note that the OBF board are not usually able to help with GSoC queries.</p> <h2 id="staff-and-org-admins">Staff and Org Admins</h2> <h4 id="organisation-administrator">Organisation administrator</h4> <p>Whenever possible please email the OBF GSoC Admin group - <a href="mailto:obf-gsoc-admins@googlegroups.com">obf-gsoc-admins@googlegroups.com</a> - this reaches all admins.</p> <h2 id="project-specific-queries">Project-specific queries</h2> <p>For prospective GSoC contributors, the first point of contact should be the mailing list or mentors of the OBF project you are interested in working with, but if ever in doubt please contact the org admin group above.</p>https://www.open-bio.org/events/gsoc/gsoc-project-ideas/Sun, 05 Jan 2020 15:45:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/gsoc/gsoc-project-ideas/<h1 id="google-summer-of-code-2022-project-ideas">Google Summer of Code 2022 Project Ideas</h1> <hr> <p>Shortcut to project ideas:</p> <ul> <li><a href="#feature-viewer">Configurable feature visualization to improve the user experience and performance of the feature viewer</a></li> <li><a href="#openms-data-format">Space- and time-efficient data format for mass spectrometry data (OpenMS)</a></li> <li><a href="#efficient-layout-openms">Efficient data layout for mass spectrometry data (OpenMS)</a></li> <li><a href="#gpu-cwl-toil">GPU support for Toil-CWL-Runner (UCSC/CWL Project)</a></li> <li><a href="#openms-autowrap">Improving automated wrapping of C++ code in Python (OpenMS/autowrap)</a></li> <li><a href="#journal-tracker-express">Migration of Journal Policy Tracker backend to Express + GraphQL</a></li> <li><a href="#journal-tracker-css">Journal tracker - finalise and deploy React front-end</a></li> <li><a href="#genestorian-data-refinement">Genestorian: data refinement</a></li> <li><a href="#citation-and-databasing-functionality-in-luox">Citation and databasing functionality in luox</a></li> </ul> <h5 id="cross-project-ideas">Cross-Project Ideas</h5> <p>OBF is an umbrella organization which represents many different programming languages used in bioinformatics. In addition to working with each of the “Bio*” projects (listed below) we also accept “cross-project” ideas that cover multiple programming languages or projects. These collaborative ideas are broadly defined and can be thought of as “unfinished” — interested contributors should adapt the ideas to their own strengths and goals, and are responsible for the quality of the final proposed idea in their application.</p> <p><strong>Feel free to propose your own entirely new idea.</strong></p> <hr> <h6 id="configurable-feature-visualization-to-improve-the-user-experience-and-performance-of-the-feature-viewer">Configurable feature visualization to improve the user experience and performance of the feature viewer</h6> <p><strong>Project description</strong></p> <p>Analyzing positional features/annotations in sequences is important in bioinformatics. Visualizing such data is quite a challenging task, considering the large amount of data to be displayed. The feature viewer is an open source javascript library developed to visualize biological data (referred to as features) mapped to a linear sequence (Paladin et al., 2020). For instance, it can be configured to visualize the location of protein domains or amino acid variations in a protein sequence. The feature viewer is being used in several popular bioinformatics resources such as neXtProt and COSMIC 3D.</p> <p>Currently, the feature viewer supports limited configurability options in the features displayed, such as the color, shape and on-click behavior. This is too restrictive for some of the possible use cases of the feature viewer, where more flexibility is required in the display of features. One such instance is when different types of amino acid variants should be displayed in a color-specific manner in the same feature track.</p> <p>The overall goal of this project is to improve the configurability of the feature viewer, such that it allows greater flexibility in the visualization of detailed biological data. Specific aims of the project are:</p> <ul> <li> <p>Simplify the configuration of new tracks</p> <p>The current version of the feature viewer requires new tracks to be hard-coded. Implementing a solution allowing new tracks to be added or existing tracks to be modified or deleted would ease the use of the viewer.</p> </li> <li> <p>Add graphical representations of numerical features</p> <p>Protein sequences can have features/annotations which are numerical. For instance, the frequency observed in a population of amino acid variants at a specific position. Such numerical data can be visualized as graphs of different types, such as line graphs or histograms.</p> </li> <li> <p>Configure the visualization of certain features in a class of feature</p> <p>Currently all the features displayed on a single track have the same color and/or shape; interesting features can not be highlighted using a different color or shape.</p> </li> <li> <p>Improve the speed of display by first displaying a summary or message</p> <p>Currently all the data displayed has to be provided before display, which results in slow loading and rendering time when there are tens of thousands of features. In order to improve the user experience, it is possible to initially show a message summarizing the data and only fetch and display the data on-demand by the user.</p> </li> <li> <p>Enable the user to download a snapshot of the current display</p> <p>The user community has requested a download button which generates a snapshot of the feature viewer. This feature will allow users to include an image of the data displayed in the feature viewer in a publication or elsewhere.</p> </li> </ul> <p><strong>Project size</strong></p> <ul> <li>350h</li> </ul> <p><strong>Languages and skills needed</strong></p> <ul> <li>Javascript</li> <li>HTML/CSS</li> <li>Git/Github</li> <li>Optionally: Java</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Medium to Hard</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>20 weeks</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Kasun Samarasinghe (<a href="mailto:kasun.wijesiriwardana@unige.ch">kasun.wijesiriwardana@unige.ch</a>)</li> <li>Lydie Lane (<a href="mailto:lydie.lane@sib.swiss">lydie.lane@sib.swiss</a>)</li> </ul> <p><strong>Contributor benefits</strong></p> <ul> <li>Gain experience in developing configurable libraries</li> <li>Gain experience in handling large amounts of data in web applications</li> <li>Gain experience on web application user experience</li> <li>Gain experience in biological data such as gene, protein sequences</li> </ul> <p><strong>How to apply</strong></p> <ul> <li>For information on how to apply, please contact mentors in the emails provided above.</li> </ul> <hr> <h6 id="space--and-time-efficient-data-format-for-mass-spectrometry-data-openms">Space- and time-efficient data format for mass spectrometry data (OpenMS)</h6> <p><strong>Project description</strong></p> <p>OpenMS is a framework for computational mass spectrometry. Modern mass spectrometers produce large files (e.g., 100 GB) that can’t be easily stored or accessed in the established XML file format mzML. Recently, an update to mzML has been developed that uses HDF5 to store Blosc compressed spectra in binary format: called mzMLb. In this project, the student will add a reader and writer for the mzMLb file format to OpenMS. To some extent, code from the OpenMS reader and writer for the mzML file format can be reused, as well as inspiration can be taken from reference implementations by other parties.</p> <p><strong>Project size</strong></p> <ul> <li>350h</li> </ul> <p><strong>Languages and skills needed</strong></p> <ul> <li>C++</li> <li>Git/GitHub</li> <li>Optionally: CMake</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Easy for experienced C++ programmers with good CMake and GitHub skills. Medium for experienced C++ programmers without CMake or GitHub skills.</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>20 weeks</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Timo Sachsenberg, GitHub: <a href="https://github.com/timosachsenberg">https://github.com/timosachsenberg</a></li> <li>Julianus Pfeuffer, GitHub: <a href="https://github.com/jpfeuffer">https://github.com/jpfeuffer</a></li> <li>Samuel Wein, GitHub: <a href="https://github.com/poshul">https://github.com/poshul</a></li> </ul> <p><strong>Contributor Benefits</strong></p> <ul> <li>Gain experience working in a friendly team of developers.</li> <li>Get a glimpse into the exciting field of bioinformatics / computational mass spectrometry.</li> <li>Obtain detailed knowledge on HDF5, which is widely used to store large data efficiently.</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>Please introduce yourself in our Gitter channel: <a href="https://gitter.im/OpenMS/OpenMS">https://gitter.im/OpenMS/OpenMS</a> and get in contact with us prior to writing a proposal.</li> </ul> <hr> <h6 id="efficient-data-layout-for-mass-spectrometry-data-openms">Efficient data layout for mass spectrometry data (OpenMS)</h6> <p><strong>Project description</strong></p> <p>OpenMS is a framework for computational mass spectrometry. It features a wide range of algorithms and data structures to process and analyze mass spectra. For some very computationally demanding parts, we performed manual code conversion to make the layout of our data better fit the data access patterns of our algorithms. We observed the biggest speedup switching the data layout from an Array of Structs (AoS) to a Structure of Arrays (SoA). In this project, the GSoC contributor will adapt our core data structure for mass spectra to AoS. Ideally, the contributor should be using a modern C++ zero-cost abstraction (e.g., building on <a href="https://github.com/crosetto/SoAvsAoS">https://github.com/crosetto/SoAvsAoS</a>) that makes the old code work without (or minimal) manual changes.</p> <p><strong>Project size</strong></p> <ul> <li>175h</li> </ul> <p><strong>Languages and skills needed</strong></p> <ul> <li>C++</li> <li>Git/GitHub</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Medium: requires a good understanding of modern C++.</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>12 weeks</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Timo Sachsenberg, GitHub: timosachsenberg</li> <li>Hannes Roest, GitHub: hroest</li> <li>Julianus Pfeuffer, GitHub: jpfeuffer</li> <li>Aditya R Rudra, Github: adityaofficial10</li> </ul> <p><strong>Contributor Benefits</strong></p> <ul> <li>Gain experience working in a friendly team of developers.</li> <li>Get a glimpse into the exciting field of bioinformatics / computational mass spectrometry.</li> <li>Learn and apply modern C++ features to a real-life project.</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>Please introduce yourself in our Gitter channel: <a href="https://gitter.im/OpenMS/OpenMS">https://gitter.im/OpenMS/OpenMS</a> and get in contact with us prior to writing a proposal.</li> </ul> <hr> <h6 id="gpu-support-for-toil-cwl-runner-ucsccwl-project">GPU support for Toil-CWL-Runner (UCSC/CWL Project)</h6> <p><strong>Project description</strong></p> <p>Teach the <a href="https://github.com/DataBiosphere/toil">TOIL workflow system</a> how to support GPUs with <a href="https://www.commonwl.org/user_guide/">CWL</a>. Optionally this can be expanded to HPC clusters. This will enable researchers to run specialized workflows that need occasional GPU support efficiently on university computing clusters.</p> <p><strong>Project size</strong></p> <ul> <li>Either 175 (basic support) or 350 hours (advanced job routing)</li> </ul> <p><strong>Languages and skills needed</strong></p> <ul> <li>Python</li> <li>Optional: HPC, Clustering</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Medium, or easier if you have experience with HPC or clustering.</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Michael Crusoe, <a href="https://github.com/mr-c">https://github.com/mr-c</a></li> <li>Lon Blauvelt, <a href="https://github.com/DailyDreaming">https://github.com/DailyDreaming</a></li> </ul> <p><strong>Contributor Benefits</strong></p> <ul> <li>Exposure to workflow engines and distributed computing</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>To get started, visit <a href="https://github.com/DataBiosphere/toil">https://github.com/DataBiosphere/toil</a>, review the readme and the contributing guidelines: <a href="https://toil.readthedocs.io/en/master/contributing/contributing.html#contributing">https://toil.readthedocs.io/en/master/contributing/contributing.html#contributing</a></li> </ul> <hr> <h6 id="improving-automated-wrapping-of-c-code-in-python-openmsautowrap">Improving automated wrapping of C++ code in Python (OpenMS/autowrap)</h6> <p><strong>Project description</strong></p> <p>Autowrap is a python package for the automated wrapping of whole C++ projects into Python via Cython. C++ developers basically need to provide a Cython header file for each C++ header file to specify what needs to be wrapped and how. It then analyses the syntax tree generated by the Cython parser for those “header” files and generates Cython source code for it. Cython then creates the necessary source code to be compiled with e.g. CPython to create a Python extension module to be imported by the end-user. While the wrappers created by autowrap are rather simple, passing templated and nested STL objects like vectors, maps, or tuples between Cython/Python and C++ with autogenerated code can become rather complex. Autowrap offers recursion for nested vectors but cannot handle mixed data structures yet. It also misses support for newer STL containers like tuples and only offers simple vector to (Python) list conversions, while numpy arrays, e.g. via the buffer protocol would sometimes be more suitable. We are seeking for a motivated GSoC contributor proficient in at least Python to tackle those improvements.</p> <p><strong>Project size</strong></p> <ul> <li>350h</li> </ul> <p><strong>Languages and skills needed</strong></p> <ul> <li>Python (advanced knowledge, for code generation)</li> <li>Cython (basic knowledge, potentially possible to be acquired, syntax similar to Python; to be generated)</li> <li>C++ (basic knowledge, potentially possible to be acquired; to be wrapped)</li> <li>Git/GitHub</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Medium: requires a deep understanding of Python and in the beginning at least some basic knowledge about its differences to C++ (regarding memory management and typing)</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>20 weeks</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Julianus Pfeuffer, GitHub: jpfeuffer</li> <li>Axel Walter, GitHub: axelwalter</li> <li>Timo Sachsenberg, GitHub: timosachsenberg</li> </ul> <p><strong>Contributor Benefits</strong></p> <ul> <li>Gain experience working in a friendly team of developers.</li> <li>Get a deep understanding of two very commonly used programming languages and how to interface between them.</li> <li>It is also possible to learn how to create your own Python package with C++ extensions.</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>Please introduce yourself in our Gitter channel: <a href="https://gitter.im/OpenMS/OpenMS">https://gitter.im/OpenMS/OpenMS</a> and get in contact with us prior to writing a proposal.</li> </ul> <hr> <h6 id="migration-of-journal-policy-tracker-backend-to-express--graphql">Migration of Journal Policy Tracker backend to Express + GraphQL</h6> <p><strong>Project description</strong></p> <p>The <strong>Journal Policy Tracker</strong> is your go-to place where you can find all the open-source scientific journals and their policies. Currently the backend of this project is on Flask and SQLite3 along with SQLAlchemy as the ORM. This project aims to migrate the backend from Flask and SQL database to Express, GraphQL using <a href="https://graphql.org/graphql-js/express-graphql/">express-graphql</a> and a NoSQL database like MongoDB.</p> <p>At the end of the program, the mentee is expected to do a successful migration of the existing server to an Express &amp; GraphQL based backend.</p> <ul> <li>Repository: <a href="https://github.com/codeisscience/journal-policy-tracker-backend/">codeisscience/journal-policy-tracker-backend</a></li> <li>Existing API documentation: <a href="https://journal-policy-tracker.herokuapp.com/swagger/">journal-policy-tracker.herokuapp.com/swagger</a></li> </ul> <p><strong>Project size</strong></p> <ul> <li>175h</li> </ul> <p><strong>Languages and skills needed</strong></p> <p>Required skills:</p> <ul> <li>JavaScript</li> <li>Express.js</li> <li>GraphQL</li> <li>MongoDB</li> <li>Documentation (Markdown knowledge preferred)</li> </ul> <p>Useful skills:</p> <ul> <li>Deployent nodejs apps to Heroku</li> <li>Familiarity with testing frameworks like Jest, Chai, Mocha in-order to write unit tests, integration tests and e2e tests.</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Easy if you have experience with GraphQL</li> <li>Medium if you are familiar with Express.js</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>Flexible, depending on contributor needs</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Pritish Samal, <a href="mailto:pritish.samal918@gmail.com">pritish.samal918@gmail.com</a></li> <li>Yo Yehudi, <a href="mailto:yochannah@gmail.com">yochannah@gmail.com</a></li> </ul> <p><strong>Contributor Benefits</strong></p> <ul> <li>Experience developing in backend js frameworks and GraphQL.</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>Please always email all mentors in the same mail if you would like to ask questions or discuss the project.</li> <li>You can also join the Code is Science <a href="https://join.slack.com/t/codeisscience/shared_invite/zt-16g3i8hr7-6j~jd_6JddhjEUBq9YUkmQ">Slack workspace</a>.</li> </ul> <hr> <h6 id="journal-tracker---finalise-and-deploy-react-front-end">Journal tracker - finalise and deploy React front-end</h6> <p><strong>Project description</strong></p> <p>The <strong>Journal Policy Tracker</strong> is your go-to place where you can find all the open-source journals and their policies. Currently the Frontend of this project is on React and React Bootstrap. This project aims to finalise the frontend after GSoC 2021, add state management and a user dashboard, and decouple the Frontend from CSS Frameworks for layout and presentation using Grid and Flex in place.</p> <p>Tasks:</p> <ol> <li>Study the existing user-interface for the journal policy tracker</li> <li>Add functionality to the existing website while developing the components</li> <li>Migrate the existing frontend CSS libraries to vanilla CSS</li> <li>Work on the user-management dashboard</li> <li>Use context/Redux for state management</li> </ol> <ul> <li>Repository: <a href="https://github.com/codeisscience/journal-policy-tracker-frontend/">codeisscience/journal-policy-tracker-frontend</a></li> <li>Frontend Preview: <a href="https://journal-policy-tracker.netlify.app/">journal-policy-tracker.netlify.app</a></li> </ul> <p><strong>Project size</strong></p> <ul> <li>175h</li> </ul> <p><strong>Languages and skills needed</strong></p> <p>Required skills:</p> <ul> <li>JavaScript</li> <li>React.js</li> <li>CSS3</li> <li>HTML5</li> <li>Grid</li> <li>Flex box</li> <li>Documentation (Markdown knowledge preferred)</li> </ul> <p>Useful skills:</p> <ul> <li>Familiarity with HTML5 and CSS3 semantics</li> <li>Familiarity with UI/UX</li> <li>Familiarity with Writing tests</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Easy if you have experience with Grid, Flex box, and CSS page layout</li> <li>Medium if you are familiar with CSS page layout</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>Flexible, depending on contributor needs</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Isaac Miti, <a href="mailto:ikayztm@gmail.com">ikayztm@gmail.com</a></li> <li>Yo Yehudi, <a href="mailto:yochannah@gmail.com">yochannah@gmail.com</a></li> </ul> <p><strong>Contributor Benefits</strong></p> <ul> <li>Experience designing and developing front-end interfaces.</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>Please visit the repo: <a href="https://github.com/codeisscience/journal-policy-tracker-frontend/">codeisscience/journal-policy-tracker-frontend</a> and make at least one contribution, and email the mentors to discuss your project proposal.</li> <li>You can also join the Code is Science <a href="https://join.slack.com/t/codeisscience/shared_invite/zt-16g3i8hr7-6j~jd_6JddhjEUBq9YUkmQ">Slack workspace</a>.</li> </ul> <hr> <h6 id="genestorian-data-refinement">Genestorian data refinement</h6> <p><strong>Project description</strong></p> <p><a href="https://www.genestorian.org/">Genestorian</a> is a web application to manage a collection of <a href="https://en.wikipedia.org/wiki/Model_organism">model organism</a> strains and <a href="https://en.wikipedia.org/wiki/Recombinant_DNA">recombinant DNA</a> in a life sciences laboratory.</p> <p>New DNA sequences (inside or outside cells) are <strong>always</strong> generated by combining existing sequences. Genestorian leverages existing <a href="https://sbolstandard.org/">semantic web tools for synthetic biology</a> and <a href="https://github.com/TeselaGen/openVectorEditor">libraries for DNA visualisation</a> to provide an intuitive interface where researchers can plan, document and revisit their experiments. <a href="https://www.genestorian.org/internship">Here</a> you can find a short summary of the problem we are adressing, adapted for the non-biologists.</p> <p>An important challenge for the project is to migrate data from spreadsheets, where most labs keep their collections, to the database. In this project, the intern will develop a first version of a tool to perform the data refinement required to migrate from spreadsheet to the database.</p> <p><strong>Project size</strong></p> <ul> <li>350h</li> </ul> <p><strong>Required skills</strong></p> <ul> <li>Good knowledge of text processing in a programming language (preferably Python).</li> <li>Willingness to learn the biology concepts that underlie the data models.</li> </ul> <p><strong>Useful skills</strong></p> <ul> <li>Experience with data refinement and approximate string matching.</li> <li>Willingness to interact with experimental researchers of which the data will be refined.</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>Flexible, depending on contributor needs</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Manuel Lera Ramirez, <a href="mailto:manulera14@gmail.com">manulera14@gmail.com</a></li> <li>Yo Yehudi, <a href="mailto:yo@openlifesci.org">yo@openlifesci.org</a></li> </ul> <p><strong>Expected outcome</strong></p> <p>Development of a first version of a tool to perform the data refinement required to migrate from spreadsheets to the database. The task could focus only on the program for refinement, but also developing a web interface for migration is a possibility. In addition to mentorship, we will organise two half-day sessions with a professional Research Software Engineer for helping and advising the contributor, and for code review.</p> <p><strong>Difficulty level</strong></p> <p>Medium if you have experience with string matching, easier if you know a bit of biology.</p> <p><strong>How to Apply</strong></p> <ul> <li>Please always email <em>all</em> mentors in the same mail if you would like to ask questions or discuss the project.</li> </ul> <hr> <h6 id="citation-and-databasing-functionality-in-luox">Citation and databasing functionality in luox</h6> <p>luox is a free, open-access and open-source platform for documenting and reporting light-related quantities from a spectrum of light written in JavaScript and React running directly in the browser. It is targeted to biomedical researchers looking for a convenient way to make their research with light(ing) interventions reproducible. Researchers can request a DOI (digital object identifier) for an uploaded spectrum, which is stored in a compressed/hashed way in the URL. The goal of this project is to develop simple database functionality to luox such that the web interface displays the DOI for any spectra that have already been assigned a DOI.</p> <ul> <li>Platform: <a href="https://luox.app/">https://luox.app/</a></li> <li>Repository: <a href="https://github.com/luox-app/luox">https://github.com/luox-app/luox</a></li> <li>Article describing the platform: <a href="https://doi.org/10.12688/wellcomeopenres.16595.2">https://doi.org/10.12688/wellcomeopenres.16595.2</a></li> </ul> <p><strong>Project size</strong></p> <ul> <li>350h</li> </ul> <p><strong>Required skills:</strong></p> <ul> <li>Good knowledge of programming in JavaScript</li> <li>Good knowledge of web development</li> <li>Version control with Git</li> </ul> <p><strong>Useful skills:</strong></p> <ul> <li>Knowledge of DOIs (digital object identifiers)</li> </ul> <p><strong>Estimated Length</strong></p> <ul> <li>Flexible, depending on contributor needs</li> </ul> <p><strong>Mentors</strong></p> <ul> <li>Manuel Spitschan, <a href="mailto:manuel.spitschan@tuebingen.mpg.de">manuel.spitschan@tuebingen.mpg.de</a></li> <li>Yo Yehudi, <a href="mailto:yo@openlifesci.org">yo@openlifesci.org</a></li> </ul> <p><strong>Expected outcome</strong></p> <ul> <li>Functionality to look up DOI from the compressed/hashed spectrum through a table</li> <li>Display of the associated DOI in the web interface</li> </ul> <p><strong>Difficulty</strong></p> <ul> <li>Medium</li> </ul> <p><strong>How to Apply</strong></p> <ul> <li>Please always email <em>all</em> mentors in the same mail if you would like to ask questions or discuss the project.</li> </ul>https://www.open-bio.org/2019/12/21/travel-fellowship-december-2019/Sat, 21 Dec 2019 23:59:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/12/21/travel-fellowship-december-2019/<p>Two awardees were chosen during the latest round of the <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship program</a>, which closed on December 1, 2019. The program, which started in 2018, provides some travel funding to selected applicants who, by attending events in open source / open science, will help to promote diversity in the community.</p> <p>One of our awardees is <a href="https://lacion.rbind.io/">Laura Acion</a> from the <a href="http://www.ic.fcen.uba.ar/en/">Instituto de Calculo</a> in Argentina, who will be attending <a href="https://2020.carpentrycon.org/">CarpentryCon 2020</a> (June 29 - July 1 in Madison, WI) and <a href="https://user2020.r-project.org/">Use R! 2020</a> (July 7-10 in St. Louis, MO). Because the two conferences will be held fairly near each other in time and geographical location, Laura is optimizing travel by attending both of these meetings.</p> <p>Our other awardee, Michael Thompson of the <a href="https://www.knust.edu.gh/">Kwame Nkrumah University of Science and Technology</a> in Ghana, will attend <a href="https://galaxyproject.org/events/2020-03-admin/">Galaxy Admin Training</a> to be held in Barcelona from 2 - 6 March 2020. This training will enable Michael to deploy Galaxy for production use at his university.</p> <h3 id="obf-travel-fellowship-review-chair-changes">OBF Travel Fellowship Review Chair changes</h3> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/12/farah-768x1024.jpg" alt="">Farah Zaib Khan</p> <p>In addition to congratulating our latest awardees, we wish to thank Farah Khan (above) for serving as our Travel Fellowship Review Chair throughout 2019. This role will now be assumed by <a href="https://malvikasharan.github.io/">Malvika Sharan</a> (below).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/Malvika-801x1024.jpeg" alt="">Incoming Travel Fellowship Review Chair Malvika Sharan</p> <p>As always, we encourage community members who are planning to attend events that promote open source software development and/or open science in biology to apply for an <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a>. We particularly welcome applications from people who are members of historically underrepresented groups and/or who work in low-income research environments. In 2020, there will be two application calls that will close on 1 March and 1 September 2020.</p>https://www.open-bio.org/2019/12/20/biopython-1-76-released/Fri, 20 Dec 2019 15:02:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/12/20/biopython-1-76-released/<p>Biopython 1.76 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.76">PyPI</a>.</p> <p>Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a <a href="https://python3statement.org/">focus hereafter on Python 3</a>. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.</p> <p>This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.</p> <p>As in recent releases, more of our code is now explicitly available under either our original &quot; <em>Biopython License Agreement</em>&quot;, or the very similar but more commonly used &quot; <em>3-Clause BSD License</em>&quot;. See the <code>LICENSE.rst</code> file for more details.</p> <p>In addition to the mainstream <code>x86_64</code> aka <code>AMD64</code> CPU architecture, we now also test every contribution on the <code>ARM64</code>, <code>ppc64le</code>, and <code>s390x</code> CPUs under Linux thanks to Travis CI. Further post-release testing done by Debian and other packagers and distributors of Biopython also covers these CPUs.</p> <p>The <code>Bio.motifs.PositionSpecificScoringMatrix.search()</code> method has been re-written: it now applies <code>.calculate()</code> to chunks of the sequence to maintain a low memory footprint for long sequences.</p> <p>Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the <code>black</code> tool.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Chris Daley (first contribution)</li> <li>Chris Rands</li> <li>Christian Brueffer</li> <li>Ilya Flyamer (first contribution)</li> <li>Jakub Lipinski (first contribution)</li> <li>Michael R. Crusoe (first contribution)</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Sergio Valqui</li> </ul>https://www.open-bio.org/2019/12/17/global-community-biosummit-2019-mit/Tue, 17 Dec 2019 18:27:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/12/17/global-community-biosummit-2019-mit/<p><em>The <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting Open Source bioinformatics software development and open science in the biological research community. Arunav Konwar&rsquo;s participation at</em> <a href="https://www.biosummit.org/">Global Community Biosummit (GCBS),</a> <em>2019 was supported by this fellowship. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p><img src="https://scontent.fgau3-1.fna.fbcdn.net/v/t1.0-9/s960x960/67842987_2309735785809363_3830016113882693632_o.jpg?_nc_cat=101&amp;_nc_oc=AQm74VYRk_p9ARtE5OLImFJCu8MxugqdsQ55hIVnqJnTXHznMYznmJQHelCqxSxfAes&amp;_nc_ht=scontent.fgau3-1.fna&amp;oh=58c849b2e805e6e004f10d37e9558771&amp;oe=5E56663C" alt="No photo description available."></p> <p>I recently had the opportunity to attend the <a href="https://www.biosummit.org/">Global Community Biosummit (GCBS),</a> which took place between October 11-13 at the Massachusetts Institute of Technology (MIT) in Cambridge, MA, USA.</p> <p>My attendance wouldn&rsquo;t have been possible without the generous support of the Open Bioinformatics Foundation (OBF). I am grateful to the OBF for the travel fellowship which enabled me to undertake the journey to travel all the way from India to the city of Boston.</p> <p>GCBS is a global conference that aims to initiate a discourse among people working in and around all aspects of biology and beyond. Biohackers, artists, scientists, geneticists, etc all under one roof. In its own words, it states <em>&ldquo;Our goal is to provide a space for the global community of DIY biologists / community biologists / biohackers / biomakers and members of independent and community laboratories to convene, plan, build fellowship, and continue the evolution of our movement.&rdquo;</em></p> <p>Conferences can be an incredible opportunity for people to learn from and connect with like-minded people. Below is a recount and reflections of my experiences after attending the conference, which I hope can inspire others to participate in this conference or other similar events in the future.</p> <p><strong>DAY 0</strong></p> <p>A day before the conference many participants could sign up for lab tours in and around Boston. This included visits to <a href="https://www.ginkgobioworks.com/">Gingko Bioworks</a>&rsquo; labs, Boslab (a local community lab in Somerville), Makers&rsquo; Asylum (hacker lab in Cambridge, MA), etc. This gave participants a better idea of the overall DIY scene and ecosystem in the area that co-exists with the big-name universities.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/12/cambridge-1024x768.jpg" alt="">Cambridge, Massachusetts, USA. Photo by Arunav Konwar</p> <p><strong>DAY 1</strong></p> <p>The conference was opened with opening remarks by David Sun Kong (Director of Community Biotechnology Initiative, MIT Media Lab), Deb Roy (Executive Director, MIT Media Lab) and Kate Darling (MIT Media Lab).</p> <p>It was followed by participants introducing themselves and their projects in under 30 seconds each, in a segment called &lsquo;Hello World&rsquo;.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/12/david-kong-intro.jpg" alt="">David Sun Kong welcoming the attendees with his opening speech.</p> <p>The day consisted of plenary talks in the first half of the day followed by parallel sessions after lunch. Notable sessions were: “Global Gender Representation in Biotech / Community Bio” and “Building and Sustaining Community Labs”. There were hands-on workshops ranging from bio-sensors to full-blown introduction labs to CRISPR, all of which were extremely popular and were overbooked by the attendees. These workshops were crucial in building a deeper connection between the attendees and everyone involved.</p> <p><a href="https://www.instagram.com/p/B3hlTu-A70a/">https://www.instagram.com/p/B3hlTu-A70a/</a></p> <p>A picture of me working on building an open-source wearable biosensor during the conference</p> <p><strong>DAY 2</strong></p> <p>Day 2 started with remarks again by David Sun Kong about the successful Day 1 and the excitement surrounding the upcoming days.</p> <p>Incredible panel discussions that I attended included <em>“Establishing and Nurturing Global Collaborations”</em> which had the presence of researchers from around the globe, a few being Anthony DiFranco (Counter Culture Labs, Open Insulin), Jenny Molloy (University of Cambridge, Biomakespace Gathering of Open Science Hardware), etc.</p> <p>Another plenary talk that I enjoyed was <em>“Superminds: the Collective Intelligence of Community Bio”</em> by Professor Thomas Malone of MIT Center for Collective Intelligence, where he talked about the immense potential of designing systems that can leverage the unique relationships that humans and machines can cultivate to become a kind of super-intelligent being in the future.</p> <p>The rest of the day involved attending parallel tracks that participants could sign-up for and attend, and also spend time around the amazing installations of bio-art, research posters and other works around the conference space.</p> <p>Day 2 of the summit ended with a party named 99Biohackers party (appropriately named after Media Lab&rsquo;s weekend parties called 99Fridays).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/12/biosummit-party.jpg" alt="">Scenes from the Biosummit party Day 2 at the MIT Media Lab (Photo Courtesy: David Sun Kong)</p> <p><strong>DAY 3</strong></p> <p>The last day intentionally started late to give people the room to recover from the previous night&rsquo;s party. The day largely consisted of hands-on workshops for which people had to move to other dedicated spaces and laboratories in other MIT buildings. Unconferences (which were held in the afternoon) were a great way for people to organize smaller talks with topics of common interests.</p> <p>There was a plenary meeting from 11-12 pm which involved the whole community to talk about &lsquo;Community Ethics&rsquo;. This was a great opportunity for the global community to discuss issues surrounding ethics that seem to be common across borders. It was also a great way to bring in everyone together to build a framework for a common cause.</p> <p>The closing session was between 5-6 pm which brought back all the attendees to the main conference space for a final vote of thanks and reflections from the community.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/12/all-attendee-group-pic.jpg" alt="">All attendee group picture GCBS 3.0</p> <p><strong>Unconferences and parallel tracks</strong></p> <p>Along with many hardware enthusiasts, the conference includes people who work on computational biology, bioinformatics, and software as well. I was able to unconference with a bunch of people working on writing and contributing to open-source software for biology and beyond. Timothy Stiles from the Boslab in Somerville, MA happened to introduce his new project <a href="https://genepool.me/">Genepool</a> to a broader crowd during the summit. More such projects were shared with the attendees by Keoni Gandall (BioBricks Foundation), Sebastian Cocioba, etc.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/12/biosummit-attendees-continents-1024x594.png" alt="">Attendees came from almost every continent (except for Antarctica) Pic courtesy: Pat Pataranutaporn</p> <p><strong>Thoughts on the venue and MIT</strong></p> <p>The conference and the workshops were primarily held at the MIT Media Lab and the MIT Biology Laboratories across the street around the East campus. With its immense resources (both infrastructure and people), MIT has been able to accommodate the needs of the participants. There have been discussions on holding the event in Europe or other continents but this currently seems unlikely for the near future due to logistical reasons.</p> <p><strong>The summit, global collaborations and sister conferences</strong></p> <p>Biosummit takes pride in creating and empowering communities around the world to organize their own events. <a href="http://www.oshafrica2019.com/">AfricaOSH</a> is one of the conferences that grew out of the Biosummit in Africa. <a href="http://thedarwin.in/">Darwin conference</a> in India is another example of a major conference started by a biosummit alumni, with a stellar lineup of speakers ranging from artists like Joe Davis to biologists like Sebastian Cocioba working on incredible flower projects.</p> <p>Biosummit also hosted its first group of Global Community Bio fellows. The <strong>Global Community Bio Fellows Program</strong> was started as a part of the summit and is designed to provide leadership, development training, and peer support for emerging leaders in the global community. This cohort of participants from all over the world attended online seminars organized by the MIT Media Lab and the Harvard Kennedy School and developed projects in groups over a period of a few months and finally showcased it during the summit in October.</p> <p><strong>Personal takeaways</strong></p> <p>Biosummit is an incredible, one of a kind conference that breaks the norm in terms of the ideas being discussed and the diversity of the people it brings in. It lives up to its goals of being inclusive and providing a safe space for people from every background to come and discuss ideas. I met some of the most impactful people in the DIY science and tech space and got to discuss and share recent developments.</p> <p>Boston is an incredible city with an amazing ecosystem of top universities and companies working to solve some of the most pressing problems facing human civilization. I had an excellent time meeting and interacting with amazingly talented and kind people at the Global Community Biosummit and I can&rsquo;t wait to attend it again next year.</p>https://www.open-bio.org/2019/11/15/creating-an-obf-wide-code-of-conduct/Fri, 15 Nov 2019 22:14:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/11/15/creating-an-obf-wide-code-of-conduct/<p>Among the core values shared across the OBF community are inclusiveness and welcoming newcomers to contribute, without discrimination. Every year at BOSC, when we ask who is at BOSC for the first time, about half of the audience&rsquo;s hands go up. To signify the importance of this, both to existing and prospective community members, BOSC successfully advocated several years ago for ISMB to adopt a Code of Conduct by ISMB (which applies to BOSC when it is held as part of ISMB).</p> <p>In the near future, OBF plans to adopt an Affiliated Project Policy to provide a transparent and documented mechanism for other open-source projects to formally join the OBF umbrella. To ensure that our larger community supports our core values, a project wishing to join will have to have, or adopt, a Code of Conduct (CoC) aligned with ours. This means that we need to document what our OBF-wide CoC is, i.e., the expectations in conduct that we want to hold ourselves accountable to across our member projects and their communities, whether at BOSC or not.</p> <p>This is in fact not the first time an official CoC has been requested outside the context of BOSC from within our project communities. Interest has been expressed both within member projects (such as Biopython), and in-person at our public board meeting at BOSC 2019. We have now begun an initiative to create, and ultimately get adopted, a Code of Conduct covering both our in-person events (BOSC, CoFest, GSoC meetings, etc) and our online activities (mailing lists, GitHub threads, Gitter conversations, etc), including those of our current and future member projects. We invite our community to engage and provide feedback.</p> <p>Thanks to the work of many other open-source communities, we don’t have to start from scratch. Specifically, having reviewed multiple existing CoC documents, one strong candidate for us is <a href="https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html">The Carpentries Code of Conduct</a>. Another one might be <a href="https://ropensci.org/code-of-conduct/">rOpenSci’s</a>.</p> <p>The OBF would provide member projects and BOSC with a somewhat external CoC point of contact for reporting and tracking any issues, and ensure training as needed. Any new member project would be able to take advantage of this CoC automatically applying to their work and interactions.</p> <p>We welcome suggestions for how to best handle any CoC violation against the OBF board itself, such as a reciprocal arrangement with another society. The Carpentries has a designated ombudsperson in this role.</p> <p>When we hold joint meetings with other organizations (such as BOSC with ISMB or Galaxy) we would expect that a single Code of Conduct is explicitly selected, and applied to the conference.</p> <p>We are inviting feedback on <a href="https://github.com/OBF/obf-docs/issues/67">this GitHub issue</a>, or email privately <a href="mailto:board@open-bio.org">to the board</a> ( <a href="mailto:board@open-bio.org">board@open-bio.org</a>), <strong>by December 1st</strong>, allowing time to put a draft CoC to formal approval at the OBF public board meeting on December 17, 2019, and then OBF member approval by ballot, followed by adoption by the member projects.</p>https://www.open-bio.org/2019/11/14/obf-travel-fellowship-december-2019/Thu, 14 Nov 2019 16:50:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/11/14/obf-travel-fellowship-december-2019/<p>The call for <a href="https://www.open-bio.org/travel-awards/">OBF travel fellowship</a> to select the next round of awardees is officially open! Please submit your application by filling out <a href="https://goo.gl/forms/btbOOfkVcXVzZXxD2">this form</a>. Deadline for this round is <strong>1 December 2019</strong>.</p> <p>This fellowship aims to support our community members in attending events that promote open source software development and/or open science in the biological research fields. As the organiser of <a href="https://www.open-bio.org/wiki/BOSC">Bioinformatics Open Source Conference (BOSC)</a> since 2000, OBF understands the role of such conferences and wants to support people who can benefit from showcasing their work, learn from each other and promote open science at BOSC or similar events.</p> <p><a href="https://docs.google.com/forms/d/e/1FAIpQLScCYMt_Id9FSKzHtOxyBgiOIXa61CLiveqh5JLx5rQsFoW8fA/viewform"><img src="https://www.open-bio.org/wp-content/uploads/2019/11/obftf-1.png" alt=""></a></p> <p>Applications are particularly encouraged from members from historically underrepresented groups, who work in low-income research environments and strive to promote diversity and inclusion in their communities. The conference or event that the applicants intend to attend must take place in 2020 (preferably during the first half of the year) and should provide them with a platform to learn or promote open science.</p> <p>Since 2018, OBF has offered this fellowship to <strong>12 awardees</strong> to defray or subsidize their travel-related cost of up to <strong>$1000 each</strong>. You can read their blog posts in <a href="https://www.open-bio.org/category/travel-fellowship/">OBF blog</a> where they have shared their experiences from attending different events as OBF travel fellows.</p> <p>In 2020, there will be two application calls that will close on 1 March and 1 September 2020. [ <strong>NOTE</strong>: This was later changed to 1 April and 1 October.] Please read more details on the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">fellowship program</a> and feel free to contact the committee by writing an email to <a href="mailto:board@open-bio.org">board@open-bio.org</a>.</p>https://www.open-bio.org/2019/11/14/obf-travel-fellowship-schedule/Thu, 14 Nov 2019 16:50:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/11/14/obf-travel-fellowship-schedule/<p>The <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship program</a>, which was started in 2016, will be making some changes to the schedule. Until now, there have been three application rounds per year, with deadlines April 15, August 15 and December 15.</p> <p>For the next round, we are moving our December deadline two weeks earlier, to December 1, 2019.</p> <p>Starting in 2020, we will move to two application deadlines per year, on March 1 and September 1. Applicants will be considered for events that take place in the year starting one month after the deadline&ndash;for example, for the December 1, 2019 deadline, we will consider applications for events scheduled to take place between January 1, 2020, and December 31, 2020.</p> <p>We have made these changes to better accommodate long-term planning and to consolidate the demands on time for our Travel Fellowship reviewers.</p>https://www.open-bio.org/2019/11/12/supercharge-your-open-project-with-leadership-training/Tue, 12 Nov 2019 21:32:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/11/12/supercharge-your-open-project-with-leadership-training/<p><em>This post is co-authored by Bérénice Batut, Malvika Sharan, Emmy Tsang, and Yo Yehudi.</em></p> <p>In 2016, Mozilla launched a program to help grow the skills of people interested in working openly and empower a generation of open-inspired leaders. The program has been through several stages of evolution, from early <a href="http://mozillascience.github.io/working-open-workshop/">Working Open Workshops</a>, and eventually to regular twice-yearly cohorts, mentoring project leads from all around the globe. Projects spanned a broad number of domains, but included a large number of research/science and tech-oriented projects, including <a href="https://www.prereview.org/">PREreview</a>, an initiative to get people involved in scientific preprint journal clubs; <a href="https://outbreakscience.org/">Outbreak science</a>, a nonprofit using technology to support disease outbreaks; <a href="https://mozilla.github.io/leadership-training/round-5/projects/#mbac-computer-vision-tool-for-bacterial-motility-assays">MBac</a>, a computer vision tool for bacterial motility assays; and <a href="https://mozilla.github.io/leadership-training/round-5/projects/#open-sourcing-duracloud-beyond-the-license">DuraCloud</a>, an open-source digital preservation storage service.</p> <p>In 2019 the Open Leaders program has re-branded: rather than training promising project leaders, it set its sights to a broader goal, creating <a href="https://foundation.mozilla.org/en/opportunity/mozilla-open-leaders/open-leaders-x/">Open Leaders X</a>, a train-the-trainers program, supporting ten teams to build open leader programmes in various areas concerning Internet Health, from science hardware to digital inclusion. These ten programmes were officially launched on October 26 at the Mozilla Festival and will run from early 2020.</p> <p>We would like to draw the open science and research software communities’ attention to two of the Open Leaders programmes. Both programmes aim to equip participants with the knowledge and experience to lead their own projects openly through <strong>1:1 mentorship</strong> and learning from peers, experts, speakers and other members in the programmes.</p> <p>The table below summarises the similarities and differences in the curricula of the two programmes:</p> <p>[table id=2 /]</p> <p>The <strong>Open Life Science</strong> programme is designed for early-career researchers and young leaders in life science to further their open science skills. Participants will receive training in open science advocacy and work on their projects to promote best open science practices in life science (from solving technical questions,  to creating an open data project or report, developing Open Source software project, writing open publications, facilitating community/team culture movements, advancing open educational resources or contributing to other existing projects/community)</p> <p>The <strong>eLife Innovation Leadership</strong> programme targets innovators who wish to create tools/platforms to advance open research communication. Participants will learn to develop their ideas into sustainable beta products through a curriculum covering topics from basic product design to communication and promotion. Some of these projects could receive support from eLife beyond the programme.</p> <p>We encourage interested readers to find out more about these programmes by visiting their respective websites. If you have any questions, please contact:</p> <ul> <li>Bérénice, Malvika, Yo at <a href="mailto:hello@openlifesci.org">hello [at] openlifesci [dot] org</a> for Open Life Science</li> <li>Emmy at <a href="mailto:innovation@elifesciences.org">innovation [at] elifesciences [dot] org</a> for eLife Innovation Leaders</li> </ul> <p>Organisers of both programmes will also be at the upcoming <a href="https://www.biohackathon-europe.org/">Biohackathon-Europe</a>.</p> <p>To answer any questions related to these programs, an online information session (webinar) will be held on <a href="https://arewemeetingyet.com/Berlin/2019-11-27/17:00/OpenLifeSci%20&amp;%20eLife%20Application%20Webinar">27 November 2019 at 4pm GMT</a> via this <a href="https://zoom.us/j/653381208">Zoom room</a>. Agenda and notes can be found <a href="https://docs.google.com/document/d/1EIDzZi5mgRiWR7cJQl0up470C87GsbcoTR_6-cs-SeE/edit?usp=sharing">here</a>.</p> <p><img src="https://images.unsplash.com/photo-1522202176988-66273c2fd55f?ixlib=rb-1.2.1&amp;auto=format&amp;fit=crop&amp;w=1000&amp;" alt="People interacting informally"><em>Image on <a href="https://unsplash.com/photos/g1Kr4Ozfoac">Unsplash by @brookecagle</a></em></p> <p>If you are interested in contributing to the programmes as a mentor or expert, please don’t hesitate to get in touch using the contact details above.</p>https://www.open-bio.org/2019/11/07/biopython-1-75-released/Thu, 07 Nov 2019 16:31:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/11/07/biopython-1-75-released/<p>Dear Biopythoneers,</p> <p>Biopython 1.75 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.75">PyPI</a>.</p> <p>This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected to work on the soon to be released Python 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.</p> <p>Note we intend to drop Python 2.7 support in early 2020.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the August 2019 release of REBASE.</p> <p><code>Bio.SeqIO</code> now supports reading and writing files in the native format of Christian Marck&rsquo;s DNA Strider program (&ldquo;xdna&rdquo; format, also used by Serial Cloner), as well as reading files in the native formats of GSL Biotech&rsquo;s SnapGene (&ldquo;snapgene&rdquo;) and Textco Biosoftware&rsquo;s Gene Construction Kit (&ldquo;gck&rdquo;).</p> <p><code>Bio.AlignIO</code> now supports GCG MSF multiple sequence alignments as the &ldquo;msf&rdquo; format (work funded by the National Marrow Donor Program).</p> <p>The main <code>Seq</code> object now has string-like <code>.index()</code> and <code>.rindex()</code> methods, matching the existing <code>.find()</code> and <code>.rfind()</code> implementations. The <code>MutableSeq</code> object retains its more list-like <code>.index()</code> behaviour.</p> <p>The <code>MMTFIO</code> class has been added that allows writing of MMTF file format files from a Biopython structure object. <code>MMTFIO</code> has a similar interface to <code>PDBIO</code> and <code>MMCIFIO</code>, including the use of a <code>Select</code> class to write out a specified selection. This final addition to read/write support for PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.</p> <p>Values from mmCIF files are now read in as a list even when they consist of a single value. This change improves consistency and reduces the likelihood of making an error, but will require user code to be updated accordingly.</p> <p><code>Bio.PDB</code> has been updated to support parsing REMARK 99 header entries from PDB-style Astral files.</p> <p>A new keyword parameter <code>full_sequences</code> was added to <code>Bio.pairwise2</code>&rsquo;s pretty print method <code>format_alignment</code> to restore the output of local alignments to the &lsquo;old&rsquo; format (showing the whole sequences including the un-aligned parts instead of only showing the aligned parts).</p> <p>A new function <code>charge_at_pH(pH)</code> has been added to <code>ProtParam</code> and <code>IsoelectricPoint</code> in <code>Bio.SeqUtils</code>.</p> <p>The <code>PairwiseAligner</code> in <code>Bio.Align</code> was extended to allow generalized pairwise alignments, i.e. alignments of any Python object, for example three-letter amino acid sequences, three-nucleotide codons, and arrays of integers.</p> <p>A new module <code>substitution_matrices</code> was added to <code>Bio.Align</code>, which includes an <code>Array</code> class that can be used as a substitution matrix. As the <code>Array</code> class is a subclass of a numpy array, mathematical operations can be applied to it directly, and C code that makes use of substitution matrices can directly access the numerical values stored in the substitution matrices. This module is intended as a replacement of <code>Bio.SubsMat</code>, which is currently unmaintained.</p> <p>As in recent releases, more of our code is now explicitly available under either our original &ldquo;Biopython License Agreement&rdquo;, or the very similar but more commonly used &ldquo;3-Clause BSD License&rdquo;. See the <code>LICENSE.rst</code> file for more details.</p> <p>Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style. We have also started to use the <code>black</code> Python code formatting tool.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Chris MacRaild</li> <li>Chris Rands</li> <li>Damien Goutte-Gattat (first contribution)</li> <li>Devang Thakkar</li> <li>Harry Jubb</li> <li>Joe Greener</li> <li>Kiran Mukhyala (first contribution)</li> <li>Konstantin Vdovkin</li> <li>Mark Amery</li> <li>Markus Piotrowski</li> <li>Mike Moritz (first contribution)</li> <li>Mustafa Anil Tuncel</li> <li>Nick Negretti</li> <li>Peter Cock</li> <li>Peter Kerpedjiev</li> <li>Sergio Valqui</li> <li>Spencer Bliven</li> </ul>https://www.open-bio.org/events/bosc-2019/Sat, 19 Oct 2019 04:57:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2019/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/lots-of-people-at-poster-session-1.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h1 id="bosc-2019">BOSC 2019</h1> <p>BOSC 2019 was a success! We look forward to <a href="https://www.open-bio.org/events/bosc/">BOSC 2020</a> (with GCC2020 as part of the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference</a>) in Toronto, Canada, July 18-21, 2020.</p> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. In 2019, BOSC was part of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB</a> in Basel. See the full <a href="https://www.open-bio.org/events/bosc-2019-schedule/">schedule of talks, posters</a> and <a href="https://www.open-bio.org/events/bosc/2019-bofs/">Birds of a Feather</a> meetups.</p> <p><a href="https://www.iscb.org/ismbeccb2019"><img src="https://www.open-bio.org/wp-content/uploads/2019/03/ismbeccb2019.jpeg" alt=""></a></p> <h1 id="overview">Overview</h1> <p>BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <p>BOSC is usually preceded or followed by what we now call <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest (CoFest</a> for short), a two-day community development session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. All are welcome to attend CoFest 2019 (whether or not you attend BOSC)!</p> <p><a href="https://www.open-bio.org/events/bosc/about/">More about BOSC&hellip;</a></p> <h2 id="important-dates">Important Dates</h2> <ul> <li>April 11, 2019: Full talk/poster <a href="https://www.open-bio.org/events/bosc/submit/">abstract submission</a> deadline</li> <li>May 9: Authors notified</li> <li>May 15: Late poster/late-breaking lightning talk <a href="https://www.open-bio.org/events/bosc/submit/">submission</a> deadline</li> <li>May 23: Late round authors notified</li> <li>June 20: Last day for <a href="https://www.iscb.org/ismbeccb2019-registration">ISMB/ECCB early registration</a> prices</li> <li>July 21-25: <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB 2019</a>, Basel, Switzerland</li> <li><strong>July 24-25: BOSC 2019</strong>, Basel, Switzerland</li> <li>July 26-27: <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest 2019</a>, Basel, Switzerland (location TBD)</li> </ul> <h2 id="session-topics">Session Topics</h2> <p>BOSC covers all aspects of bioinformatics software and open science,  including (but not limited to) these topics:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Open Approaches to Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach and Training</li> <li>Bioinformatics Open Source Project Reports (about new or existing projects)</li> </ul> <h2 id="registration">Registration</h2> <p>BOSC 2019 will take place the last two full days of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB 2019</a>. You can <a href="https://www.iscb.org/ismbeccb2019-registration">register</a> for the full ISMB/ECCB meeting (July 21-25) or just for the two days of BOSC (July 24-25).</p> <p>When you register for ISMB, you will select a primary COSI (such as BOSC) but you will be able to move freely between all of the <a href="https://www.iscb.org/ismbeccb2019/2209">COSIs</a> that take place as parallel tracks during the days for which you register.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/farah-yo-angel-GCCBOSC-1024x683.jpg" alt=""></p> <h2 id="sponsors">Sponsors</h2> <p>Sponsorships from private companies and organizations help to defray some of our costs. Please see the <a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsors</a> page for more information.</p> <p>If you would like to be a sponsor of BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <h3 id="bosc-2019-sponsors">BOSC 2019 Sponsors</h3> <h3 id="cofest-2019-sponsors">CoFest 2019 Sponsors</h3> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/07/BOSC2019-organizers-1.jpg" alt="">Members of the BOSC 2019 organizing committee</p> <h2 id="organizing-committee">Organizing Committee</h2> <p><strong>Chair: Nomi L. Harris</strong> (Lawrence Berkeley National Laboratory) <strong>Co-Chair: Heather Wiencko</strong> ( <a href="https://www.hostedgraphite.com/">Hosted Graphite</a>)</p> <ul> <li> <p><a href="http://www.scri.ac.uk/staff/petercock">Peter Cock</a> ( <a href="http://biopython.org/">Biopython developer</a>; <a href="http://www.hutton.ac.uk/">James Hutton Institute</a>)</p> </li> <li> <p>Christopher Fields (National Center for Supercomputing Applications)</p> </li> <li> <p>Bastian Greshake Tzovaras ( <a href="https://www.openhumans.org/">Open Humans</a>)</p> </li> <li> <p><a href="https://github.com/heuermh">Michael Heuer</a> ( <a href="https://rise.cs.berkeley.edu/">UC Berkeley</a>)</p> </li> <li> <p>Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)</p> </li> <li> <p>Monica Munoz-Torres (Oregon State University)</p> </li> <li> <p><a href="http://yo-yehudi.com/">Yo Yehudi</a>(University of Cambridge)</p> </li> </ul> <h2 id="review-committee">Review Committee</h2> <p>Kai Blin*, Christian Brueffer*, Brad Chapman, Anamaria Crisan, Arun Decano*, Gianluca Della Vedova*, Christopher Fields*, Konrad Förstner*, Bastian Greshake Tzovaras*, Nomi Harris*, Michael Heuer*, Karsten Hokamp*, Anisha Keshavan, Farah Z Khan, Radhika Khetani*, Aleix Lafita*, Jessica Maia, Hervé Ménager, Monica Munoz-Torres, Frank Nothaft, Kieran O&rsquo;Neill, Konstantin Okonechnikov, Lorena Pantano*, Bastian Rieck, Surya Saha*, Malvika Sharan, Nicole Vasilevsky*, Heather Wiencko, Jason Williams, Yo Yehudi*</p> <p>*: reviewed both rounds</p> <h2 id="previous-boscs">Previous BOSCs</h2> <p>BOSC has been held yearly since 2000. See <a href="https://www.open-bio.org/events/bosc/about#Past_BOSCs">information about the first 19 BOSC conferences.</a></p> <p><strong><a href="https://www.open-bio.org/wiki/BOSC_2018">BOSC 2018</a> was held June 26-27, 2018</strong> (with training days June 24-25 and a CollaborationFest June 28-29) at Reed College in Portland, Oregon as part of <a href="https://gccbosc2018.sched.com/">the GCCBOSC 2018 bioinformatics community conference</a> co-hosted with the Galaxy Community Conference. Check out the <a href="https://gccbosc2018.sched.com/">complete schedule</a>, or visit the <a href="https://www.open-bio.org/wiki/BOSC_2018">BOSC 2018 page</a> for links to conference reports.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/bosc-crowd-by-james-taylor-1024x340.jpg" alt="">A full room at BOSC 2017</p> <h1 id="code-of-conduct">Code of Conduct</h1> <p>As part of ISMB/ECCB 2019, BOSC 2019 will be covered by <a href="https://www.iscb.org/ismbeccb2019-codeofconduct">ISMB&rsquo;s Code of Conduct.</a></p>https://www.open-bio.org/2019/10/15/computational-biology-without-borders/Tue, 15 Oct 2019 20:52:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/10/15/computational-biology-without-borders/<p><em>This is a guest blog post from <a href="https://twitter.com/khanaziz84">Aziz Khan</a>, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship</a> program to attend the <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB</a> and <a href="https://www.open-bio.org/events/bosc/">BOSC 2019</a> meeting in Basel, July 2019. The OBF’s Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <hr> <p>Computational tools and software are now becoming the core of scientific discovery, and making it open source and sharing it freely with the community helps to take scientific discoveries to the next level. We live in an era where international and interdisciplinary collaborations become very central to answer big scientific questions. Given science is becoming more collaborative and data-intensive, we need intelligent and robust computational algorithms to help us to understand and interpret such big-data.</p> <p>Biology is no longer limited to PCR or gel electrophoresis. The high-throughput approaches to DNA sequencing at the genome and exome level are the state-of-the-art. For example, genomics and epigenomics are shifting from bulk sequencing to single-cell sequencing, which produces even more and sparse data. The (epi)genomics at single-cell can help us to understand the molecular mechanisms more precisely to understand disease and tumor biology. Integrative methods and software are needed to interpret multi-omics data at bulk and single-cell resolution to better understand the heterogeneity between cells, patients, or multi-region biopsies from a tumor. All these require open-source bioinformatics software and resources that are free and accessible for everyone.</p> <p>The international community that develops such software and methods need a diverse and multidisciplinary platform to meet and share the latest developments in the field, fostering fresh dialogues and perspectives to learn about and shape the future of bioinformatics. And such a platform is provided by ISCB&rsquo;s Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB) when they both meet in Europe every second year with diverse Communities of Special Interest (COSI) such as the <a href="https://www.open-bio.org/events/bosc/">Bioinformatics Open Source Conference (BOSC)</a>.</p> <p>ISMB/ECCB is the world’s largest bioinformatics/computational biology meeting. I’ve been very lucky to attend three of those so far. I started my ISMB/ECCB journey when I was a Ph.D. student at Tsinghua University, China. In fact, first I joined the <a href="https://www.iscbsc.org/">ISCB Student Council</a>, a wonderful forum for early career researchers (ECR) in bioinformatics. I was part of the web-committee and later served as co-chair of the committee. I helped the community to organize and review student symposiums. If you’re an ECR in bioinformatics, I would definitely recommend joining the community. So, back to ISMB/ECCB, it was July 2015, I was accepted to present a poster and also to volunteer at ISMB/ECCB 2015 in Dublin. Of course, I saved the registration fee by volunteering but it also gave me an excellent opportunity to network. I met some of the great people in that meeting and we’re still connected. My second ISMB/ECCB was in 2017 in the beautiful city of Prague. Again, I signed up to volunteer and had a wonderful meeting and presented one of our open-source <a href="https://github.com/asntech/intervene">projects</a> both at the Student Symposium and at the Regulatory and Systems Genomics (RegSys) COSI.</p> <p>This year, 2019, the ISMB/ECCB came to Basel, a city in the heart of Europe, which shares its borders with France and Germany.</p> <p><img src="https://i.ibb.co/1QRqzGT/IMG-20190726-084155-HDR.jpg" alt=""></p> <p><em>The tripoint (Dreiländereck) where the borders of France, Germany and Switzerland meet.</em></p> <p>I knew I wanted to attend, especially my favorite ISMB/ECCB COSI on the Regulatory and Systems Genomics (RegSys). And this year, my PI Anthony Mathelier was one of the organizers of RegSys. I always wanted to attend <a href="https://www.open-bio.org/events/bosc/">BOSC</a>, so I submitted our community initiative, ECRcentral, that aims to bring ECRs together to discuss funding opportunities, share experiences, and create impact through community engagement. ECRcentral was accepted for a long talk and on top of that, I got a <a href="https://www.open-bio.org/2019/05/31/travel-award-recipients-for-april-2019/">travel fellowship</a> from the <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> to attend <a href="https://twitter.com/hashtag/ISMBECCB2019?src=hash">#ISMBECCB2019</a> and present <a href="https://twitter.com/ECRcentral">@ECRcentral</a> at <a href="https://twitter.com/hashtag/BOSC2019?src=hash">#BOSC2019</a>. What else do you need, right?</p> <blockquote> <p><strong>Welcome to Basel</strong>! We arrived in Basel on July 21st from Oslo, Norway.</p> </blockquote> <blockquote> <p>In Basel for <a href="https://twitter.com/hashtag/ISMBECCB19?src=hash&amp;ref_src=twsrc%5Etfw">#ISMBECCB19</a>! My 3rd <a href="https://twitter.com/hashtag/ISMBECCB?src=hash&amp;ref_src=twsrc%5Etfw">#ISMBECCB</a> conference, looking forward to meet the community and 4 days of exciting science.</p> <p>— Aziz Khan (@khanaziz84) <a href="https://twitter.com/khanaziz84/status/1152994355537502208?ref_src=twsrc%5Etfw">July 21, 2019</a></p> </blockquote> <p>Basel was on fire (~40°C), compared with 20°C in Oslo. While walking from the train station towards the hotel, we passed through a bridge (Basel has many bridges over the river Rhine) and saw many people floating down the Rhine to escape from the heat. For a while, it felt like liquid-liquid phase separation in biology, or maybe solid-liquid!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/Rhine-swimmers-1.jpg" alt=""></p> <p><em>People are escaping from the heat by floating down the Rhine. <a href="https://www.open-bio.org/2019/08/01/meeting-report-bosc-2019/">Picture credit</a></em></p> <p>I quickly checked-in, got fresh and ran to the conference venue. The conference kicked off in the San Francisco hall at Congress Center Basel with over 2,000 participants from all over the world, mainly from developed countries. I love the idea of naming conference rooms of Congress Center after different cities around the world like you could bump in Montreal from Delhi without border control. Anyway, I am not sure how many researchers couldn&rsquo;t make it due to visa denials or solely due to lack of funding. I made it because as a European resident I don&rsquo;t need a visa to enter Switzerland.</p> <p>I found that at this year&rsquo;s ISMB/ECCB “ <strong>3</strong>” was my lucky number. As I mentioned earlier, this was my 3rd ISMB/ECCB meeting with 3 participations (2 posters and 1 talk). And surprisingly, three of my mentors were in Basel for the meeting who came from three different continents, Asia, Europe, and North America. My former Ph.D. advisor <em>Xuegong Zhang</em> from Tsinghua University, my current Postdoc PI <em>Anthony Mathelier</em> from the University of Oslo and my next PI <em>Christina Curtis</em> from Stanford University. This is the beauty of ISMB/ECCB, which connects us without borders although many of us have to cross several man-made borders. By the way, I am joining the Curtis lab this fall at Stanford as a research scientist. And congratulations to <em>Xuegong</em> on getting elected as ISCB Board of Directors. Back to lucky number 3, I visited three countries (Switzerland, Germany, and France) in one day with a lunch in Switzerland, dinner in Germany and went for a walk to France.</p> <p>Anyway, the first day of the conference started with an exciting <a href="https://youtu.be/2OEQ0x7CdV0?t=595">keynote talk</a> by <em>Nikolaus Rajewsky</em> from MDC Berlin on the principles of gene regulation in space and time at single-cell resolution. He also shared a great European research initiative, The <a href="https://lifetime-fetflagship.eu/">LifeTime Initiative</a> which aims to use single-cell multi-omics and machine learning techniques to map disease progression to improve medicine.</p> <p>We started the second day with a fascinating <a href="https://youtu.be/CeCLk1jyeAg?t=1294">keynote</a> by <em>William Stafford Noble</em> of the University of Washington on traveling across spaces: the power of embedding genomic and proteomic data into a latent space. He shared three powerful applications of machine learning and deep learning to make sense of complex genomic or proteomic data into latent representation.</p> <p>After the keynote, participants started traveling to different &ldquo;cities&rdquo; to attend their favorite COSIs. My favorite COSI at ISMB has been SysReg. But this time, I stayed in San Francisco (the main hall) to attend the first keynote of HiTSeq COSI by <em>Christina Curtis</em> from Stanford University on quantifying the rates and routes of metastasis.</p> <p>After Christina&rsquo;s talk, I was back to RegSys which was on in the Singapore room with a great line of keynote speakers in the field of gene regulation. The exceptional keynote talks demonstrated the power of using model organisms for important discoveries including interpretation of genetic variants and characterization of different roles and usages of cis-regulatory regions. Other talks highlighted novel experimental and computational methods for characterizing the 3D organization of the genome, TF co-binding, chromatin accessibility, and linking them to different cellular and molecular outcomes. Transcriptional enhancers and their diverse roles in gene regulation were common themes across many talks highlighting the importance of studying these non-coding regulatory regions.</p> <p><img src="https://pbs.twimg.com/media/EAJoUsqXsAAa-FT?format=jpg&amp;name=4096x4096" alt=""><em>The Singapore room is full on the 2nd day of RegSys&rsquo;s morning session on single-cell. Photo by @ferhatay</em></p> <p>The second day of RegSys started in the Singapore room with sessions on the bleeding edge developments in the field of single-cell and transcription factor binding. The three amazing keynotes and other selected talks were full of exciting discoveries enabled by comparing single-cell data from different organisms or by integrating multi-omics such as scRNA-seq and scATAC-seq. Other talks demonstrated the power of machine learning and deep learning techniques at the base-pair resolution, in enabling a better understanding of gene regulatory programs through refined characterization of transcription factor binding.</p> <p>On the 4th day, BOSC 2019, the 20th annual Open Source Bioinformatics Conference, was kicked off in Delhi room by BOSC Chair Nomi Harris followed by an introduction to the Open Bioinformatics Foundation by Heather Wiencko. This was my first official BOSC meeting although I dropped by at the BOSC 2015 in Dublin and BOSC 2017 in Prague while volunteering at ISMB/ECCB. This year the BOSC community presented some excellent open-source bioinformatics resources, tools, and workflows through talks and poster sessions. <em>Nicola Mulder</em> of the University of Cape Town gave a <a href="https://youtu.be/xShfwiDCQL0?t=366">keynote talk</a> on building infrastructure for responsible open science in Africa. She discussed the technical, ethical and social challenges of sharing data in Africa. She said, “It&rsquo;s really hard to convince people to share their data and their tools when they have such a history of being exploited”. She and her team under the umbrella of <a href="https://www.h3abionet.org/">H3ABioNet</a> consortium are making progress in building a Pan-African bioinformatics network.</p> <p>And then came the fifth and last day of ISMB/ECCB 2019. It was also the second and last day of BOSC 2019 which started with interesting talks on open-source, open science and reproducible research using containers and workflows. The last session of BOSC 2019 was on Building Open Source Communities, where I was given the opportunity to introduce our community initiative, <a href="https://ECRcentral.org">ECRcentral</a>. I made my <a href="https://f1000research.com/slides/8-1185">slides</a> and <a href="https://f1000research.com/posters/8-1144">poster</a> publicly available on F1000 Research.</p> <p><a href="https://twitter.com/khanaziz84/status/1154329690154438656">https://twitter.com/khanaziz84/status/1154329690154438656</a></p> <blockquote> <p><strong>ECRcentral</strong> is a community-driven initiative for early career researchers to find research fellowships and travel grants and to share experiences, resources and get feedback.</p> <p><a href="https://elifesciences.org/inside-elife/85999196/elife-ambassadors-introducing-ecrcentral">Read more here</a>&hellip;</p> </blockquote> <p>I co-founded ECRcentral as part of eLife Ambassadors program in collaboration with other eLife Ambassadors. We are a group of ECRs advocating for best practices in science to make science open and reproducible. As an advocate for open science and open-source, I do share all of my code on <a href="https://github.com/asntech">GitHub</a> and also the source code for the ECRcentral platform is openly available on <a href="http://github.com/ecrcentral">GitHub</a>.</p> <blockquote> <p>My talk about <strong>ECRcentral</strong> was well received by the community!</p> </blockquote> <p><a href="https://twitter.com/yoyehudi/status/1154390803248287746">https://twitter.com/yoyehudi/status/1154390803248287746</a></p> <p>And ISMB/ECCB 2019 concluded after an inspiring keynote talk by <em>Bonnie Berger</em> of Massachusetts Institute of Technology on Biomedical Data Sharing and Analysis at Scale. Bonnie Berger started her talk with a powerful statement to emphasize the importance of computational biology. She said:</p> <blockquote> <p>“Biology used to be biology. Now biology is inseparable from computer science.”</p> <p>Bonnie Berger</p> </blockquote> <p><em>I loved it and tweeted right away!</em></p> <p><a href="https://twitter.com/khanaziz84/status/1154410102901923841">https://twitter.com/khanaziz84/status/1154410102901923841</a></p> <blockquote> <p><strong>And I would say that this inseparable biology now needs to be more open and reproducible without borders.</strong></p> </blockquote> <p>Along the lines of openness to science, <a href="https://www.youtube.com/channel/UCN9kqT7pfOzZddPJHqWSuyA/playlists">ISMB/ECCB</a> and <a href="https://www.youtube.com/playlist?list=PLmX8XnLr6zeHofbRXbVg0vShC5RwuElj4">BOSC</a> are setting an example for many other conferences and organizations by recording talks and making those publicly available with the consent of speakers licensed under CC-BY 4.0. I have noticed that most of the talks at several other conferences are recorded but sadly these are put behind the paywalls and community need subscriptions to watch these talks later. There is a great need to digitize conferences and make the recorded talks freely available to everyone, and especially for researchers from developing countries who can not attend these events due to lack of funding or visa restrictions.</p> <p>To conclude, I would like to thank the OBF for providing the travel fellowship to participate in ISMB/ECCB and BOSC 2019. This travel fellowship was a great opportunity to connect with open source and open science enthusiasts, and I strongly believe that this community will push the boundaries even further to grow and diversify in the years to come.</p> <p><a href="https://twitter.com/khanaziz84/status/1155005378079395841">https://twitter.com/khanaziz84/status/1155005378079395841</a></p> <hr> <p><em><a href="https://asntech.github.io/">Aziz</a> is a computational biologist interested in gene regulation, machine learning, cancer, and regulatory genomics and epigenomics. He is a strong advocate of open science, open-source, preprints, and reproducible research and often <strong><a href="http://twitter.com/khanaziz84">tweets</a></strong> about it. He is also an eLife and ASAPbio Ambassador and co-founded ECRcentral, which is powered by eLife.</em></p> <hr>https://www.open-bio.org/2019/09/30/obf-travel-fellowship-august-2019-awards/Mon, 30 Sep 2019 08:38:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/09/30/obf-travel-fellowship-august-2019-awards/<p>A record number of people applied for the latest round of the <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a>, which closed on August 15, 2019. Out of this great set of applicants, we offered travel awards to three who epitomize the goal of the awards: to promote diversity in the world of open source bioinformatics / open science.</p> <p>The awardees are <strong>Arunav Konwar,</strong> <strong>Fernanda Troyner and Nicolás Palopoli</strong>.</p> <p><strong>Arunav</strong> has contributed to open source projects including <a href="https://github.com/deep-learning-indaba/Baobab">Deep Learning Indaba</a> (an African Machine Learning community), Wikimedia, and <a href="https://metafluidics.org">Metafluidics.</a> He will give a talk and lead a workshop at the <a href="https://www.biosummit.org/">Global Community Bio Summit 3.0,</a> which aims to democratize biotechnology by building an inclusive global network of people in the life sciences.</p> <p><strong>Fernanda</strong>, who participated in &quot; <a href="https://www.reprodutibilidade.bio.br/nobudgetsciencehackweek">No Budget Science Hack Week</a>&quot;, is fairly new to open science; she attended the Hack Week to learn about software tools for open science and launch her own open science project. She participates in the <a href="https://www.reprodutibilidade.bio.br/home">Brazilian Reproducibility Initiative</a>.</p> <p><strong>Nicolás</strong> will be co-leading the first <a href="https://carpentries.org/become-instructor/">Carpentries Instructor training</a> in Lima, Peru, in October. He later declined the fellowship as the local organizers offered to cover his travel expenses.</p> <p>Big congratulation to our awardees! We look forward to hearing more about their open source/science projects in future.</p>https://www.open-bio.org/2019/08/27/tips-for-informal-discussions/Tue, 27 Aug 2019 22:36:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/27/tips-for-informal-discussions/<p><em>The <a href="https://www.open-bio.org">Open Bioinformatics Foundation (OBF)</a> sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Malvika&rsquo;s participation at <a href="https://www.open-bio.org/events/bosc/about/">Bioinformatics Open Source Conference</a> 2019 was supported by this fellowship granted to her in January 2019. Find more information <a href="https://www.open-bio.org/travel-awards/">here.</a></em></p> <p>The phrase ‘water cooler effect’ is derived from informal gatherings and connections made around water coolers (or vending machines these days!) at the workplace or other formal situations. Such unplanned encounters lead to genuine connections between people resulting in meaningful and productive collaborations. Many research organizations value the importance of such serendipitous interactions, and actively promote them in their work-culture. Conference organizers also recognize its effectiveness and design their program with longer coffee breaks, dedicated slots for informal discussions and designated venues for breakout sessions.</p> <p><img src="https://images.unsplash.com/photo-1563461661026-49631dd5d68e?ixlib=rb-1.2.1&amp;ixid=eyJhcHBfaWQiOjEyMDd9&amp;auto=format&amp;fit=crop&amp;w=1500&amp;q=80" alt="People interacting informally"></p> <p><em>Image on <a href="https://unsplash.com/photos/5H0p6JPUHbI">Unsplash by @productschool</a></em></p> <p>Since 2000, the <a href="https://www.open-bio.org/events/bosc/about/">Bioinformatics Open Source Conference (BOSC)</a> has been bringing together bioinformaticians and computational researchers interested in Open Science, to provide opportunities for them to discuss their projects, exchange ideas, learn about the latest practices in bioinformatics, and collaborate with each other. These meetings are attended by participants with different backgrounds, which provides them with a unique environment to gain multiple perspectives into different technical and social issues within the bioinformatics community. To facilitate informal interactions that promote the water cooler effects, attendees are encouraged to lead or take part in the participant-driven discussion sessions called <a href="https://en.wikipedia.org/wiki/Birds_of_a_feather_(computing)">Birds of a feather (BoF)</a> on topics of interest to them. Since these sessions are very short, session facilitators try to encourage interactions between the participants, while making effective use of the allocated time, welcoming different viewpoints, and finishing the session with some defined outcome or future directions.</p> <p><img src="https://images.unsplash.com/photo-1557734864-c78b6dfef1b1?ixlib=rb-1.2.1&amp;auto=format&amp;fit=crop&amp;w=1782&amp;q=80" alt="discussion session"></p> <p><em>Image on <a href="https://unsplash.com/photos/QiIxg_q2vh0">Unsplash by @zainulyasni6118</a></em></p> <p>I attended my first BoF on the topic of <a href="http://www.hub-hub.de/wordpress/?p=327">“Unseminar”</a> at the BOSC 2013, where I first met <a href="https://twitter.com/AidanBudd">Aidan Budd</a> who was leading this session. Aidan chose the <a href="http://www.theworldcafe.com/key-concepts-resources/world-cafe-method/">World Cafe method</a> to facilitate this session, where participants could form smaller groups to discuss related topics and switch groups to join different discussions. This informal setting was quite different from the usual speaker-centric format of conferences because it was participant-driven. Everyone immediately felt welcome and included in this session because the emphasis was on learning about the topic at hand together as a group. For a fresh grad student like me, this was a very special experience because I could truly co-exist as a scientist with people of varying levels of experience without feeling like an imposter or someone who didn’t belong there. This discussion didn’t end with the session itself, but catalyzed a much longer discussion after the conference over emails and shared documents, which finally led to a crowdsourced <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003905">publication on “Ten Simple Rules for Organizing an Unconference”</a>, several long-lasting collaborations among the participants, and Aidan became my mentor and a close friend.</p> <p>As a community manager, informal discussion sessions are hands-down my favourite way to connect with others, promote collaborations between the existing members of the community and welcome new members while encouraging active participation from them. Since my first encounter with BoFs, I have participated in and led several discussion sessions. In particular, I facilitated one BoF session at BOSC 2017 in Prague, and one session this year in Basel during my participation at BOSC 2019, which was supported by the <a href="https://www.open-bio.org/travel-awards">OBF fellowship</a>, granted to me in December 2018 application round.</p> <blockquote> <p>off = BoF* :), i.e. Birds of a feather - where people with a common interest can discuss the topic together.</p> <p>— Malvika Sharan (@MalvikaSharan) <a href="https://twitter.com/MalvikaSharan/status/1154007583730126848?ref_src=twsrc%5Etfw">July 24, 2019</a></p> </blockquote> <p>Here are my <strong>top 5 tips for facilitating BoFs</strong> or similar discussion sessions that promote the informal and unplanned aspects of the water cooler effect.</p> <p>1. <strong>Set the ground rules</strong></p> <p>Start your session by welcoming everyone and highlighting the main points of your organization’s/conference’s Code of Conduct. By choosing an inclusive discussion format (see <a href="https://acrl.ala.org/IS/is-committees-2/committees-task-forces/discussion-group-steering/possible-discussion-format-options/">this post by The Instruction Section, ACRL</a> for ideas) we can provide a platform for our attendees to participate equitably. It is also useful to introduce a few simple tips for effective discussions, for example, by inviting volunteers to take different roles such as notetaker, timekeeper, or chair in different groups to ensure that everyone’s voice is heard and noted (see <a href="https://files.adainitiative.org/wiki_binaries/role_cards.pdf">this role card by Ada Initiative</a>).</p> <p><strong>2. Get everyone on the same page</strong></p> <p>State the objective of your sessions clearly so that your participants know what to expect. You shouldn’t assume that participants will know the specific details essential to discuss the topic (we can always ask!), therefore, you can take the first few minutes to briefly introduce the topic and the main terminologies. It’s important to clarify what they will and will not discuss in your session.</p> <p><strong>3. Manage your time effectively</strong></p> <p>Be thoughtful and appreciative of people’s time that they invest in your sessions. Conferences can be stressful. Listening to talks, taking down notes, and getting introduced to new topics while coping with the busy schedule, new venues, and jet-lag can be both mentally and physically exhausting. Therefore informal sessions should not demand too much effort from our attendees and should allow them to decompress. To make everyone’s time count, you can share a clear agenda and divide your session into short rounds. When a session is attended by a large number of participants, it’s more effective to split them into smaller groups where they can discuss different aspects of the given topic. We should also encourage people to switch groups to maximize their chances for personal interactions. As facilitators, we should minimize our own contribution but shouldn&rsquo;t hesitate to bring the focus back to the topic when the discussions derail.</p> <p><strong>4. Make it truly collaborative</strong></p> <p>Short sessions are great for brainstorming and generating new ideas. To ensure that these ideas don’t get lost after the session is over, there should be possibilities for your participants to collaboratively explore the topic and take notes. Each group can be provided with pens, sticky notes, flip charts, and/or whiteboards to facilitate note-taking or drawing concept maps. Online documents such as Etherpad, google docs and GitHub are generally used for sharing details of the sessions, offering a place for everyone to exchange their contact information, store their notes, add questions, and refer back to after the session is over. These online tools can be distracting if not balanced well with in-person collaborative activities (see this excellent <a href="https://uwaterloo.ca/centre-for-teaching-excellence/teaching-resources/teaching-tips/alternatives-lecturing/discussions/facilitating-effective-discussions">post on facilitating discussions</a> by University of Waterloo). Each group discussion can be guided by a set of questions or scenarios and the chair of each group can be asked to share the outcome of their discussion with everyone.</p> <p><strong>5. Communicate your next steps</strong></p> <p>Even though these events are short, it’s always useful to use a few minutes towards the end of the sessions to bring the entire group together to invite final thoughts and possible directions for the discussed topic and ideas. You can set a few channels of communication that the attendees can use in order to connect with each other and continue the discussion afterward. Since we want to be mindful of the contributions made by our participants, it’s important to let them know where and how the outcome of their discussions will be used, how they can reuse the material, and where they can access them in the future. After the conference, a summary of the session in a collaborative document and further details can be shared with a “Thank You” email.</p> <p><img src="https://pbs.twimg.com/media/DFVqupbXoAI9eCV?format=jpg&amp;name=medium" alt="BOSC 2017"></p> <p><em>Picture from a BoF I facilitated during BOSC 2017 on &lsquo;Promoting Diversity at Bioinformatics Conferences&rsquo;</em></p> <p>To conclude, informal discussion sessions are useful for collecting ideas, gaining perspectives, and engaging with others over informal conversations on topics of mutual interests. With a little pre-planning, these meetings can turn an idea discussed over coffee or by the water coolers into useful community-driven projects. I hope you find these tips useful and take advantage of this format at the next BOSC or in your community events.</p> <p>Do let me know on twitter ( <a href="https://twitter.com/MalvikaSharan">@malvikasharan</a>) which of your favourite tips are missing in the post.</p>https://www.open-bio.org/2019/08/27/dos-and-donts-for-computational-training/Tue, 27 Aug 2019 09:49:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/27/dos-and-donts-for-computational-training/<h6 id="thanks-to-obf-support-with-a-travel-grant-i-was-able-to-attend-the-first-european-carpentryconnect-event-in-manchester-ccmcr19-organized-by-thesoftware-sustainability-institute">Thanks to OBF support with a <a href="https://www.open-bio.org/travel-awards/">travel grant</a>, I was able to attend the first European CarpentryConnect event in Manchester CCMcr19 organized by The Software Sustainability Institute.</h6> <p><img src="https://i.imgur.com/rKTSHED.png" alt="">Colourful Manchester days post Pride weekend</p> <p><strong>The <a href="https://carpentries.org/">Carpentries</a> is a global community with a mission to teach</strong> essential data and foundational computational skills to researchers for conducting efficient, open, and reproducible research. The community includes instructors, trainers, maintainers and many more helpers and supporters on a global scale.</p> <p>This was my first CCMcr19 and first Carpentry event. I was curious to know more about the community, their computational efforts and inclusive practices and CCMcr19 seemed like a good place to start.</p> <p>I joined the computational world a few years ago, after moving from “wet” to “dry” lab. Shortly after the transition, I started delivering computational training and naturally, as a novice trainer, my main focus was on the material in terms of what to cover, how relevant it is, in what order do I present it and so on.</p> <p>When I faced my first classroom, I quickly realized that prepping the material and doing my research was the easy part. Instead, I found myself thinking of the other factors that contribute to the participants&rsquo; learning experience such as; how do I address and interact with them, how do I account for their very diverse demographics such as gender, age and language.</p> <p><img src="https://i.imgur.com/5ppP8SE.jpg" alt="">Diversity and Inclusion CCMcr19 Ms. Brönte</p> <p>Our classrooms today are not what they used to be 10 years ago. Participants come from all over the world and all walks of life, in other words, very diverse. This is especially true in computational training. For instance, bioinformatics training events in EMBL-EBI have two different types of attendees, one of which is made of plastic; <a href="https://www.ebi.ac.uk/about/news/announcements/bioinformatics-training-with-robot-avatars">robot avatars</a> allowing students to participate virtually without having to be physically there.</p> <p>Providing training and access to computational and cloud-based resources, enables researchers, especially those with limited resources, to work along with international partners, thereby contributing to open, reproducible research and helping improve research quality by bringing new perspectives.</p> <blockquote> <p>Question is, how do we improve and adapt our training sessions to be more inclusive accounting for a diverse range of demographics?</p> </blockquote> <p>I turned to the Carpentries community to learn from their collective experiences to help create a Dos and Don’ts checklist for computational teaching. The continuous contributions from trainers, as well as trainees, will help build a resource with advice on how to be mindful of diversity, equality and inclusion issues that play a role in training practices.</p> <p>CCMcr19 was a three-day event with a very dynamic and interactive format with a twist.</p> <p>Unlike many tech-oriented events, CCMcr19 covered a wide range of topics related to computational training, including advancing inclusive practices in the community and <a href="https://software.ac.uk/blog/2019-04-24-can-we-increase-our-impact-reducing-it-thoughts-environmental-sustainability">environmental initiatives</a>.</p> <blockquote> <p>My first day &amp; first <a href="https://twitter.com/hashtag/CCMcr19?src=hash&amp;ref_src=twsrc%5Etfw">#CCMcr19</a>, I&rsquo;m impressed!! Lovely people, great food, environmental awareness, dog, magician, doodler and above all interesting discussions and tons of things to learn! Defo a conference with a twist 😉! Thanks to the organisers! <a href="https://twitter.com/hashtag/Day2?src=hash&amp;ref_src=twsrc%5Etfw">#Day2</a> <a href="https://twitter.com/hashtag/BringItOn?src=hash&amp;ref_src=twsrc%5Etfw">#BringItOn</a> <a href="https://t.co/Dslqiz1HOe">https://t.co/Dslqiz1HOe</a></p> <p>— Dr. Sara El-Gebali (@yalahowy) <a href="https://twitter.com/yalahowy/status/1143776558651514881?ref_src=twsrc%5Etfw">June 26, 2019</a></p> </blockquote> <p>To encourage attendees to contribute to reducing impact on the environment at the conference, the <strong>Reusable Cup Raffle</strong> was introduced. We took a photo of our reusable cup/other reusable items such as reusable lanyards and badges, then tweeted about it using the hashtag # <a href="https://twitter.com/hashtag/CCMcr19ReusableLanyards?src=hashtag_click">CCMcr19ReusableLanyards</a> &amp; # <a href="https://twitter.com/hashtag/CCMcr19ReduceCO2?src=hashtag_click">CCMcr19ReduceCO2</a> and the raffle was drawn.</p> <blockquote> <p>Guess who won?</p> </blockquote> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/Sara-Elgebali-we-won-1024x768.jpg" alt="">We won!</p> <p>After learning about the Carpentries and their inspiring work on day 1. I carried out my workshop titled Dos and Don’ts for computational training on day 2. I was joined by 10 participants, all of whom have experience in delivering training.</p> <p><img src="https://i.imgur.com/gruhfO3.jpg" alt="">Group discussions</p> <p>The first exercise we did was getting to know each other; background, expectations and anticipated outcomes.</p> <blockquote> <p><strong><em>“Know your audience”</em></strong></p> </blockquote> <p>After the groups formed organically, people started sharing their experiences and each group started noting down their observations, contributing to the list of advice.</p> <blockquote> <p><strong><em>“</em> Do’s and Don’ts in computational training”</strong></p> </blockquote> <p>As the discussion became more lively and engaging, it was evident that we needed a <strong>gatekeeper;</strong></p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>a person who can make sure that everyone is participating and getting along in an orderly fashion. </span></span></code></pre></div><p>There were some interesting examples from the trainers which led to some thought-provoking advice, for example;</p> <blockquote> <p><strong><em>“Hands off my keyboard”</em></strong></p> </blockquote> <p>As a trainer, when asked for help, there is a tendency to grab the keyboard to “show” the students how to work out the task at hand. In doing so, we inadvertently diminish their autonomy, reduce their confidence and invade their personal space.</p> <p>Other practical advice to display an open and inclusive space include introducing our pronouns at the start of the session. In doing so, the participants become aware that this is an inclusive environment where they are encouraged to express themselves.</p> <p>We also discussed breaks during sessions, such as;</p> <p><strong>“Bio breaks”</strong>, short breaks of 5-10 minutes to allow participants time to go to the bathroom, drink water, and stretch to prevent people from taking breaks at different times and miss out on something.</p> <p><strong>“Brain Breaks”</strong>, a mental break of 1-3 minutes each hour of the session, to help participants to re-energize, re-focus and relax, allowing people to reflect or clear their minds.</p> <h2 id="since-we-are-focused-on-computational-teaching-it-didnt-go-amiss-to-include-advice-on-technological-solutions-to-facilitate-training-sessions-while-catering-for-different-abilities-and-needs">Since we are focused on computational teaching, it didn’t go amiss to include advice on technological solutions to facilitate training sessions while catering for different abilities and needs.</h2> <p>Check out the list of Do&rsquo;s and Don&rsquo;ts in computational training and please feel free to share your tips and advice on <a href="https://github.com/selgebali/CCMcr19_dos">GitHub</a>.</p> <h4 id="sara-el-gebali">Sara El-Gebali</h4> <p>Email: <a href="mailto:selgebali@gmail.com">selgebali@gmail.com</a> Twitter: @yalahowy GitHub: @selgebali</p>https://www.open-bio.org/2019/08/25/cordon-bleu-bioinformatics/Sun, 25 Aug 2019 18:08:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/25/cordon-bleu-bioinformatics/<p>I attended the Bioinformatics Open Source Conference ( <a href="https://www.open-bio.org/events/bosc/">BOSC</a> 2019) organized this year along with <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB</a> in Basel, Switzerland from July 21st-25th. BOSC 2019 was in multiple ways a lot of &lsquo;firsts&rsquo; for me. I was attending my first ISMB/ECCB. It also happened to be my first time in Europe. It was the first time I was putting faces and voices to a lot of names. Like in most of the conferences these days, I met a lot of Twitter-verse friends for the very first time. And above all, this was my first ever BOSC.  I was funded in part by the Open Bioinformatics Foundation’s <a href="https://www.open-bio.org/travel-awards/">Travel Award</a> and ISMB/ECCB’s Travel Fellowship. My travel and the learnings I summarize here would have been impossible without both.</p> <p><img src="https://lh3.googleusercontent.com/2hnxxOt_KWFjNV-q51dGeodBwJQ_LjK9bom4AP2irMkBE1I6d5YE0eCZ_NrQqqT9_MCJAUAUnfV3cXMzj6CkySLpqdm6u8Pef25o76H9K4BPhMup6DwhNFN1Zf8mKd_fl63fKpCb" alt="">Nomi Harris introducing the 20th BOSC 2019 (Couldn&rsquo;t capture Nomi at this angle)</p> <h3 id="bosc-and-me"><strong>BOSC and me</strong></h3> <p>I had been trying to go to BOSC for around three years. I submitted three abstracts over the three years which were all accepted for a lightning talk. However, a lack of funding made it impossible for me to make it to  BOSC 2016 and BOSC 2018. I submitted my abstract for a poster and talk about <a href="https://github.com/saketkc/pysradb">pysradb</a> that was selected for a lightning talk (a short five-minute talk) and a poster.</p> <h3 id="ismbeccb-single-cell-workshop"><strong>ISMB/ECCB Single Cell Workshop</strong></h3> <p>I arrived in Switzerland on July 19th, two days earlier than the official start date of the meeting and a day earlier than the Tutorial tracks.</p> <p>OBF’s Travel award not only covered my ISMB registration but was also generous enough to cover the registration costs for Tutorial(s). ISMB/ECCB 2019 had multiple tutorial tracks spanning the fields of interpretation of deep learning in biology, computational drug discovery, statistical methods for single-cell RNA-seq, biological data visualization, biomarker discovery and tools for reproducible analysis. I decided to attend the tutorial on statistical methods for single-cell RNA-seq primarily to get an overview of the single-cell world, which is not very distant from my current research interest of deciphering translation regulation. The <a href="https://github.com/rhondabacher/ISMB2019_SingleCellTutorial">tutorial</a> was very comprehensive and gave an overview of the technology, its nuances and the methods developed to tackle them. I expected it to be a bit more methods oriented, but it is difficult to have the best of everything for a diverse audience. </p> <h3 id="keynotes-at-ismbeccb"><strong>Keynotes at ISMB</strong>/ECCB</h3> <p>ISMB/ECCB being a large conference (owing to the fact that it is two conferences combined into one) is organized into multiple tracks. The upside of a large conference is that there is so much new to learn. An obvious downside is that it could be overwhelming. I followed an “on-the-day” optimization strategy where I would look up schedules for the talks for a day in the early morning. This would have been practically impossible without the ISMB’s conference app. Though there are traditional conference booklets, an app comes in handy in scheduling. Given the multitude of tracks involved, I would keep running from one room to other. The calm dusk at Rhine river came to the rescue after each day&rsquo;s heated effort, <a href="https://www.washingtonpost.com/climate-environment/2019/08/05/heres-how-hottest-month-recorded-history-unfolded-around-globe/">quite literally</a>,</p> <p>I made sure I attended all the keynotes. Day 1 had Dr. Nikolaus Rajewsky’s keynote on how single-cell RNA-seq is making it easier to improve our understanding of gene regulation on a much granular scale in space and time. Day 2’s Keynote had Dr. William Noble walking us through the applied machine learning world in genomics: an embedding method for inferring the corresponding cells given two biological assays data and an imputation method for learning the latent representation of the epigenome. Day 3 had Dr. Alexis Battle talking about modeling the complex impact of common and rare genetic variation on gene expression. The field of Genomics is full of examples of missing ground truth. On Day 4, Dr. Christophe Dessimoz talked on “Challenges and rewards of benchmarking – how to cope with a biased, incomplete, or even entirely missing ground truth”. I had been aware of Dr.Christophe’s work through his paper on the <a href="http://doi.org/10.1371/journal.pcbi.1002514">ortholog-paralog conjecture</a>. Finally, Dr. Bonnie Berger’s keynote introduced me to the perils of data sharing in the genomic world and the solutions her lab has worked on over the years.</p> <h3 id="poster-sessions"><strong>Poster Sessions</strong></h3> <p>The poster sessions were spread over 4 days of ISMB/ECCB. With approximately 1000 posters, it is overwhelming to digest all the information you obtain. I again relied on the ISMB/ECCB mobile app to shortlist ones that I really wanted to learn about. I am sure I still missed out on a bunch.</p> <h3 id="keynote-at-bosc"><strong>Keynote at BOSC</strong></h3> <p>Dr. Nicola Mulder’s keynote introduced us to the challenges faced by African countries, owing to their history of exploitation and inequitable scientific partnerships.</p> <p><a href="https://twitter.com/GigaScience/status/1154012905639206912?ref">https://twitter.com/GigaScience/status/1154012905639206912?ref</a>_src=twsrc%5Etfw</p> <p><a href="https://www.h3abionet.org">H3ABioNet</a> is a Pan-African bioinformatics network that is trying to address this challenge by making the controlled access data findable and interoperable for both data providers and users.</p> <h3 id="bosc-takeaways"><strong>BOSC Takeaways</strong></h3> <p>BOSC happens over two days of the main conference that is often followed by another two days of <a href="https://www.open-bio.org/wiki/Codefest">C</a> <a href="https://www.open-bio.org/events/bosc/collaborationfest/">oF</a> <a href="https://www.open-bio.org/wiki/Codefest">est</a>. Unfortunately, I was not able to participate in CoFest. BOSC was packed with sessions on data crunching, data modeling and formats,  containers, open science, workflows and building open source communities. Besides these sessions there were also independent Birds of a Feather sessions (BoFs) which are informal self-organized meetups on <a href="http://bit.ly/BOSC2019-bofs">a myriad of topics</a>, spread over the two days. I participated in the “Reimaging the paper” BoF organized by Dr. Emmy Tsang of eLife Innovation. We discussed how the traditional model of publishing is limited in terms of reproducibility. The journals need to define a minimum standard for ensuring reproducibility, but defining what these gold standards should be, still remains a challenge in itself.</p> <p>Summarizing all the talks at BOSC would be near impossible here. So I will describe the ones that got me super excited. The first one was by Dr. Malvika Sharan, on how promoting inclusiveness in Open Science communities requires an “open by design” approach where information sharing is scalable, the community is welcoming and supportive of newcomers and there are appropriate channels for skill transfer.</p> <p><a href="https://twitter.com/yoyehudi/status/1154384936893329408">https://twitter.com/yoyehudi/status/1154384936893329408</a></p> <p>Dr. Devon Ryan’s talk on <a href="https://github.com/maxplanck-ie/snakepipes">snakePipes</a> was another talk that stuck around with me as it solves a critical problem that I have faced as a computational biology PhD student. A lot of data analysis requires mundane steps in analysis. snakesPipes is designed to make this useful for everyone with such a need, without forcing them to be familiar with CLI.</p> <p><a href="https://twitter.com/dpryan79/status/1154277950151372800?ref">https://twitter.com/dpryan79/status/1154277950151372800?ref</a>_src=twsrc%5Etfw</p> <p>If you are wondering what “eierlegendewollmilchsau” is, to the best of my knowledge (and memory), it translates to “has only advantages, satisfies all needs, meets all demands” and probably fits in well with the ideology behind snakePipes.</p> <p>Mateusz Kuzak from Elixir in his talk “ELIXIR Europe on the Road to Sustainable Research Software” encouraged everyone to open source their work from day one. No, there is no evidence of your work being scooped if you choose to do so. Here is his advice:</p> <p><a href="https://twitter.com/morgantaschuk/status/1154326308203257857">https://twitter.com/morgantaschuk/status/1154326308203257857</a></p> <p>I need to mention my fellow OBF Travel awardee Dr. Aziz Khan&rsquo;s efforts at building <a href="https://ecrcentral.org/">ECRcentral</a> that helps early-stage researches find and discuss funding opportunities besides providing them a platform to share their experiences and mentor peers. As an early stage researcher myself, I have found the resources there extremely useful.</p> <p>Finally, a project that I will keep a lookout on is <a href="https://www.biotite-python.org/">Biotite</a> by Patrick Kunzmann designed as a  comprehensive and efficient computational molecular biology library. But we already have <a href="https://biopython.org">Biopython</a>? Well, yes and no. Extensive usage of numpy and cythonization results in reduced runtimes.</p> <p><img src="https://lh4.googleusercontent.com/npS5DuQPIX_4hhHWCzDthPHDjRCykY8e4dAZeCkWxcP9G6i3C2nLMyELMo4QkXdGxgVwmyB7PzgfQNfq1gVXBRfYa0Tz2Ssjz3MzE04hIqrqxskrjGOKRZM1exhsmpvOndIq9BWt" alt="">Biotite and Biopython: Open source wins</p> <p><img src="https://lh3.googleusercontent.com/5s1J3ioUYM2APb1TziwU046t17pcbNVPSwZmazeWNPmTiEwsK-7U2LXjNLjWsP3m1MHnK4_oTTFSrFMKyQZ81-n7_uP9s_nL5agnZ2KxXHQEAEeHQBlu72FqPq7ZsMAPjcYKQ2Ys" alt="">Biotite&rsquo;s perfomance compared at multiple tasks</p> <p><strong>My lightning talk at BOSC</strong></p> <p>My schedule before leaving for ISMB/ECCB 2019 from Los Angeles was jam-packed. I did the grave mistake of overestimating my ability to make a presentation for a 5-minute lightning talk. You just have to talk for 5 minutes, but then you have <strong>only</strong> five minutes. My presentation was only complete the night before my actual talk and would not have been possible without the feedback of Meghna Verma, a PhD candidate at Virginia Tech. I met her also for the first time at ISMB. I had a lightning talk on Day 1 where I talked about <a href="https://f1000research.com/articles/8-532">pysradb</a>, which I built over the last year to help me in my Ph.D. project. In the future, I plan to not overestimate my abilities, they are not worth the potential ill-effects they can have.</p> <p><a href="https://twitter.com/yoyehudi/status/1153969142665502720?ref">https://twitter.com/yoyehudi/status/1153969142665502720?ref</a>_src=twsrc%5Etfw</p> <p>I also had a poster on pysradb on the day of my lightning talk. I got a lot of visitors and a bunch of feedback. I hope pysradb also gets more contributors in the days to come!</p> <p><img src="https://lh3.googleusercontent.com/lLZ26IxGrCPVJRK-Khv_Ljy7hPpP_w6MiSOCl6qoJOqRUYbCHsOJfYuefKPsc0tgSPQizZAYnZtChcT4b3hzxqO1_6XX98jVFrntGnChIjNrkFhkQ-pCy9Yyj-Mgv0zNyqhxVA38" alt="">P-01: pysradb poster</p> <h3 id="applying-for-bosc-travel-award"><strong>Applying for BOSC Travel Award</strong></h3> <p>If you are thinking of traveling to any event promoting open-source bioinformatics software development and open science in the biological research community, OBF covers up to USD 1000 and it is possible to request a higher amount. The <a href="https://www.open-bio.org/travel-awards/">application process</a> is one of the smoothest I have ever come across!</p> <p>Application Deadlines: April 15, August 15, December 15 every year.</p> <h3 id="applying-for-ismb-travel-fellowship"><strong>Applying for ISMB Travel Fellowship</strong></h3> <p>ISCB also provides Travel Fellowships that can come in handy if your original source of funding is not sufficient. Switzerland travel was a bit expensive, so I had applied for a travel fellowship once I got an acceptance. If you are submitting to ISMB in the future, you will receive instructions via email if you want to apply for a Travel Fellowship. Both the OBF and ISMB applications are very easy to fill out.</p> <h3 id="cordon-bleu"><strong>Cordon Bleu?</strong></h3> <p>Though more often associated with a <a href="https://en.wikipedia.org/wiki/Cordon_bleu_(dish)">dish</a>, I chose the title of this post as such for the high quality of talks at ISMB/ECCB and BOSC. I learned a lot in the span of five days and look forward to participating in the future as well. Again, I can’t thank enough the Open Bioinformatics Foundation and ISMB/ECCB for making this cordon bleu experience possible.</p> <p><img src="https://lh3.googleusercontent.com/2fp5QayJNDfcjc7XBlMiOTpYKkYmYY_tq_QI4gWo9BCdgo0lTzieGmH3Qa3MPUCkKf5CSKtAw_ZCZdwkXinl2bSuek7tFzGL5AKPDDvKpaIbaVfgWOa0Y5kmRzUdyo4RKDyNOEG0" alt="">Cordon Bleu - the dish</p> <p><img src="https://lh6.googleusercontent.com/fzuwof2uE2o3YR58i2-1pIf10d8HtdcujGxopihgSooY0YMaJ3V_53KY6J6xgts1hUgTGKtjlHA6bXfj70fejtzWdiXUYDGLii7wkqEIUYgDCqkYsp9mrPfPmX14tgl42hrJHv86" alt="">Dusk at the Rhine river, a few minutes walk away from the conference venue</p>https://www.open-bio.org/2019/08/17/malvika-sharan-elected-to-obf-board/Sat, 17 Aug 2019 13:36:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/17/malvika-sharan-elected-to-obf-board/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/Malvika-cropped-1.jpg" alt="Photo of Malvika Sharan"> At the OBF’s July 2019 <a href="https://www.open-bio.org/2019/08/16/obf-public-board-meeting-july-2019/">public Board meeting</a> (held at BOSC 2019), Malvika Sharan was unanimously elected as a new at-large Board member. Malvika, who earned a PhD in bioinformatics at the University of Würzburg, is a community outreach coordinator at the European Molecular Biology Laboratory (EMBL), Heidelberg. She is passionate about promoting the inclusion of historically underrepresented groups in bioinformatics and STEM in general. Malvika recently won a fellowship from the <a href="https://software.ac.uk/programmes-and-events/fellowship-programme">Software Sustainability Institute</a> to support her research into identifying and developing effective training strategies in low-income research environments (limited resources, lack of funding, etc.). She was also a recipient of an <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> that helped defray her cost of attending BOSC.</p> <p>As a new OBF Board member, Malvika looks forward to helping the organization undertake more efforts to grow and support a vibrant, diverse open science community.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/OBF-Board-July-2019-1.jpg" alt="Photo of OBF Board members, July 2019"> Above: OBF Board members Malvika Sharan, Nomi Harris, Bastian Greshake Tzovaras, Hilmar Lapp, Yo Yehudi, Heather Wiencko, Peter Cock. (Not shown: Chris Fields)</p>https://www.open-bio.org/2019/08/16/obf-public-board-meeting-july-2019/Fri, 16 Aug 2019 03:55:21 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/16/obf-public-board-meeting-july-2019/<p>On July 25, 2019, the OBF held a public Board meeting in Basel, Switzerland. Organized as a Birds of a Feather session at BOSC 2019, the meeting was open to all attendees at ISMB. All but one of the current Board members were present (Secretary Chris Fields called in), as well as a number of ISMB/BOSC attendees. At the meeting, Malvika Sharan was elected as a new Board member. Other topics of discussion included the need for a Code of Conduct that applies to member projects as well as covering the yearly BOSC meeting; the policy for accepting new member projects; revisiting the OBF’s mission statement; and considering whether the OBF should issue position statements. The meeting minutes are <a href="https://github.com/OBF/obf-docs/blob/master/minutes/2019-July.md">here</a>. There will be another public Board meeting near the end of 2019 to vote on Board members whose terms are ending.</p>https://www.open-bio.org/2019/08/07/travel-fellowship-deadline-august-15-2019/Wed, 07 Aug 2019 23:12:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/07/travel-fellowship-deadline-august-15-2019/<p>The <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> program, established in 2016, aims to increase diverse participation at events related to open source bioinformatics. Applications are reviewed three times a year. Applicants may apply for attending any event that develops or promotes open source development and open science in the biological research community. It doesn’t have to be an OBF-related event, and it can be one that you already attended in the recent past. For example, if you attended BOSC 2019 and your travel expenses were not covered by your employer or university, you could apply for a travel fellowship to help defray those expenses (up to a maximum of $1000, in most cases). Travel fellowship awardees are required to write a blog post about their experience attending the event; you can see some past such posts on our <a href="https://www.open-bio.org/tag/travel-fellowship/">blog</a>.</p> <p>The next application deadline is August 15, 2019. We encourage you to apply if you are attending an event that promotes open source bioinformatics software development or open science, and your participation will contribute to diversity in the wider community.</p>https://www.open-bio.org/2019/08/01/meeting-report-bosc-2019/Thu, 01 Aug 2019 20:45:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/01/meeting-report-bosc-2019/<p>As Europe experienced a record-breaking heat wave, <a href="https://www.open-bio.org/events/BOSC/">BOSC 2019</a> attendees stayed cool in the Basel Congress Center (and many took breaks by floating down the Rhine). This was the 20th annual BOSC. In 2018, BOSC partnered with the Galaxy Community Conference in <a href="https://www.google.com/url?q=https://gccbosc2018.sched.com/&amp;sa=D&amp;ust=1564688159135000">GCCBOSC2018</a>; this year, it returned to <a href="https://www.google.com/url?q=https://www.iscb.org/ismbeccb2019&amp;sa=D&amp;ust=1564688159135000">ISMB</a> as one of over a dozen “Communities of Special Interest” (COSIs).</p> <p><a href="https://www.google.com/url?q=/events/bosc/&amp;sa=D&amp;ust=1564688159135000">BOSC 2019</a> opened on July 24 with chair Nomi Harris noting that <a href="https://www.google.com/url?q=/events/bosc/about/&amp;sa=D&amp;ust=1564688159135000">over its 20 years</a>, BOSC has been held in 12 different countries, 6 US states and 2 Canadian provinces. Next, Heather Wiencko introduced the <a href="https://www.google.com/url?q=/&amp;sa=D&amp;ust=1564688159136000">Open Bioinformatics Foundation</a>, BOSC’s parent organization, and Kai Blin discussed the OBF’s participation in <a href="https://www.google.com/url?q=https://obf.github.io/GSoC/&amp;sa=D&amp;ust=1564688159136000">Google’s Summer of Code</a>. The two morning sessions focused on data&ndash;representing it, storing it, crunching it. Open Data was covered in another session later in the day.</p> <p>The second day started with Late-Breaking Lightning Talks, which offered peeks at the latest open source / open science research. Next up was a popular new session on Containers, followed by an Open Science session. Our ever-popular Workflows session was followed by a session called Building Open Source Communities (check out the acronym!), which opened with a talk by newly-elected (at the public OBF Board Meeting held during BOSC) OBF Board member Malvika Sharan on Inclusiveness in Open Science Communities.</p> <p>This year’s <a href="https://www.google.com/url?q=/events/bosc/keynotes/&amp;sa=D&amp;ust=1564688159137000">keynote speaker</a> was University of Cape Town professor Nicola Mulder, who spoke on “Building infrastructure for responsible open science in Africa.” Sharing data in Africa involves technical, ethical and social challenges (“It&rsquo;s really hard to convince people to share their data and their tools when they have such a history of being exploited,” she observed), but despite these obstacles, the H3ABioNet Consortium (of which Prof. Mulder is lead PI) is making progress in building a pan-African bioinformatics network.</p> <p>The two-day meeting included a total of <a href="https://www.google.com/url?q=/events/bosc/schedule/&amp;sa=D&amp;ust=1564688159137000">46 talks and 55 posters</a>. During the meeting, attendees generated over 1500 <a href="https://www.google.com/url?q=https://twitter.com/search?q%3D%2523BOSC2019%26src%3Dtyped_query%26f%3Dlive&amp;sa=D&amp;ust=1564688159137000">tweets mentioning #BOSC2019</a>(you can find them in JSON format <a href="https://www.google.com/url?q=https://www.dropbox.com/s/phznj50qkjet1lh/twitter_BOSC.json.gz?dl%3D0&amp;sa=D&amp;ust=1564688159138000">here</a>).</p> <p>BOSC closed with an announcement that next year’s meeting will be held in collaboration with Galaxy’s Community Conference as the Bioinformatics Community Conference (BCC 2020), which will be held in Toronto, Canada, July 18-22, 2020. We may return to ISMB in 2021 (this has not yet been decided).</p> <p>The two days after BOSC, about 50 people participated in the OBF-run <a href="https://www.google.com/url?q=/events/bosc/collaborationfest/&amp;sa=D&amp;ust=1564688159138000">CollaborationFest</a> (or CoFest for short), an event at which participants work together to contribute to bioinformatics software, documentation, training materials, and use cases. CoFest 2019 was held at The Swiss Innovation Hub for Personalized Medicine in Basel.</p> <p>The OBF/BOSC thank our <a href="https://www.google.com/url?q=/events/bosc/sponsors/&amp;sa=D&amp;ust=1564688159139000">sponsors</a> for helping to support BOSC, the CoFest and our ongoing <a href="https://www.google.com/url?q=/travel-awards/&amp;sa=D&amp;ust=1564688159139000">Travel Fellowship</a> program: <a href="https://www.google.com/url?q=https://aws.amazon.com/hpc&amp;sa=D&amp;ust=1564688159139000">AWS</a>, <a href="https://www.google.com/url?q=https://cloud.google.com/&amp;sa=D&amp;ust=1564688159139000">Google Cloud</a>,<a href="https://www.google.com/url?q=https://elifesciences.org/&amp;sa=D&amp;ust=1564688159140000">eLIFE</a>, <a href="https://www.google.com/url?q=https://journals.plos.org/ploscompbiol/&amp;sa=D&amp;ust=1564688159140000">PLOS Comp. Biol.</a>, <a href="https://www.google.com/url?q=https://academic.oup.com/gigascience&amp;sa=D&amp;ust=1564688159140000">GigaScience</a>, <a href="https://www.google.com/url?q=https://thehyve.nl/&amp;sa=D&amp;ust=1564688159140000">The Hyve</a>, <a href="https://www.google.com/url?q=https://www.knime.com/&amp;sa=D&amp;ust=1564688159140000">KNIME</a>. and the <a href="https://www.google.com/url?q=https://www.software.ac.uk/&amp;sa=D&amp;ust=1564688159140000">Software Sustainability Institute</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-organizers-1.jpg" alt=""> Figure 1: The BOSC 2019 Organizing Committee (from left to right: Peter Cock, Karsten Hokamp, Yo Yehudi, Nomi Harris, Monica Munoz-Torres, Heather Wiencko, Michael Heuer, Bastian Greshake Tzovaras; not shown: Chris Fields)</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""> Figure 2: A rapt audience at BOSC 2019</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/Rhine-swimmers-1.jpg" alt=""> Figure 3: Many people escaped from the heat by swimming in the Rhine, which runs right through the middle of Basel</p> <hr>https://www.open-bio.org/2019/07/23/minutes2019-bosc/Tue, 23 Jul 2019 14:22:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/07/23/minutes2019-bosc/<p>The July 2019 Open Bioinformatics Foundation Public Board Meeting was held in person, as a Birds-of-Feather during the 2nd day lunch period of the 2019 BOSC.</p> <h2 id="date-location-and-dial-in">Date, Location and Dial-In</h2> <p>Date and time: July 25, 12:45pm CEST Venue: Congress Center Basel, Switzerland, in the Dehli Room (ground floor, same room as BOSC) Dial-In for participating remotely: <em>expired</em></p> <h2 id="agenda">Agenda</h2> <p><strong>Old business:</strong></p> <ol> <li>Approve <a href="https://www.open-bio.org/2018/03/16/minutes2018-mar-confcall/">minutes from March 2018 Public Board Meeting</a></li> </ol> <p><strong>New business:</strong></p> <ol> <li>Term expirations and Elections to the Board ( <a href="https://vote.heliosvoting.org/helios/e/obf-july-2019">electronic ballot</a>) <ul> <li>Malvika Sharan, running for Board member at-large</li> <li>Karen Cranston&rsquo;s term as Board member at-large expired in 2018, and she chose not to run for another term.</li> <li>The terms of several current Board members (Hilmar Lapp, Peter Cock, Chris Fields, Nomi Harris) are expiring this year, but are deferred to later this year for re-election.</li> </ul> </li> <li>Fiscal sponsor <ul> <li>Update on fiscal sponsor situation</li> <li>Revamping the process for OBF&rsquo;s financial reports</li> </ul> </li> <li>OBF Code of Conduct</li> <li>Open floor <ul> <li>Opportunities to engage</li> <li>Revisiting vision and mission</li> </ul> </li> </ol> <h2 id="minutes">Minutes</h2> <p>The meeting minutes are <a href="https://github.com/OBF/obf-docs/blob/master/minutes/2019-July.md">available in the obf-docs Github repository</a>.</p>https://www.open-bio.org/2019/07/16/biopython-1-74-released/Tue, 16 Jul 2019 19:39:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/07/16/biopython-1-74-released/<p>Dear Biopythoneers,</p> <p>Biopython 1.74 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.74">PyPI</a>.</p> <p>This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However, it will be the last release to support Python 3.4 which is now at end-of-life. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.</p> <p>(Please note we will be dropping support for Python 2.7 in early 2020.)</p> <p>Over half our code is now explicitly available under either our original &ldquo;Biopython License Agreement&rdquo;, or the very similar but more commonly used &ldquo;3-Clause BSD License&rdquo;. See the <code>LICENSE.rst</code> file for more details.</p> <p>Our core sequence objects ( <code>Seq</code>, <code>UnknownSeq</code>, and <code>MutableSeq</code>) now have a string-like <code>.join()</code> method.</p> <p>The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning the fields may not always follow the historical column based positions. We no longer give a warning when parsing these. We now allow writing such files (although with a warning as support for reading them is not yet widespread).</p> <p>Support for the <code>mysqlclient</code> package, a fork of MySQLdb, has been added.</p> <p>We now capture the IDcode field from PDB Header records.</p> <p><code>Bio.pairwise2</code>&rsquo;s pretty-print output from <code>format_alignment</code> has been optimized for local alignments: If they do not consist of the whole sequences, only the aligned section of the sequences are shown, together with the start positions of the sequences (in 1-based notation). Alignments of lists will now also be prettily printed.</p> <p><code>Bio.SearchIO</code> now supports parsing the text output of the HHsuite protein sequence search tool. The format name is <code>hhsuite2-text</code> and <code>hhsuite3-text</code>, for versions 2 and 3 of HHsuite, respectively.</p> <p><code>Bio.SearchIO</code> HSP objects has a new attribute called <code>output_index</code>. This attribute is meant for capturing the order by which the HSP were output in the parsed file and is set with a default value of -1 for all HSP objects. It is also used for sorting the output of <code>QueryResult.hsps</code>.</p> <p><code>Bio.SeqIO.AbiIO</code> has been updated to preserve bytes value when parsing. The goal of this change is make the parser more robust by being able to extract string-values that are not utf-8-encoded. This affects all tag values, except for ID and description values, where they need to be extracted as strings to conform to the <code>SeqRecord</code> interface. In this case, the parser will attempt to decode using <code>utf-8</code> and fall back to the system encoding if that fails. This change affects Python 3 only.</p> <p><code>Bio.motifs.mast</code> has been updated to parse XML output files from MAST over the plain-text output file. The goal of this change is to parse a more structured data source with minimal loss of functionality upon future MAST releases. Class structure remains the same plus an additional attribute <code>Record.strand_handling</code> required for diagram parsing.</p> <p><code>Bio.Entrez</code> now automatically retries HTTP requests on failure. The maximum number of tries and the sleep between them can be configured by changing <code>Bio.Entrez.max_tries</code> and <code>Bio.Entrez.sleep_between_tries</code>. (The defaults are 3 tries and 15 seconds, respectively.)</p> <p>All tests using the older print-and-compare approach have been replaced by unit tests following Python&rsquo;s standard testing framework.</p> <p>On the documentation side, all the public modules, classes, methods and functions now have docstrings (built in help strings). In addition to displaying the <a href="https://biopython.org/DIST/docs/api/">Biopython API documentation via epydoc</a>, we now also have the <a href="https://biopython.org/docs/1.74/api/">Biopython API documentation via Sphinx</a> (which we hope to make the default in future). Furthermore, the PDF version of the <em>Biopython Tutorial and Cookbook</em> now uses syntax coloring for code snippets.</p> <p>Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Andrey Raspopov (first contribution)</li> <li>Antony Lee</li> <li>Benjamin Rowell (first contribution)</li> <li>Bernhard Thiel</li> <li>Brandon Invergo</li> <li>Catherine Lesuisse</li> <li>Chris Rands</li> <li>Deepak Khatri (first contribution)</li> <li>Gert Hulselmans</li> <li>Jared Andrews</li> <li>Jens Thomas (first contribution)</li> <li>Konstantin Vdovkin</li> <li>Lenna Peterson</li> <li>Mark Amery</li> <li>Markus Piotrowski</li> <li>Micky Yun Chan (first contribution)</li> <li>Nick Negretti</li> <li>Peter Cock</li> <li>Peter Kerpedjiev</li> <li>Ralf Stephan</li> <li>Rob Miller</li> <li>Sergio Valqui</li> <li>Victor Lin</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Zheng Ruan</li> </ul> <p>For reference, checksums:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.74* </span></span><span style="display:flex;"><span> 808a8cc83ef7ae8328de47112a9619c9 biopython-1.74-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> bc71b115d62fa0505b05dcb8d51ebbb3 biopython-1.74-cp27-cp27m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> eb9b68d29187208688f3763d7f9b4443 biopython-1.74-cp27-cp27m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> e060e2971cb64488392690f2b49a894a biopython-1.74-cp27-cp27mu-manylinux1_i686.whl </span></span><span style="display:flex;"><span> 69e2b9aea866248dcb250b0d4749347c biopython-1.74-cp27-cp27mu-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 301964b516d9a1af29db36c45e97857c biopython-1.74-cp27-cp27m-win32.whl </span></span><span style="display:flex;"><span> 72549961e56ba7c00ddf5aa4d4a2c4b7 biopython-1.74-cp27-cp27m-win_amd64.whl </span></span><span style="display:flex;"><span> 7545b99fe59e820b3e5343463df9bf61 biopython-1.74-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> a18c82789358cd3a6cf854750bbf9216 biopython-1.74-cp34-cp34m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> 33f5c75fe0fd63bba49afb19077a6067 biopython-1.74-cp34-cp34m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 2d42a3e23b976a4a7db837b9d2782df1 biopython-1.74-cp34-cp34m-win32.whl </span></span><span style="display:flex;"><span> 9a74dbfa0c81848ce107ad3c169ce1d3 biopython-1.74-cp34-cp34m-win_amd64.whl </span></span><span style="display:flex;"><span> 6fc5cce9f94e5cac1aa4b57774e8626b biopython-1.74-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> 7c8e4473a474c05e39d70d8106dbd641 biopython-1.74-cp35-cp35m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> dc9710022e6409590fc99bc82309cd8d biopython-1.74-cp35-cp35m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> fe2623ea21ca2e9f057eae333d0ae386 biopython-1.74-cp35-cp35m-win32.whl </span></span><span style="display:flex;"><span> b4b59bbf517e42c8e1abfbe7af2a6893 biopython-1.74-cp35-cp35m-win_amd64.whl </span></span><span style="display:flex;"><span> a28eaf891cd04af42ea6391477c968d8 biopython-1.74-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> 74761f292187cfc06166107230d94dcd biopython-1.74-cp36-cp36m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> 62e7696d4597d7b7ff8bbf157191c284 biopython-1.74-cp36-cp36m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 419f489831ec20aa1e11384d2991676c biopython-1.74-cp36-cp36m-win32.whl </span></span><span style="display:flex;"><span> 743a888661c48b66d41de2e6c04890d5 biopython-1.74-cp36-cp36m-win_amd64.whl </span></span><span style="display:flex;"><span> 025d4a914ad515b0181bdb0f8b1e8a2e biopython-1.74-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> db5ee8837a887188bcef09f57b5bf12f biopython-1.74-cp37-cp37m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> f7602a46d3e2e3302f99437739652727 biopython-1.74-cp37-cp37m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 20075d6abfbdb011460829f624de0832 biopython-1.74-cp37-cp37m-win32.whl </span></span><span style="display:flex;"><span> ffdd7986cb63dedf8daa4fb78140bbac biopython-1.74-cp37-cp37m-win_amd64.whl </span></span><span style="display:flex;"><span> cead2bfe9e7be45267eba00635f68d5c biopython-1.74.tar.gz </span></span><span style="display:flex;"><span> ff21159f333f433f3fa5a01a791cf717 biopython-1.74.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ sha256sum biopython-1.74* </span></span><span style="display:flex;"><span> 6182f8c17c81aa40987b018e6241719137e463f5bb263c423db6180d118d3a03 biopython-1.74-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> 7103f3dd3cef9f6ae52c0c3275ecb65121f3935b90d25c5e149ce62f684fbaf2 biopython-1.74-cp27-cp27m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> bb302ad68a133ed3ae26efa0a0c82a0905c8b9b85a70fa6626611a882a65ec61 biopython-1.74-cp27-cp27m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 77145b88a74c89f752db2ed11f64737161cc337c9e520e3853c945bd1d9866e6 biopython-1.74-cp27-cp27mu-manylinux1_i686.whl </span></span><span style="display:flex;"><span> 022909d10bbdfbc70eba6ea1c06ff573444e26e40ef0899025fb269898604b16 biopython-1.74-cp27-cp27mu-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 540f9df15e11f091e2d92959b891d2001bb59660ca806d51ca30d76dab60d39e biopython-1.74-cp27-cp27m-win32.whl </span></span><span style="display:flex;"><span> 36c35d93d16c9270303bfc755d2364171a1aaebd75f3bfa97179712a3ac09e2d biopython-1.74-cp27-cp27m-win_amd64.whl </span></span><span style="display:flex;"><span> d6a310fab78e11dba51b55a2b194a79128d202584127e17952f7f64b52da83e2 biopython-1.74-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> d3bf43ea45859bec05e8496c39dbd614c75520a832da20d826fdbd7e83105414 biopython-1.74-cp34-cp34m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> 8b7a3edd0dcc9eae3020849ad6110c721399f2c8dd71e54317dcc50035f9ebf9 biopython-1.74-cp34-cp34m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 32c50dd9450ac780d640baa212ecde22fcc98dc0de472b40296968df2385c824 biopython-1.74-cp34-cp34m-win32.whl </span></span><span style="display:flex;"><span> 015b79eea59bb5ccf7abef2ab17a813540c5c1969a8def2148fe3d529ff405a3 biopython-1.74-cp34-cp34m-win_amd64.whl </span></span><span style="display:flex;"><span> 1324bd2f6ea1dbad748085875d4c206f08748bb7848355f365d31fcd771dfa75 biopython-1.74-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> 6d9a39f295d97ed953a48c1cde635b35205ed25034015238776dbd2a8afbb2a7 biopython-1.74-cp35-cp35m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> 273c524550aaad3284edbdacecdf66cfd880dac580a5f6c5f80a9925a70144fb biopython-1.74-cp35-cp35m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> e6cc6e725a5fb628d41ed675bb74aa5eb03763e1ccd3111d0f73f739c7263ab4 biopython-1.74-cp35-cp35m-win32.whl </span></span><span style="display:flex;"><span> aa07bcf7def1c270c1fc1bab25f72a34f1ba24ab0a2d680f0a8466b39a2a7660 biopython-1.74-cp35-cp35m-win_amd64.whl </span></span><span style="display:flex;"><span> efee2f77cef1b65a76fe27af83c05774329b481c2da71d0580fcbcf92d6e9988 biopython-1.74-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> f50ee861a67e96488d21bc210ea72250df8cb7578351366f52c3904b841b5fbe biopython-1.74-cp36-cp36m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> fa8ed2c3fec5dc45f9b750bd5da386f82cddb7944b456bfd0472106050efa397 biopython-1.74-cp36-cp36m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 7c32c37b20843e1d22e76c889f1733097e27996d1ec0fe54d84e5f737c9ff65e biopython-1.74-cp36-cp36m-win32.whl </span></span><span style="display:flex;"><span> 046510af3cbaaf822e7451f0772e3e3f327916edbfd1f34798e6b8cbf60e8aa3 biopython-1.74-cp36-cp36m-win_amd64.whl </span></span><span style="display:flex;"><span> 67144db2defb3b49d505c7c4c676ca80b3451a0764f507b930b86031b7ebde5c biopython-1.74-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> b8cdfaf2963b7ef24497aa82e60bfc86267989f32a49b4edd4a67aba75202834 biopython-1.74-cp37-cp37m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> a117596b366e2226e2bf0adaf87f32cda495357c398b1b2ca2ada9f54c386718 biopython-1.74-cp37-cp37m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> 3a802aba32b64aee9c3b92d8b5d50aa3d0a95c8188b69a78a2cbc292578dae08 biopython-1.74-cp37-cp37m-win32.whl </span></span><span style="display:flex;"><span> ca627475233f698ede17b5adb169ed10b44ab4dc3a48d71069d7ab0086bdbc1c biopython-1.74-cp37-cp37m-win_amd64.whl </span></span><span style="display:flex;"><span> 25152c1be2c9205bf80901fc49adf2c2efff49f0dddbcf6e6b2ce31dfa6590c0 biopython-1.74.tar.gz </span></span><span style="display:flex;"><span> 546dd36c5ba18696d6b4673d8f68c01bd27b016f2e3fdefb5ff848f646a91ba4 biopython-1.74.zip </span></span></code></pre></div>https://www.open-bio.org/2019/06/01/obf-travel-fellowship-for-africaosh-summit-2019/Sat, 01 Jun 2019 02:14:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/06/01/obf-travel-fellowship-for-africaosh-summit-2019/<p><em>Note: This is a guest blog post from Angela Muraya, who was supported by the ongoing</em> <a href="https://www.open-bio.org/travel-awards/"><em>Open Bioinformatics Foundation travel fellowship program</em></a> <em>to attend the Africa Open Science Hardware Summit 2019. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. If you are hoping to attend an open source / open science bioinformatics event and travel costs are a barrier, we encourage you to</em> <a href="https://www.open-bio.org/travel-awards/"><em>apply for one of our $1000 travel fellowships</em></a> <em>. The next deadline is August 15, 2019.</em></p> <p>The Africa Open Science Hardware Summit 2019 brought citizens from about 10 African countries and overall, 15 nationalities worldwide. We gathered for the much awaited <a href="https://africaosh.com/">AfricaOSH</a> version 2.0 in Dar es Salaam, Tanzania. <a href="https://africaosh.com/">AfricaOSH</a> connected makers, educators, researchers and innovators from Africa and around the world to dialogue and collaborate on how to use open science and hardware to change the world. It brought together various stakeholders to explore and try to understand the place of open science principles in the African context with particular attention to Open Hardware. Various stakeholders included innovators of Open Innovations such as SangaBoard, OpenFlexture Microscope, Biomaker Training Kit, Hack-A-Toy; representatives of Open Labs such as  <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwi3gOPclr_iAhVmxYUKHSVWADEQFjAAegQIBBAD&amp;url=https%3A%2F%2Fsticlab.co.tz%2F&amp;usg=AOvVaw3I4ighz4RsPZRGeSyRpqEH">SticLab</a>, <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=2&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwiYgcT8lb_iAhUOJhoKHThmBi4QFjABegQIABAB&amp;url=https%3A%2F%2Fjogl.io%2F&amp;usg=AOvVaw19kZJNHU_K6uSwm8QC2MKj">Just-One-Giant-Lab</a> and <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=2&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjW9syllr_iAhVKx4UKHYb0BzgQFjABegQIARAB&amp;url=https%3A%2F%2Fvc4a.com%2Fkumasi-hive%2F&amp;usg=AOvVaw07RkjlynPUe1rH-fZ0auhW">Kumasi Hive</a>, and, Open Knowledge platforms such as <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=4&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjIxLn2lr_iAhWjxoUKHdT-CywQFjADegQIARAB&amp;url=http%3A%2F%2Fwww.openair.org.za%2F&amp;usg=AOvVaw1dFEOpJDBOzxVwq9rh-VGs">OpenAIR</a>, <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=3&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwiuz8Sgl7_iAhUryIUKHeoCDi0QFjACegQIARAB&amp;url=https%3A%2F%2Finfo.africarxiv.org%2F&amp;usg=AOvVaw3va5RNhvAsn0nk29Dx7NE5">AfricArxiv</a>.</p> <p>This auspicious summit was carried out in the beautiful city of Dar es Salaam in Tanzania at three venues. The first was the <a href="https://dlab.or.tz/">D-Lab</a> within the University of Dar es Salaam (UDSM) courtesy of Dr. Christine Mwase, an assistant lecturer in telecommunications and a co-founder of <a href="https://www.coict.udsm.ac.tz/index.php/about-us">UDICTI</a>, the first ICT incubator in the university. The second host was <a href="https://twitter.com/bunihub">BuniHub</a>. The third host was <a href="http://sticlab.co.tz/">SticLab</a>.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/05/keynote1-2.jpg" alt=""></p> <p><strong>Day 1</strong></p> <p>The team started the summit by touring Buni Innovation hub, open space at the Commission of Science and Technology (COSTECH) for Tanzania’s tech community to foster innovation, entrepreneurship and the culture of co-creation. Their aim is to bridge the skill gap among the youth and to make them competent enough to create innovations for self-sustenance and for solving community problems. We attended a presentation from Dr Christine on ‘Experiences of CoICT in supporting Innovation in Tanzania’. She highlighted that direction towards use of technology is exponentially expanding in Africa especially among the youth. She explained various ways in which UDICTI are empowering the youth to use technology to drive socio-economic development, especially in the informal sector, given the fact that there is a high rate of unemployment in the country.</p> <p>Later, we visited SticLab – the House of Innovation, an open maker space co-founded by AfricaOSHers: Paul Nyakyi and Eng. Valerian Sanga. We saw the various on-going projects such as green farming using hydroponics, green fish farming, the MAJIPesa – water vending pump and the e-waste 3D printers and the SangaBoard they designed. They support open science by making the prototype, blueprints and codes available for the public to use and modify. As a result of embracing openness, several collaborations from other innovators enabled then redesign and modify SangaBoard v1.0 to the more improved version 2.0. I led a breakout session on Open Access Journals. During that discussion, we highlighted the various principles of Open Science which are accessibility, sharing, inclusiveness, collaboration, quality and integrity. We agreed that open is not necessarily free but can also mean that open innovations are more affordable than the traditional models thus making them easier to access, and in addition, the prototypes are available for modification. This was the motivation behind the innovation of the OpenFlexure Microscope. We covered various topic such as types of open access – green and gold, open access versus predatory journals, methods of identifying genuine open access journals, among other issues.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/05/keynote2-3-1024x1024.jpg" alt=""></p> <p><strong>Day 2</strong></p> <p>The day started with a powerful presentation from Prof. Jeremy de Beer, a lecturer at Ottawa University and a co-founder of OpenAIR. Prof Jeremy’s talk was about ‘Open Innovation and Intellectual Property Rights – Solving the Paradox’ He pointed out the dilemma open innovators face when they want to legally protect their innovations through intellectual property rights and commercialize them while also keeping them open access. He proposed a third option of allowing a certain degree of porosity between the openness of ideas and knowledge which is seen in the reemerging African indigenous knowledge systems that involve passing down of knowledge from one generation to the next.</p> <p><strong>Day 3</strong></p> <p>Dr EliAmani, an associate professor at the <a href="https://www.4icu.org/reviews/15060.htm">Nelson Mandela African Institution of Science and Technology</a> expounded on the types of property rights legally recognized: Patents, Trademarks, Copyrights, Trade secrets. He mentioned the use of open licensing as one of the policies used to protect open innovations. He leads the discussion on the fears that arise from the use of open innovations where the following were a few mentioned: challenges of sustainability of open innovations, the uncertainty of trust/goodwill, compounding effects of community ownership of innovations whereby consistent contribution to support and maintain the innovations is not guaranteed. It was established that in the African context, the greatest challenge with open innovations is that they are only used and embraced up to some time and then they are abandoned. In rare occasions, open innovations are improved and eventually commercialized.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/05/slide-1.png" alt=""></p> <p>Inclusivity was discussed focusing mainly on the role of women in open science during a breakout session and also a panel discussion in which I participated. We discussed how we can, as the scientific community, increase the interest of girls to STEM subjects. One solution was to increase mentorship to them through achieved female scientists o cab be their role models. In terms of open science, we discussed that as open science philosophy, principles and policies are being gradually developed, they should not inherit the exclusive tendencies that affect the scientific world.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/05/groupphotot-1024x682.jpg" alt=""></p> <p>Overall, I had a beautiful experience visiting my neighbor country, Tanzania, for the first time. I can hardly wait for next year&rsquo;s in Cameroon! I wish to thank the Open Bioinformatics Foundation for supporting me with a Travel fellowship.</p>https://www.open-bio.org/2019/05/31/travel-award-recipients-for-april-2019/Fri, 31 May 2019 02:55:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/05/31/travel-award-recipients-for-april-2019/<p>We are pleased to announce the April 2019 OBF Travel Fellowship recipients. The <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> program, established in 2016, aims to increase diverse participation at events related to open source bioinformatics. After carefully evaluating a competitive set of applications submitted from all around the globe, we were able to extend offers to five deserving applicants: Sara El-Gebali, Angela Wanjugu Muraya, Saket Choudhary, Aziz Khan and Vid Ayer. They have all accepted the award, and we are looking forward to hearing about their experiences.</p> <p>Congratulations to our April 2019 recipients:</p> <p>·      <strong>Sara El-Gebali</strong> will be attending CarpentryConnect Manchester 2019 ( <a href="https://www.software.ac.uk/ccmcr19">CCMcr19</a>). Sarah has been involved in delivering workshops and breakout sessions at various events including Mozilla Festival, Cambridge Science Festival and international Data curation conference. During CarpentryConnect, she intends to invite participants to create a comprehensive “Do’s and Don’ts” checklist when preparing for a training session for different countries and audiences.</p> <p>·      <strong>Angela Wanjuga Muraya</strong> participated in an Open Science hackathon as a member of the Open ScienceKe team at <a href="http://africaosh.com/aosh-summit-2019/">Africa Open Science and Hardware Summit 2019</a> where she researched and explored the status of <a href="https://github.com/BioinfoNet/Status-of-OpenScienceKE-LiteratureSearch">Open Science in the local institutions</a>.</p> <p>·      <strong>Saket Choudhray</strong> will attend <a href="https://www.open-bio.org/events/bosc/">BOSC 2019</a>, where will he give a talk about his Python package <a href="https://github.com/saketkc/pysradb">pysradb</a>, which provides a collection of command line methods to query and download metadata and data from SRA utilizing the curated metadata database available through the SRAdb project. Saket has been actively involved in open source software development contributing to Biopython, Galaxy, bcbio-nextgen and Bioconda recipes.</p> <p>·      <strong>Aziz Khan</strong> will be attending <a href="https://www.open-bio.org/events/bosc/">BOSC 2019</a> to give a presentation about <a href="https://ecrcentral.org/">ECRcentral</a> platform that helps early career researchers to find research fellowships and travel grants and to share experiences, resources and feedback. Aziz has been involved in the <a href="https://github.com/asntech/">development</a> of several open-source bioinformatics tools and resources.</p> <p>·      <strong>Vid Ayer</strong> will attend <a href="https://www.open-bio.org/events/bosc/">BOSC 2019</a> and plans to conduct a Bird Of Feathers (BOF) session on Research Data Management. Having completed her Software Carpentry training, Vid has been actively mentoring and inspiring fellow women researchers to be more involved in open source software development.</p> <p>The next deadline for <a href="https://www.open-bio.org/travel-awards/">travel awards</a> is August 15, 2019. You can apply to travel to participate in any event that develops or promotes open source development and open science in the biological research community. The program is aimed at increasing diverse participation at such events.</p>https://www.open-bio.org/2019/05/09/bosc-2019-late-round/Thu, 09 May 2019 23:48:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/05/09/bosc-2019-late-round/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/nomi-at-podium-open-data-slide-gigascience.jpg-1.jpg" alt=""> If you&rsquo;d like the opportunity to present your work at <a href="https://www.open-bio.org/events/bosc/">BOSC 2019</a> (which will take place in Basel, Switzerland, on July 24-25, the last two days of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB 2019</a>), now&rsquo;s your chance! The late round of <a href="https://www.open-bio.org/events/bosc/submit">abstract submission</a> is open, and we will be choosing a few abstracts for &ldquo;Late-Breaking Lightning Talks&rdquo; as well as posters.</p> <p>BOSC welcomes submissions about all aspects of open source bioinformatics, open science and open data. More information, and a link to the EasyChair submission portal, can be found at <a href="https://www.open-bio.org/events/bosc/submit/">/events/bosc/submit/</a> .</p> <p>A few tips to increase your chances of success: 1. Work discussed in BOSC presentations must be open source, with a recognized open source license and a URL for accessing your code. Submissions that don&rsquo;t meet those requirements will be rejected. 2. We look for impact in building or sustaining open source communities. It&rsquo;s ok if your project is just getting started&ndash;tell us about how it will help the community, and how others will be able to contribute to it in the future. 3. If you submitted an abstract in the first round and didn&rsquo;t get selected for a talk, you can revise your abstract and make a new submission in the late round. (You can&rsquo;t just update your previous submission&ndash;you must start a new one in order to be considered for the late round.) 4. All submissions must include a 200-word summary. A one- or two-page PDF is also encouraged, though not required for poster-only submissions. We hope you&rsquo;ll use the extra space to tell us more about your project and how it fits into the bioinformatics open source ecosystem, and maybe add some cool pictures, too!</p> <p>Note that the deadline for submissions is Thursday, May 15, at 23:59 in the <a href="https://time.is/Anywhere_on_Earth">&ldquo;Anywhere on Earth&rdquo; time zone</a>, which is UTC-12. That means that for almost everyone, the deadline is effectively the morning of May 16.</p> <p>Please spread the word about BOSC&ndash;we welcome everyone, and are actively seeking to increase the diversity of our participants.</p> <p>To keep informed, <a href="https://twitter.com/OBF_BOSC">follow us on Twitter</a> or join our public <a href="https://gitter.im/OBF/BOSC_community">Gitter room</a>.</p>https://www.open-bio.org/events/bosc-2019/bosc-2019-keynote/Wed, 01 May 2019 20:27:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2019/bosc-2019-keynote/<p><em>We&rsquo;re excited to announce that Nicola Mulder will be delivering the keynote at BOSC 2019. Read the abstract below for a taster of the talk to come&hellip;</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/nicky-mulder.jpg" alt="Dr. Nicola Mulder">Dr Nicola Mulder</p> <p>Due to a history of exploitation and inequitable scientific partnerships, many African researchers are reluctant to fully embrace open science practices. Recent investment in genomics research on the continent and associated capacity development initiatives have enabled the development of research infrastructures and data related skills. This is helping to narrow the gap in expertise and access to data analysis capacity and facilitate more equitable engagement in international collaboration or more importantly, more independent research.</p> <p>H3ABioNet is a Pan African bioinformatics network that has been instrumental in building capacity for genomics data analysis on the continent. The network has an ethos of openness and is promoting open science practices among its members. This is exercised through many different activities, including open source software and workflow development, open science training, and efforts to make our data, tools and training materials FAIR. Though the genomic data we work with is controlled access, H3ABioNet is working to ensure the data are findable, harmonized and interoperable to increase the value for both data providers and users who are granted access for responsible secondary use.</p> <p>In this talk I will describe some of our activities in data, tool and training material curation, standardization and dissemination. Our approach considers past inequities and tries to promote responsible openness that ensures protection of privacy and recognition of scientific contributions.</p>https://www.open-bio.org/2019/04/08/goodbye-mediawiki-hello-new-website/Mon, 08 Apr 2019 12:15:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/04/08/goodbye-mediawiki-hello-new-website/<p><img src="https://lh3.googleusercontent.com/JQD9onWD94c-30bU-yDdFRRtx4OG1TEw06wKDHsksZmmpEdNm3qhQZnY2s1LvfuihdF8ye3Ut5DTYamGrOAdZrEA8164wlDn1vc6IEkfGW8xn3sTpcxAM2L5Z6hID0wMvwBbDZWz" alt=""></p> <p>Above: the old BOSC page. Below: the <a href="https://www.open-bio.org/events/bosc/">new one</a>.</p> <p><img src="https://lh4.googleusercontent.com/DySsict0S9ROodG_qjzQ20qLu77TEoYYPsQVL-86m0XjsUUGSp9KFcemiKK-0v7ev2iNVeWBEt5pUa-wP47lUg3BMjbRZ28ADD3E4u2ft4vZaLOz2y-Mun9uQfuRRpImJYXkEQtU" alt=""></p> <p>If you’ve been around the OBF and BOSC community, you’re probably familiar with our slightly rusty old site, which ran on <a href="https://www.mediawiki.org/wiki/MediaWiki">MediaWiki</a>, the same open source software that runs <a href="https://en.wikipedia.org/wiki/Main_Page">Wikipedia</a>. While they’re both awesome tools, <a href="https://www.open-bio.org/2018/11/19/updates-are-coming/">we decided it was time for a refresh</a>.</p> <p>Over the last few months, our <a href="https://www.outreachy.org/alums/">Outreachy</a> Intern <a href="https://github.com/kushinauwu/">Deepashree Deshmukh</a> designed and implemented the <a href="https://www.open-bio.org/">new OBF website</a>(with supervision by OBF Board member Yo Yehudi). The goal was an attractive and easily-updatable site that can function as a community-oriented hub. Did we accomplish that? Your feedback on the <a href="https://www.open-bio.org/">new site</a> is welcome!</p> <p><strong>What’s going to happen to the old OBF and BOSC websites?</strong></p> <p>The two old sites - the old wiki / main site at <a href="https://www.open-bio.org/wiki">/wiki</a> and the blog at <a href="http://news.obf.org">http://news.obf.org</a> - will stick around for a while, but they won’t be updated any more. One of our goals was to make sure not to break any of our old links - some of them have been around for years. You’ll probably notice a banner at the top of the old pages, pointing towards the new site. Longer term, we’re hoping to redirect all our old URLs directly to their equivalents on the new website.</p> <p><strong>What to do if you spot any bugs or strange things</strong></p> <p>We’ve spent a lot of time testing, updating content, tweaking things, and squashing bugs - but no site is ever perfect so it’s possible (probable?!) we’ve missed things. If you spot broken links, layout problems, browser compatibility issues, or anything else, please let us know. If you have a GitHub account, you can <a href="https://github.com/OBF/homepage/issues/new">log an issue directly</a>, or if it’s easier drop by our <a href="https://gitter.im/OBF/homepage">gitter homepage chat</a> and let us know there. You’re also welcome to pick the issue up if you know how to fix it!</p> <p><strong>Acknowledgements</strong></p> <p>As well as the fantastic hands-on work from Deepashree, we’d like to thank Yo Yehudi for her excellent mentorship of our first OBF intern, Nomi Harris for updating the content and reporting bugs, Hilmar Lapp for setting up a staging server and migrating content to the live site, and the rest of the OBF board and BOSC committee for proofreading and bug reports. A lot of people put time and effort info this and we couldn’t have done it without you!</p>https://www.open-bio.org/2019/04/06/us2ts/Sat, 06 Apr 2019 20:10:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/04/06/us2ts/<p><em>This is a guest blog post from Md Kamruzzaman Sarker, who was supported by the ongoing <a href="https://www.open-bio.org/travel-awards/#fellowships-selection-criteria">Open Bioinformatics Foundation travel fellowship program</a> to attend <a href="http://www.us2ts.org/">2nd U.S. Semantic Technologies Symposium Series</a> (US2TS). The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes on 15 April 2019. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships.</em></p> <p>To discuss and solve open problems of using Semantic Web technologies US2TS symposium is being arranged for the last 2 years. To bring diverse United State semantic web researchers into a common platform where they can discuss ongoing problems, share ideas to improve those this symposium started at 2018.</p> <p>The first symposium was held at my university (Wright State University). This year’s symposium was at Duke University, Durham, NC so I travelled from west coast to east coast to attend this symposium as I was doing my internship at Intel, Oregon. I flew from Portland, Oregon to Durham, North Carolina. The picturesque views, architecture and the surrounding atmosphere at Duke university creates a pleasant environment for brainstorming.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/04/us2ts-2019-duke-2-1024x767.png" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/04/us2ts-2019-duke-1-1024x764.png" alt="">Duke University</p> <p>I was expecting more participation this year but, the number of participants was more or less the same as last year. The program started with the keynote speech by Deborah McGuinness. She gave an excellent overview of the knowledge graph. My takeout from her keynote is:</p> <ul> <li>Knowledge graph is essentially A-Box.</li> <li>We need system which don’t require a PhD to maintain.</li> <li>Tools are important to support the infrastructure.</li> <li>Why industry is not using/being able to use semantic web technologies in large scale?</li> </ul> <p>The last question is actually an ongoing open-ended issue for over a decade and we as a semantic web community don’t have a clear answer to this. In my opinion, the technology behind the semantic web (Description Logic and others) is not really easy to grasp by an undergrad student. Unless we can create some technology, which is easy to understand or it gives tremendous economic benefit, it will not be used by mass people.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/04/us2ts-2019-program-overview-970x1024.png" alt="">Program overview</p> <p>In total there were 11 tutorial/workshop sessions this year. I also organized a <a href="https://semanticsforxai.github.io/">tutorial on Explainable Artificial Intelligence</a> (XAI). Because of the schedule conflict, two organizers, Dr Derek Doran, and Freddy Lecue could not come to present on the tutorial, but I and my advisor <a href="http://www.pascal-hitzler.de">Dr Pascal Hitzler</a> were able to present. I discussed the current state of the art of the XAI, it’s limitations and how semantic web can help to enhance explainability. Dr Hitzler presented a broad picture of neural semantic integration and its benefits.</p> <p><a href="https://twitter.com/smkpallob/status/1105117560918425602">https://twitter.com/smkpallob/status/1105117560918425602</a></p> <p>He also briefly mentioned our current work on this approach which is published at AAAI-2019 ( <a href="http://www.aaai.org/Papers/AAAI/2019/AAAI-SarkerM.3637.pdf">Efficient Concept Induction for Description Logics</a>). We also made the source code open access and published at GitHub ( <a href="https://github.com/md-k-sarker/ecii">https://github.com/md-k-sarker/ecii</a>).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/04/us2ts-2019-pascal-xai-1024x769.png" alt="">Pascal Hitzler presenting XAI tutorial</p> <p>Another breakout session titled <a href="https://deepsemantic2019.github.io/">Fusion of Semantic Knowledge into Deep Learning Models</a> organized by Monireh Ebrahimi, Jonathan Francis, Alessandro Oltramari was particularly interesting. They discussed how semantic web can help deep learning models to get the common sense of the real world.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/04/us2ts-2019-monireh-1024x692.png" alt="">Monireh Ebrahimi presenting fusion of semnatic web into deep learning</p> <p>On the first day, there was also knowledge graph, food and agriculture session. I attended the knowledge graph session and my takeaways from that session are:</p> <ul> <li>Knowledge graph is a marketing term.</li> <li>Don’t waste time on defining knowledge graph, spend your time to work on knowledge graph.</li> </ul> <p>Another interesting session was the past, present, and future of semantic web. Researchers shared their views on working on semantic web and what may be the future situation of semantic web technologies. Alessandro Oltramari presented a long term goal stating that deep learning needs the semantic web to get the common sense of this real world.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/04/us2ts-2019-alesandro-10-years-1024x687.png" alt="">Alessandro Oltramari on the 10 years perspective of semantic web</p> <p>Because of my job I had to come back early, so I returned from the event after attending the first day&rsquo;s sessions. It was an excellent experience for me to discuss and get and share ideas with other researchers from our community.</p> <p><strong>My biased summary of this trip:</strong></p> <ol> <li>People want to see industry/mass people are using their technology.</li> <li>We need to simplify semantic web technology infrastructure to engage more industry/people.</li> <li>Representing knowledge is still a big challenge, especially on large scale.</li> </ol> <h3 id="acknowledgment"><strong>Acknowledgment</strong>:</h3> <p>I acknowledge the support of Open Bioinformatics Foundation (OBF) which helped me to attend the conference.</p>https://www.open-bio.org/2019/03/13/a-week-of-open-source-adventures-in-san-diego/Wed, 13 Mar 2019 11:19:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/03/13/a-week-of-open-source-adventures-in-san-diego/<p><em>This is a guest blog post from Lindsay Rutter, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> to attend a <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2018/11/09/ncbi-sdsu-virus-hunting-data-science-hackathon-january-2019/">National Center for Biotechnology Information (NCBI) hackathon</a> and the <a href="https://www.intlpag.org/2019/">Plant and Animal Genome Conference (PAG)</a>. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes on 15 April 2019. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships.</em></p> <p>I would like to thank the Open Bioinformatics Foundation (OBF) for promoting open source bioinformatics. Many people believe that transparency in science and software helps us procure the most we can out of increasingly large biological datasets. Your support allowed me to embark on a week-long &ldquo;open source adventure&rdquo; in San Diego, where I participated in a data science hackathon and introduced my new software package at a conference workshop.</p> <p>I was up early the first morning for the same reason anyone would be when visiting sunny Southern California - to hunt for viruses computationally! It was great to participate in my third <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2018/11/09/ncbi-sdsu-virus-hunting-data-science-hackathon-january-2019/">National Center for Biotechnology Information (NCBI) hackathon</a>. The three-day event was hosted by the Computational Sciences Research Center at San Diego State University and our mission was to develop virological indices using 141,000 metagenomic datasets from the <a href="https://www.ncbi.nlm.nih.gov/sra">NCBI Sequence Read Archive (SRA)</a>. Improving the usability of the sheer volumes of data publicly available on the NCBI SRA could potentially facilitate important public health analyses. Hackathon participants split into nine working groups to build a scientific pipeline for metadata processing and novel virus discovery in the cloud infrastructure. Data preparation teams filtered assembled contigs, supervised machine learning teams cleaned metadata, and phylogenetic association teams clustered any matches. Contigs that did not map to known viruses were sent to teams that mapped domains and open reading frames with virus gene families. Based on these results, certain contigs were then sent to &ldquo;viral dark matter&rdquo; teams that identified novel viral contigs.</p> <p>[caption id=&ldquo;attachment_2181&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;640&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2019/03/hackathon1-1024x768.jpg" alt=""> Hackers meeting. (Image shared by <a href="http://joanmarticarreras.com">Joan Martí-Carreras</a>)[/caption]</p> <p>[caption id=&ldquo;attachment_2183&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;640&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2019/03/hackathon2-1024x768.jpg" alt=""> Hackers at work (Image shared by <a href="https://twitter.com/DCGenomics">Ben Busby</a>)[/caption]</p> <p>There is a lot of problem-solving in hackathons. A lot of divergent thinking. Some sinking or swimming. This particular hackathon was even more animated than usual because all forty participants were working toward the same end pipeline and teams needed to pitch new prototypes to other teams each time a problem was encountered. Hackathon participants ranged from unseasoned students to computational virology experts and travelled from around the world. In the &ldquo;viral dark matter&rdquo; team that I led, one teammate flew in from Australia and another teammate flew in from Columbia. Many of us have used version control platforms to <em>remotely</em> collaborate with peers when writing code, but collaborating with people from different experience levels and backgrounds <em>all together in the same room</em> is a unique environment that I believe fosters creativity.</p> <p>[caption id=&ldquo;attachment_2184&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;640&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2019/03/hackathonScribbles1-1024x768.jpg" alt=""> Defining virus indices (Image shared by <a href="https://twitter.com/DCGenomics">Ben Busby</a>)[/caption]</p> <p>In the end, we produced eight free software artifacts, which are available on <a href="https://github.com/NCBI-Hackathons/VirusDiscoveryProject">GitHub</a>. Annotations and associated metadata will also be freely available in a Jupyter notebook-driven API. Many participants believed the event provided evidence that hackathon settings can be effective for demonstration projects indexing large datasets. We celebrated our work each evening by enjoying delicious food at nearby restaurants. Dinner topics ranged from ancient viruses beneath Arctic ice to synthetic viruses to future virus-hunting hackathons. The daily time reserved for casual discussion with other hackers is a great attribute of NCBI hackathons.</p> <p>[caption id=&ldquo;attachment_2185&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;640&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2019/03/socialHackathon-1024x768.jpg" alt=""> Hackers know how to have fun, even when separated from their computers! (Image shared by <a href="https://twitter.com/DCGenomics">Ben Busby</a>).[/caption]</p> <p>The <a href="https://www.intlpag.org/2019/">Plant and Animal Genome Conference (PAG)</a> commenced the day after the hackathon ended. The conference encourages forum on recent developments and future plans for plant and animal genome projects, an internationally important topic. I was invited to give a talk during their annual workshop <a href="https://pag.confex.com/pag/xxvii/meetingapp.cgi/Session/5455">&ldquo;Big Data: Manage your data before your data kills you&rdquo;</a>. Indeed, big datasets can almost feel like numerical avalanches that we should run away from, but the workshop encouraged attendees to transcend such grim thinking and instead was motivated to spark discussions on how we can properly create, interpret, and share such large datasets.</p> <p>[caption id=&ldquo;attachment_2187&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;640&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2019/03/bigDataWorkshop-999x1024.png" alt=""> Twitter feeds for the Big Data workshop.[/caption]</p> <p>One speaker discussed guidelines on how to effectively manage and document large datasets. Another speaker tackled a modern bioinformatics nightmare: The maize community had strict rules for gene naming that were rigorously followed for decades until about ten years ago when scientists began assigning names to genes that already had names. Now, the same gene could have multiple names across multiple databases. The speaker suggested developing and abiding by nomenclature committees to fight the problem.</p> <p>[caption id=&ldquo;attachment_2188&rdquo; align=&ldquo;alignright&rdquo; width=&ldquo;165&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2019/03/logo.png" alt=""> Hexagonal representation for the bigPint package.[/caption]</p> <p>I presented my open-source software package called <a href="https://lindsayrutter.github.io/bigPint/">bigPint</a>, which provides interactive visualization methods for large datasets. I was excited to demonstrate the visualization toolkit to a room full of biologists because I think it can be useful for people possessing all levels of statistical background. Scientists need to apply normalization techniques and models to analyze their datasets but this can be difficult for people with little statistical knowledge. Visualization is inherently intuitive and can be used in a complementary fashion with models to allow scientists to better understand which analytical approaches may be the most suitable for their data. I think the workshop all together was aimed at democratizing data. Making data more accessible to more people. Making data easier to share.</p> <p>After the conference, everyone seemed to want to go to &ldquo;Charlie’s&rdquo;. I imagined Charlie was a well-liked and kind intellect who was hosting everyone and who I should probably want to meet, but eventually realized it was just a popular restaurant connected to the conference hotel. I am still glad I went. I met up with the NCBI hackathon organizer Ben and a fellow hacker Jan, two-spirited and sharp-witted individuals who have contributed vastly toward open science. I know firsthand that many hackathon organizers are working hard to increase the inclusiveness at their events. If you are interested in open source software development but are worried whether you will &ldquo;measure up&rdquo; or &ldquo;fit in&rdquo;, keep in mind that many hackathons do not require advanced computer skills and are a great way to network with other enthusiasts while building those very skills in a supportive environment. One of the most valuable parts of this fellowship was the opportunity to reconnect with old and connect with new open science enthusiasts, and I hope the community continues to grow and diversify in the years to come. Thank you again to the OBF for supporting such a meaningful theme.</p>https://www.open-bio.org/events/bosc-2020/panel-2/Tue, 12 Mar 2019 00:38:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/panel-2/<h1 id="bosc-20xx-panel">BOSC 20xx panel</h1> <h3 id="open-data-standards-opportunities-and-challenges">Open Data: Standards, Opportunities and Challenges</h3> <p>Every year, BOSC includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. This year, our panel discussion will focus on open data: how it can help to catalyze scientific and preserve knowledge, standards for sharing data, and some of the challenges (for example, protecting privacy of human health data).</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2018/12/member2-1.png" alt=""></p> <h4 id="name-of-panel-member">Name of panel member</h4> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2018/12/member2-1.png" alt=""></p> <h4 id="name-of-panel-member-1">Name of panel member</h4> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2018/12/member2-1.png" alt=""></p> <h4 id="name-of-panel-member-2">Name of panel member</h4> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2018/12/member2-1.png" alt=""></p> <h4 id="name-of-panel-member-3">Name of panel member</h4> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2018/12/member2-1.png" alt=""></p> <h4 id="name-of-panel-member-4">Name of panel member</h4> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.</p>https://www.open-bio.org/events/bosc-2019/bosc-2019-schedule/Sun, 10 Mar 2019 01:26:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2019/bosc-2019-schedule/<h2 id="bosc-2019-schedule-2020-schedule-is-coming-soon">BOSC 2019 Schedule (2020 schedule is coming soon!)</h2> <h4 id="schedule-at-a-glance">Schedule at a glance</h4> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/06/bosc-schedule-15june.jpg" alt=""></p> <p><a href="https://www.open-bio.org/wp-content/uploads/2019/07/BOSC2019-program-no-abstracts-17Jul2019.pdf">Download the program without the abstracts [PDF, 15 pages]</a></p> <p><a href="https://drive.google.com/open?id=16jt37tmTXG4z6JqBKJ0TYGDPrdzcyyND">Download the complete program including abstracts [PDF, 147 pages]</a></p> <h4 id="note-to-speakers">Note to speakers</h4> <p>Please copy your slides to the podium computer during the break before your session. Also, we encourage presenters to upload their slides to the <a href="https://f1000research.com/collections/bosc?selectedDomain=slides">BOSC F1000 collection</a>.</p> <h4 id="full-schedule">Full Schedule</h4> <h4 id="posters">Posters</h4> <p>We encourage presenters to upload their posters to the <a href="https://f1000research.com/collections/bosc?selectedDomain=posters">BOSC F1000 collection</a>.</p> <h2 id="post-bosc-collaborationfest">Post-BOSC CollaborationFest</h2> <p>BOSC runs a collaborative work event (formerly called CodeFest, and now called <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest, or CoFest</a> for short) before or after the conference. At these events, participants work together to contribute to bioinformatics software, documentation, training materials, and use cases. <a href="https://www.open-bio.org/events/bosc/collaborationfest/">This year&rsquo;s CoFest</a> will take place the two days after BOSC, July 26-27, at <a href="https://www.dayone.swiss/dayone.html">The Swiss Innovation Hub for Personalized Medicine</a> in Basel, Switzerland. <a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit#gid=0">Registration is informal and free.</a></p> <p><a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit#gid=0"><strong>Sponsors</strong></a></p> <p><a href="https://docs.google.com/spreadsheets/d/1KmUvbKo7AXwivjCLkFv3Dd-z4fhNrS2pXotMse9QGCg/edit#gid=0">Sponsorships from private companies and organizations help to defray some of our costs. Please see the</a> <a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsors</a> page for more information. If you would like to be a sponsor of BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <h3 id="bosc-2019-sponsors"><strong>BOSC 2019 Sponsors</strong></h3>https://www.open-bio.org/events/bosc-2022/sponsors/Sat, 02 Mar 2019 06:24:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2022/sponsors/<h1 id="sponsoring-bosc">Sponsoring BOSC</h1> <p>Page with current BOSC Sponsors: <a href="https://www.open-bio.org/events/sponsors/">open-bio.org/events/sponsors/</a></p> <h2 id="bosc-2022-platinum-sponsors">BOSC 2022 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a></p> <h2 id="bosc-2022-gold-sponsors">BOSC 2022 Gold Sponsors</h2> <p><a href="https://www.broadinstitute.org/data-sciences-platform"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/Broad-DSP-logo-1.png" alt="Broad Institute Data Science Platform"></a><a href="https://datascience.nih.gov/"><img src="https://www.open-bio.org/wp-content/uploads/2022/04/NIH-ODSS_Horizontal_1Color-653.jpg" alt="NIH Office of Data Science Strategy"></a></p> <h3 id="bosc-2022-silver-sponsors">BOSC 2022 Silver Sponsors</h3> <p><a href="https://arvados.org"><img src="https://www.open-bio.org/wp-content/uploads/2022/05/ArvadosCurii.png" alt="Arvados, supported by Curii"></a><a href="https://academic.oup.com/gigascience"><img src="https://www.open-bio.org/wp-content/uploads/2019/05/Gigascience.png" alt="Gigascience"></a></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Geraldine-BoF-composite.png" alt="Screenshot from BOSC 2021"></p> <p>Sponsorships from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some conference participants. In 2021, thanks to our sponsors&rsquo; generous support, we were able to grant free registration to 20 participants at <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, offer honoraria to keynote speakers, and cover other expenses.</p> <p>If you’re interested in sponsoring BOSC 2022, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p>Thanks to our 2021 sponsors, we were able to offer free ISMB/ECCB 2021 registration to 20 participants from all over the world! <iframe loading="lazy" src="https://www.google.com/maps/d/embed?mid=1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width="640" height="480"> </iframe> </p> <h2 id="what-is-bosc">What is BOSC?</h2> <p>BOSC is an annual meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. Whether in-person or online, each BOSC ​includes ​talks,​ ​poster​ ​sessions,​ ​birds-of-a-feather gatherings, and ​lots​ ​of​ ​opportunities​ ​for​ ​networking. It is followed by​ ​collaborative​ ​working​ ​sessions​ ​at the CollaborationFest.​ ​These​ ​events​ ​bring​ ​together​ ​software​ ​engineers,​ ​bioinformaticians,​ ​and​ ​researchers​ ​to collaborate​ ​and​ ​extend​ ​open​ ​source​ ​bioinformatics​ ​tools.</p> <p>Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB). In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>. In July 2020, BOSC again joined forces with GCC to form the <a href="https://bcc2020.github.io/">Bioinformatics Community Conference (BCC2020)</a>. Held online, BCC2020 attracted over 600 participants from 62 countries. <a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a> was part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021</a>, and took place July 29-30, 2021 (followed by a two-day <a href="https://www.open-bio.org/events/bosc-2021/collaborationfest/">CollaborationFest</a>).</p> <p>BOSC 2022 will take place July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a>. The meeting will be held both in person in Madison, Wisconsin, USA, and simultaneously online.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/OBF-BoF-2018-25-300x225.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/43248502932_2395bc3cc6_z-300x200.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2017-panel-1.jpg" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/Jason-PeterSelby-FotisPsomopoulos-DhrithiDespande.png" alt=""></p> <p>BOSC​ ​participants​ ​come​ ​from​ ​a​ ​wide​ ​variety​ ​of​ ​research​ ​environments​ ​and​ ​backgrounds:</p> <ul> <li> <p>Biological​ ​researchers,​ ​students,​ ​and​ ​post-docs​ ​who​ ​​ ​are​ ​learning​ ​bioinformatics​ ​analysis tools and techniques</p> </li> <li> <p>Power​ ​bioinformatics​ ​users</p> </li> <li> <p>Bioinformatics​ ​tool​ ​and​ ​workflow​ ​developers</p> </li> <li> <p>Bioinformatics​-focused​ ​principal​ ​investigators​ ​and​ ​researchers</p> </li> <li> <p>Sequencing​ ​core​ ​facility​ ​staff</p> </li> <li> <p>Industry​ ​scientists​ ​and​ ​bioinformaticians</p> </li> <li> <p>Data​ ​producers</p> </li> </ul> <h1 id="previous-events">Previous Events</h1> <p>The​ ​OBF​ ​has​ ​organized​ ​BOSC​ ​ <a href="https://www.open-bio.org/events/bosc/about/">every​ ​year​ ​since​ ​2000</a>.​ From 2000 to 2017 and again in 2019,​ ​BOSC​ ​was ​run​ ​as​ ​part​ ​of​ ​the​ ​large​ ​ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference.​ ​The​ ​OBF​ ​CodeFest​s (now renamed CollaborationFest, or CoFest) have ​been​ ​held​ ​every​ ​year​ after BOSC ​since​ ​2010.</p> <p>The table below shows the approximate number of participants in BOSC and the CoFest. Figures​ ​for​ ​the​ ​CoFest​ ​and​ ​BOSC​ ​are​ ​number​ ​of​ ​people​ ​registered​ ​for​ ​at​ ​least​ ​one​ ​day​ ​of​ ​the​ ​meeting.​ ​The​ ​BOSC figures​ ​do​ ​not​ ​include​ ​drop-in​ ​attendees​ ​from​ ​the​ ​parallel​ ​sessions​ ​organized​ ​by​ ​other​ ​groups.​ ​The​ ​figures​ ​for CoFest​ ​do​ ​not​ ​include​ ​remote​ ​participants.</p> <p>YearLocation BOSC ParticipantsCoFest Participants 2020BCC2020 (BOSC + Galaxy): virtual<del>300</del>1502019Basel, Switzerland109352018 Portland, OR, USA1501002017 Prague, Czech Republic 230652016 Orlando, FL, USA90362015Dublin, Ireland125352014Boston, MA, USA100602013Berlin, Germany100372012Long Beach, CA, USA 100132011 Vienna, Austria 12035</p> <h1 id="sponsorship">Sponsorship</h1> <p>We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to</p> <ul> <li>offer free registration to some BOSC participants</li> <li>support the <a href="https://www.open-bio.org/travel-awards/">OBF&rsquo;s Event Fellowship program</a>, increasing participation from underrepresented groups</li> <li>provide child care at the conference</li> <li>underwrite the cost of conference events such as dinners or refreshments at poster sessions</li> <li>help defray the cost of videography</li> <li>provide space and catering at the CoFest</li> <li>offer honoraria to keynote speakers</li> <li>pay for captioning and translations</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/BOSC2020-party-attendees-e1609719125821.png" alt=""></p> <h2 id="sponsoring-bosc-1">Sponsoring BOSC</h2> <p>Sponsorships from private companies and organizations help to defray some of our costs and allow us to offer registration fee waivers to some attendees. If you are interested in becoming a BOSC sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <h1 id="benefits-of-sponsorship">Benefits of Sponsorship</h1> <p>We acknowledge our sponsors before, during and after the event in multiple ways:</p> <ul> <li>We list our sponsors on the BOSC website</li> <li>Sponsors are thanked and named in the introduction/closing slides during the meeting</li> <li>We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area</li> <li>The sponsors are thanked in selected emails to our mailing list, tweets and blog posts (with your logo) that go out before, during and after the event</li> <li>The sponsors are listed in our published reports after the meeting, e.g., <a href="https://f1000research.com/articles/7-1309/v1">https://f1000research.com/articles/7-1309/v1</a></li> <li>We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.</li> </ul> <h2 id="bosc-2021-platinum-sponsors">BOSC 2021 Platinum Sponsors</h2> <p><a href="https://chanzuckerberg.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/CZI_Logotype_RGB.jpg" alt="Chan Zuckerberg Initiative"></a><a href="https://www.alzheimersdata.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/ADDI_Logo_FullColor_Vert_RGB.png" alt="Alzheimer’s Disease Data Initiative"></a></p> <h2 id="bosc-2021-gold-sponsors">BOSC 2021 Gold Sponsors</h2> <p><a href="http://aws.amazon.com"><img src="https://www.open-bio.org/wp-content/uploads/2021/05/AWS_logo_RGB.png" alt="Amazon Web Services"></a><a href="https://www.broadinstitute.org/"><img src="https://www.broadinstitute.org/files/news/media-images/logos//BroadInstLogoforDigitalRGB.png" alt="Broad Institute Logo"></a></p> <h2 id="bosc-2021-silver-sponsors">BOSC 2021 Silver Sponsors</h2> <p><a href="https://elifesciences.org/"><img src="https://www.open-bio.org/wp-content/uploads/2021/04/image.png" alt=""></a> <a href="https://geneviatechnologies.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/genevia_logo_cmyk.png" alt="Genevia"></a> <a href="https://oup.com/"><img src="https://www.open-bio.org/wp-content/uploads/2021/06/OUP_logo_navy.png" alt="Oxford University Press"></a><a href="https://bioteam.net"><img src="https://www.open-bio.org/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png" alt=""></a></p> <p>If you are interested in becoming a sponsor, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>!</p>https://www.open-bio.org/2019/02/22/google-summer-of-code-2018-wrap-up/Fri, 22 Feb 2019 17:19:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/02/22/google-summer-of-code-2018-wrap-up/<p>We have recently applied to Google for the OBF to be part of the Google Summer of Code 2019 programme, again with Kai Blin and Michael Crusoe as joint administrators. Last year, <a href="https://summerofcode.withgoogle.com/archive/2018/organizations/5813329234755584/">OBF GSoC 2018</a>, was another good year with five students successfully completing their projects:</p> <ul> <li>Synchon Mandal (mentor Moritz Beber) &ldquo;Adding methods to cobrapy for improved constraint-based metabolic modelling.&rdquo; ( <a href="https://medium.com/@synchon_mandal/my-journey-to-gsoc-18-d46b59c3d4e">first blog bost</a>; <a href="https://medium.com/@synchon_mandal/gsoc-2018-with-open-bioinformatics-foundation-dc201bf945b9">final report</a>)</li> <li>Sophia Mersmann (mentors Oliver Alka, Julianus Pfeuffer, and Timo Sachsenberg) &ldquo;Improve Posterior Error Probability Estimation For Peptide Search Engine Results&rdquo; <a href="https://sophiamersmann.github.io/">(blog posts</a>; <a href="https://sophiamersmann.github.io/2018/08/08/final-report/">final report</a>)</li> <li>Edgar Garriga Nogales (mentors Paolo Di Tommaso, Michael R. Crusoe, and Stian Soiland-Reyes) &ldquo;Implement the support for Research Object specification into Nextflow framework&rdquo; ( <a href="https://github.com/edgano/nextflow/tree/663a933db47a246cae35703892bebd4b03e97b5b/subprojects/nxf-prov">repository</a>; <a href="http://edgargarriga.com/">homepage</a>; <a href="https://github.com/edgano/nextflow/tree/663a933db47a246cae35703892bebd4b03e97b5b/subprojects/nxf-prov">final report</a>).</li> <li>Sarthak Sehgal (mentors Yo Yehudi, Dennis Schwartz, and Rowland Mosbergen) &ldquo;Frontend Website Student Project for BioJS&rdquo; ( <a href="https://github.com/biojs/biojs-frontend">repository</a>; <a href="http://blog.biojs.net/tags/#frontend">blog posts</a>; <a href="http://blog.biojs.net/2018-08-12-final-report-frontend/">final report</a>).</li> <li>Megh Thakkar (mentors Yo Yehudi, Dennis Schwartz, and Rowland Mosbergen) &ldquo;Backend Website Student Project for BioJS&rdquo; ( <a href="https://github.com/biojs/biojs-backend">repository</a>; <a href="http://blog.biojs.net/tags/#backend">blog posts</a>; <a href="http://blog.biojs.net/2018-08-12-final-report-backend/">final report</a>).</li> </ul> <p>In some cases there isn&rsquo;t a single code repository to link to, rather their work included pull requests to the main project etc.</p> <p>Thank you to all our volunteer GSoC administrators and mentors - and of course thank you to the students - we hope you&rsquo;ll continue to work in bioinformatics and/or open source.</p>https://www.open-bio.org/about/Fri, 22 Feb 2019 08:44:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/about/<h1 id="history">History</h1> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/pear-transparent.png" alt=""></p> <p><div class="splitbox"><div class="left"> <img src="https://www.open-bio.org/wp-content/uploads/2019/02/bioperl.jpg" alt=""> <img src="https://www.open-bio.org/wp-content/uploads/2019/02/biojava-1.jpg" alt=""> </div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2019/02/biopython.png" alt=""> </div><div style="clear:both"></div></div> </p> </div><div class="right"> <h2 id="2000">2000</h2> <p>First Bioinformatics Open Source Conference (BOSC).</p> <h2 id="2001">2001</h2> <p>OBF grows out of volunteer projects BioPerl, BioJava and BioPython and is formally incorporated.</p> <h2 id="2005">2005</h2> <p>Bylaws enacted for the first time and formal membership created.</p> <h2 id="2012">2012</h2> <p>OBF becomes an associate project of Software in the Public Interest, Inc., a fiscal sponsorship organization.</p> </div><div style="clear:both"></div></div> <h1 id="who-we-are">Who we are</h1> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/attendees_stairs-1024x683.jpg" alt=""></p> <p>The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>The OBF is governed by a Board of Directors. Our bylaws lay out how the Board is elected, holds public meetings, and conducts its business, as well as the scope and role of our membership. OBF is an associated project with Software In The Public Interest, Inc., a fiscal sponsorship organization, and through SPI we can accept tax-exempt charitable donations.</p> <p>The OBF is open to anyone who is interested in promoting open source bioinformatics / open science. Please see the <a href="https://www.open-bio.org/membership/">Membership page</a> for more information.</p> <h1 id="main-activities">Main Activities</h1> <ul> <li>Running the yearly <a href="https://www.open-bio.org/events/bosc/about/">BOSC</a> conference.</li> <li>Organizing the <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a> collaborative work events (which usually follow or precede BOSC).</li> <li>Running the <a href="https://www.open-bio.org/event-awards/">OBF Event Award program</a> (launched March 2016), aimed at increasing diverse participation at events promoting open-source bioinformatics or open science.</li> <li>Participating in the Google Summer of Code program as an umbrella mentoring organization for member projects and related open source bioinformatics efforts, when there is sufficient interest.</li> <li>If member projects wish, managing servers, bank account (via our fiscal sponsor), domain names, and other assets for their benefit.</li> <li>Occasionally issuing public opinion and policy statements about matters related to Open Source and Open Science in bioinformatics.</li> </ul>https://www.open-bio.org/2019/02/13/travel-award-recipients-for-december-2018/Wed, 13 Feb 2019 13:56:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/02/13/travel-award-recipients-for-december-2018/<p>We had a great round of OBF travel fellowship candidates in our last round of applications, and after review we extended offers to three deserving applicants: Malvika Sharan, Lindsay Rutter, and Sarker Kamruzzaman. They’ve all accepted the award, and we’re looking forward to hearing about their experiences!</p> <p>Congratulations to our December 2018 recipients:</p> <p><strong>Malvika Sharan</strong> will be attending <a href="https://www.open-bio.org/wiki/BOSC_2019">BOSC</a> at <a href="https://www.iscb.org/ismbeccb2019">ISMB 2019</a> in Basel this July. Abstract submissions have only just opened, but she intends to submit an abstract expanding on the idea “Inclusiveness in Open Science” that she spoke about last year ( <a href="https://speakerdeck.com/malvikasharan/inclusiveness-in-open-science">slides</a>). She’s been active in the BOSC community for several years, participating in abstract review and BoF organisation, and she plans to continue this for 2019.</p> <p><strong>Lindsay Rutter</strong> attended the <a href="http://www.intlpag.org/2019/">Plant and Animal Genome Conference</a> to give an invited workshop talk for the “ <em>Big Data: Manage your data before your data kills you</em>” session. Her software &quot; <a href="https://lindsayrutter.github.io/bigPint/">bigPint</a>&quot; allows biologists to visualize genomics data, especially RNA-sequencing data, and was recently submitted and accepted to <a href="https://bioconductor.org/packages/devel/bioc/html/bigPint.html">Bioconductor</a>.</p> <p><strong>Sarker Kamruzzaman</strong> will be attending the <a href="http://www.us2ts.org/">2019 U.S. Semantic Technologies Symposium</a> in March. He’ll be presenting a tutorial &quot; <a href="http://us2ts.org/2019/posts/program-session-iii.html">On the Role of Data Semantics for Explainable AI</a>&quot; as well as a poster. The conference is meant to bring together specialists in many different fields, including natural sciences, so they can benefit from emerging semantic web technologies.</p> <p>Watch this space for blog posts from each of the awardees.</p> <p>The next deadline for travel awards is April 15, 2019. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. The program is aimed at increasing diverse participation at such events. See the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel award</a> page for details and how to apply.</p>https://www.open-bio.org/events/bosc-2021/collaborationfest/Fri, 08 Feb 2019 16:51:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2021/collaborationfest/<h1 id="collaborationfest-2021">CollaborationFest 2021</h1> <p>In conjunction with our annual meeting, <a href="https://www.open-bio.org/events/bosc-2021/">BOSC</a>, the OBF runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you.</p> <p>The 2021 BOSC CoFest, which will follow ISMB/ECCB 2021, will take place July 31 - August 1 online. We encourage you to register for the conference, but the CoFest itself is free.</p> <p>Please add yourself to this <a href="https://docs.google.com/spreadsheets/d/12liEMy5QL1UAG-PrqQgjEaizVqAUMgfS1-uS9Vr97bw/edit#gid=0">spreadsheet</a> to help gauge interest and coordinate topic groups. Please stay tuned as more details are worked out!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/attendees_stairs.jpg" alt="Attendees at the 2018 GCCBOSC CoFest"></p> <h2 id="history">History</h2> <p>This will be the 12th annual pre- or post-BOSC collaboration fest. Previous fun and successful events were <a href="https://www.open-bio.org/wiki/Codefest_2010">Codefest 2010</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> in Vienna, <a href="https://www.open-bio.org/wiki/Codefest_2012">Codefest 2012</a> in Los Angeles, <a href="https://www.open-bio.org/wiki/Codefest_2013">Codefest 2013</a> in Berlin, <a href="https://www.open-bio.org/wiki/Codefest_2014">Codefest 2014</a> in Boston, <a href="https://www.open-bio.org/wiki/Codefest_2015">Codefest 2015</a> in Dublin, <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a> in Orlando, <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> in Prague, <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC Collaboration Fest 2018</a> in Portland, <a href="https://www.open-bio.org/events/bosc/bosc-2019-collaborationfest">Collaboration Fest 2019</a> in Basel, and <a href="https://www.open-bio.org/events/bosc-2020/bosc-2020-collaborationfest/">BOSC 2020 CollaborationFest</a>/ <a href="https://bcc2020.github.io/cofest/">BCC2020 CollaborationFest</a> worldwide virtually.</p>https://www.open-bio.org/events/bosc-2020/bofs/Fri, 08 Feb 2019 16:50:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/bofs/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/OBF-BoF-2018-25.jpg" alt=""></p> <h2 id="birds-of-a-feather-bofs">Birds of a Feather (BoFs)</h2> <p>Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.</p> <p>The <a href="https://bcc2020.sched.com/overview/subject/BoF">BCC2020 BoF schedule is here</a>. BoFs are held just before and after each day of the main conference. BCC2020 attendees are also welcome to organize informal BoFs as table chats.</p>https://www.open-bio.org/events/bosc-2020/panel/Fri, 08 Feb 2019 16:50:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/panel/<p>BOSC typically includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. Past panel topics have included:</p> <ul> <li>2018: Training and documentation in bioinformatics</li> <li>2017: Open Data: Standards, Opportunities and Challenges</li> <li>2016: Growing and sustaining Open Source communities</li> <li>2015: Open Source, Open Door: increasing diversity in the bioinformatics open source community</li> <li>2014: Reproducibility: Rewards and Challenges</li> <li>2013: Strategies for funding and maintaining open source software</li> <li>2012: Should we have standard bioinformatics review criteria?</li> <li>2011: Meeting the challenges of inter-institutional collaboration</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/BOSC2015-panel-1-1024x521.jpg" alt="">Panelists at BOSC 2015</p>https://www.open-bio.org/events/bosc-2020/keynotes/Fri, 08 Feb 2019 16:49:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/keynotes/<h1 id="bcc2020-keynote-speakers">BCC2020 Keynote Speakers</h1> <p>The 2020 Bioinformatics Community Conference is pleased to announce our exceptional keynote speakers for <a href="http://bcc2020.github.io">BCC2020</a>:</p> <h4 id="lincoln-stein">Lincoln Stein</h4> <h6 id="head-adaptive-oncology-at-ontario-institute-for-cancer-research">Head, Adaptive Oncology at Ontario Institute for Cancer Research</h6> <p><img src="https://bcc2020.github.io/img/people/lincoln-stein.jpg" alt="Lincoln Stein"></p> <h5 id="how-open-source-has-changed-the-world"><a href="https://bcc2020.sched.com/event/cXDt"><em>How Open Source has Changed the World</em></a></h5> <p><a href="https://oicr.on.ca/investigators/lincoln-stein/">Lincoln Stein</a> focuses on supporting biomedical research both in Ontario and around the world by making large and complex biological datasets findable, accessible and usable.</p> <p>Prior to joining <a href="https://oicr.on.ca/">OICR</a> in 2006, Dr. Stein played an integral role in many large-scale data initiatives at <a href="https://www.cshl.edu/">Cold Spring Harbor Laboratory</a> and at the <a href="http://www.mit.edu/">Massachusetts Institute of Technology (MIT)</a> Genome Center. He led the development of the first physical clone map of the human genome, and ran the data coordinating centre and the data portal for the SNP Consortium and the HapMap Consortium. Lincoln has also led the creation and development of <a href="https://wormbase.org/">Wormbase</a>, a community model organism database for <em>C. elegans</em>, and <a href="https://reactome.org/">Reactome</a>, the largest open community database of biological reactions and pathways.</p> <p>At OICR, Dr. Stein has led several international cancer data sharing and research initiatives, including the creation and development of the data coordination centre for the <a href="https://icgc.org/">International Cancer Genome Consortium</a> and other related projects.</p> <p>Lincoln was also a keynote speaker at the very first BOSC in 2000. We are looking forward to welcoming him back.</p> <h4 id="abigail-cabunoc-mayes">Abigail Cabunoc Mayes</h4> <h6 id="working-open-practice-lead-at-mozilla-foundation">Working Open Practice Lead at Mozilla Foundation</h6> <p><img src="https://bcc2020.github.io/img/people/abby-cabunoc-mayes.jpg" alt="Abigail Cabunoc Mayes"></p> <h5 id="biased-by-default-exploring-discrimination-in-research-code"><a href="https://bcc2020.sched.com/event/cXmw"><em>Biased by Default: Exploring Discrimination in Research Code</em></a></h5> <p><a href="https://acabunoc.github.io/">Abigail Cabunoc Mayes</a> is the <a href="https://foundation.mozilla.org/en/initiatives/open-leadership-events/">Working Open Practice Lead at the Mozilla Foundation</a>. Abby mobilizes leaders in the Internet health movement through mentorship and training on open practices and open source. Before this, she was Lead Developer of the <a href="https://science.mozilla.org/">Mozilla Science Lab</a>, transforming science on the web. Prior to joining Mozilla, Abby worked as a bioinformatics software developer at the <a href="https://oicr.on.ca/">Ontario Institute for Cancer Research</a> and at <a href="https://msu.edu/">Michigan State University</a> where she applied open source and to research problems. With a background in open source and community organizing, she is fueling a culture of openness in research and innovation.</p> <h4 id="prashanth-n-suravajhala">Prashanth N Suravajhala</h4> <h6 id="senior-scientist-at-birla-institute-of-scientific-research">Senior Scientist at Birla Institute of Scientific Research</h6> <p><img src="https://bcc2020.github.io/img/people/prashanth-n-suravajhala.jpeg" alt="Prashanth N Suravajhala"></p> <h5 id="open-minds-bring-open-collaborations"><em><a href="https://bcc2020.sched.com/event/cXkH/east-keynote-1-open-minds-bring-open-collaborations#">Open minds bring open collaborations</a></em></h5> <p><a href="https://www.bioinformatics.org/wiki/Prash">Prashanth N Suravajhala</a> is a senior scientist at Birla Institute of Scientific Research, Jaipur. A PhD in Systems Biology, he went on to gain more than 7 years of postdoctoral experience across four different laboratories. He has interests exploring the known unknown regions in the human genome, primarily working on the top-down systems biology approaches of hypothetical proteins. Over the last five years, he has developed an interest in long noncoding RNAs in humans, elucidating the mechanisms underpinning small molecular interactions through clinical exomes. He founded <a href="https://bioclues.org/">Bioclues.org</a> in 2005, India’s largest bioinformatics society which advocates open access. The organization aims to bridge mentor-mentee relationships and has been successful in mentoring as many as 2000 graduate students across 30 countries. He is also associated with <a href="http://www.bioinformatics.org/">Bioinformatics.Org</a> and a host of other humanitarian organizations, such as <a href="https://www.rotary.org/en/our-programs/rotary-community-corps">Rotary Community Corps</a>.</p>https://www.open-bio.org/events/bosc-2020/2017-bosc-schedule/Fri, 08 Feb 2019 16:49:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/2017-bosc-schedule/<h1 id="bosc-2017-schedule">BOSC 2017 Schedule</h1> <p>This page has links to all the publicly available talk slides, videos and posters. Most of the slides and posters are on our <a href="http://f1000research.com/collections/BOSC">BOSC F1000 Research Collection</a>(others are on SlideShare and FigShare), while the videos are on the <a href="https://www.youtube.com/watch?v=tV6hAWreTSY&amp;list=PLir-OOQiOhXZX_2zmUJz0fx8RLALi3tkK">BOSC 2017 YouTube playlist</a>.</p> <ul> <li><a href="https://www.open-bio.org/w/images/4/42/BOSC2017-complete-program-compressed.pdf">Download the complete program (including all talk and poster abstracts) as a PDF</a></li> <li><a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2017/bosc.php">ISMB/ECCB schedule for BOSC, including brief descriptions of each talk topic</a></li> </ul> <h2 id="pre-bosc-codefest-2017">Pre-BOSC: Codefest 2017</h2> <p><a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> (a pre-BOSC hackathon) will take place July 20-21 at <a href="https://brmlab.cz/">Brmlab, Prague</a> (a non-profit, community-run hackerspace). Codefest is FREE and open to all (even if you&rsquo;re not attending BOSC). See <a href="https://www.open-bio.org/wiki/Codefest_2017">Codefest 2017</a> for details and to sign up.</p> <h2 id="schedule-at-a-glance">Schedule at a Glance</h2> <h2 id="complete-schedule-of-talks">complete Schedule of talks</h2> <h2 id="complete-program">Complete Program</h2> <ul> <li><a href="https://www.open-bio.org/w/images/4/42/BOSC2017-complete-program-compressed.pdf">Download the complete program (including all talk and poster abstracts) as a PDF</a></li> <li><a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2017/bosc.php">ISMB/ECCB schedule for BOSC, including brief descriptions of each talk topic</a></li> </ul> <h2 id="posters">Posters</h2> <ul> <li><a href="https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B">BOSC posters at ISMB/ECCB 2017</a></li> <li><a href="https://www.open-bio.org/w/images/8/82/BOSC2017-PosterOverview.pdf">PDF poster list</a></li> </ul> <h2 id="sponsors">Sponsors</h2> <p>We are grateful to and welcome <a href="http://thehyve.nl/">The Hyve</a> (open source solutions for bioinformatics), <a href="https://science.mozilla.org/">Mozilla Science Lab</a> (a community of researchers, developers, and librarians making research open and accessible), <a href="https://repositive.io/">Repositive Limited</a> (connecting the genomics community with the data they need), <a href="https://www.sevenbridges.com/">Seven Bridges</a> (the Biomedical Data Analysis Platform) and <a href="https://elifesciences.org/labs">eLife</a> (cutting-edge technology for cutting-edge research) as new sponsors for BOSC 2017, and <a href="http://gigasciencejournal.com/">GigaScience</a> (an open access, open data, open peer-review journal) as a returning sponsor.</p> <p>If you would like to be a sponsor of BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>.</p> <ul> <li><img src="https://www.open-bio.org/wp-content/uploads/2019/02/200px-Thehyve-logo-small-1.png" alt=""></li> <li><img src="https://www.open-bio.org/wp-content/uploads/2019/02/220px-MSLLogo_small-1.png" alt=""></li> <li><img src="https://www.open-bio.org/wp-content/uploads/2019/02/220px-Repositive_logo_long-1.png" alt=""></li> <li><img src="https://www.open-bio.org/wp-content/uploads/2019/02/200px-Gigascience-07-1.png" alt=""></li> <li><img src="https://www.open-bio.org/wp-content/uploads/2019/02/220px-SB_logo_navy-1.png" alt=""></li> <li><img src="https://www.open-bio.org/wp-content/uploads/2019/02/200px-ELife-1.png" alt=""></li> </ul>https://www.open-bio.org/events/bosc/about/Fri, 08 Feb 2019 16:46:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc/about/<h1 id="what-is-bosc">What is BOSC?</h1> <p>The <strong>B</strong> ioinformatics <strong>O</strong> pen <strong>S</strong> ource <strong>C</strong> onference promotes and facilitates the <a href="https://en.wikipedia.org/wiki/open_source">open source</a> development of <a href="https://en.wikipedia.org/wiki/bioinformatics">bioinformatics</a> tools and open science.</p> <p>Since it launched in 2000, BOSC has been part of ISMB every year except for 2018 and 2020, when it partnered with the Galaxy Community Conference.</p> <p><strong><a href="https://www.open-bio.org/events/bosc/">BOSC 2026</a> will take place July 14-15 as part of <a href="https://www.iscb.org/ismb2026/home">ISMB 2026</a>) in Washington DC (and online).</strong></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/codefest-some-people.jpg" alt=""></p> <h3 id="bosc-aims-to">BOSC aims to:</h3> <div class="splitbox"><div class="left"> <ul> <li>Inform the research community of important developments in open source bioinformatics and open science</li> <li>Provide a focused environment for developers and users to interact and share ideas about open source approaches in bioinformatics</li> <li>Make connections between participants that could enhance the open source ecosystem and lead to collaborations</li> <li>Promote open science, with its focus on sharing data and tools, transparency, reproducibility, and data provenance</li> </ul> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/12/Jason-at-mic-cropped-1.jpeg" alt="Jason Williams at BOSC 2024"></p> </div><div style="clear:both"></div></div> <h3 id="previous-boscs">Previous BOSCs</h3> <ul> <li><a href="https://www.open-bio.org/events/bosc-2025/">BOSC 2025</a> took place July 21-22, 2025 in Liverpool, UK (as part of <a href="https://www.iscb.org/ismbeccb2025/home">ISMB/ECCB 2025</a>).</li> <li><a href="https://www.open-bio.org/events/bosc-2024/">BOSC 2024</a> The 25th annual BOSC was held July 15-16, 2024, as part of <a href="https://www.iscb.org/ismbeccb2024">ISMB 2024</a>, in person in Montréal, Canada, and online.</li> <li><a href="https://www.open-bio.org/events/bosc-2023/">BOSC 2023</a> took place July 26-27, 2023 as part of <a href="https://www.iscb.org/ismbeccb2023">ISMB/ECCB 2023</a>, in person in Lyon, France, and online.</li> <li><a href="https://www.open-bio.org/events/bosc-2022/">BOSC 2022</a> took place July 13-14, 2022, as part of <a href="https://www.iscb.org/ismb2022">ISMB 2022</a>, in person in Madison, Wisconsin, USA, and also online.</li> <li><a href="https://www.open-bio.org/events/bosc-2021/">BOSC 2021</a>, part of <a href="https://www.iscb.org/ismbeccb2021">ISMB/ECCB 2021 online</a>, took place July 29-30, 2021.</li> <li><a href="https://www.open-bio.org/events/bosc/">BOSC 2020</a> online (as part of Bioinformatics Community Conference, <a href="https://bcc2020.github.io/">BCC2020</a>)</li> <li><a href="https://www.open-bio.org/events/bosc-2019/">BOSC 2019</a> Basel, Switzerland (as part of ISMB/ECCB 2019)</li> </ul> <div class="splitbox"><div class="left"> <ul> <li><a href="https://www.open-bio.org/wiki/BOSC_2018">BOSC 2018</a> Portland, Oregon (with the Galaxy Community Conference as <a href="https://www.open-bio.org/2018/07/27/gccbosc-2018-post-meeting-report/">GCCBOSC 2018</a>)</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2017">BOSC 2017</a> Prague, Czech Republic</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2016">BOSC 2016</a> Orlando, FL, USA</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a> Dublin, Ireland</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a> Boston, MA USA</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2013">BOSC 2013</a> Berlin, Germany</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2012">BOSC 2012</a> Long Beach, CA, USA</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2011">BOSC 2011</a> Vienna, Austria</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2010">BOSC 2010</a> Boston, MA USA</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2009">BOSC 2009</a> Stockholm, Sweden</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2008">BOSC 2008</a> Toronto, Ontario, Canada</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2007">BOSC 2007</a> Vienna, Austria</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2006">BOSC 2006</a> Fortaleza, Brasil</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2005">BOSC 2005</a> Detroit, MI USA</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2004">BOSC 2004</a> Glasgow, UK</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2003">BOSC 2003</a> Brisbane, Australia</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2002">BOSC 2002</a> Edmonton, Canada</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2001">BOSC 2001</a> Copenhagen, Denmark</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2000">BOSC 2000</a> San Diego, CA USA</li> </ul> <p></div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2025/01/Marcin-talking-to-Susannah-Tringe.jpg" alt="Marcin Joachimiak and Susannah Tringe at BOSC 2024"></p> </div><div style="clear:both"></div></div> <h3 id="collaborationfest">CollaborationFest</h3> <p>In recent years, the BOSC meetings have been preceded or followed by a two-day <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a>, an informal collaborative work event. Initially called CodeFest, the event was renamed CollaborationFest in 2018 to reflect the fact that it&rsquo;s not just about coding.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2024/12/BOSC-audience-with-Jessica-1.jpeg" alt="Part of the audience of BOSC 2024"></p> <h2 id="get-involved">Get involved</h2> <p>There are many ways to get involved with the conference:</p> <h3 id="attend">Attend</h3> <div class="splitbox"><div class="left"> <p>There&rsquo;s no conference without attendees! Your presence is crucial to the success of the event, and we&rsquo;re always happy to see new faces. We encourage everyone to attend the main meeting and/or CollaborationFest, interact with other attendees, and post about their experience. And tell your colleagues and friends who aren&rsquo;t there that they should attend next year!</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/Sehrish-Kanwal-poster-1-1.jpg" alt=""></p> </div><div style="clear:both"></div></div> <h3 id="present-your-work">Present your work</h3> <p>Our focus is on open source work and communities. Code presented at BOSC must be open and properly licensed. If your work is more about training materials than code, we want your materials to be open and licensed so others can benefit from it!</p> <p>We try to provide a platform to everyone who wants to present appropriate work. We have &ldquo;long&rdquo; talks (typically 17 minutes + 3 minutes for questions), short/&ldquo;lightning&rdquo; talks (5 minutes), and posters.</p> <p><a href="https://www.open-bio.org/events/bosc-2026/submit/" class="btn btn-lg btn-primary">Submit an abstract</a></p> <h3 id="review-abstracts">Review abstracts</h3> <div class="splitbox"><div class="left"> <p><img src="https://www.open-bio.org/wp-content/uploads/2025/01/Idowu-Olawoye-presenting.jpeg" alt="Idowu Olawoye presenting at BOSC 2024"></p> </div><div class="right"> <p>Conference abstracts are reviewed by volunteers who express their interest and have appropriate experience. We encourage reviewers to be constructive in their comments, and some choose to sign their reviews. Reviewers are typically assigned about 6-8 abstracts to review. We acknowledge our reviewers on the conference website.</p> <p><a href="https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md" target="_new" class="btn btn-lg btn-primary">More about the review process</a></p> </div><div style="clear:both"></div></div> <h3 id="join-the-organizing-committee">Join the Organizing Committee</h3> <p>The organizing committee does most of the work to make BOSC a successful meeting. Committee members help write communications to reviewers, participants, and attendees; decide on the program; design conference materials; find dinner locations; chair sessions during the conference; and more! The workload gets heavy in two waves: first when abstracts are being reviewed and the program is being put together, and again as the conference gets closer. Most organizing committee members start out by becoming abstract reviewers.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2022/01/BOSC-roundtable-2021-Jul-29-1-1.jpeg" alt=""></p> <h3 id="sponsor-bosc-andor-collaborationfest">Sponsor BOSC and/or CollaborationFest</h3> <p>The Open Bioinformatics Foundation welcomes sponsorships to help support the BOSC and <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a> events. Please see the <a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsors</a> page for more information.</p>https://www.open-bio.org/events/bosc-2020/Thu, 07 Feb 2019 18:28:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/bosc-2020/<h3 id="check-out-the-complete-bosc-2020-conference-schedule">Check out the complete <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2020 conference schedule</a>!</h3> <h4 id="blog-posts-about-bcc2020-lessons-learned-from-organizing-a-virtual-conference-why-planning-an-online-conference-is-hard">Blog posts about BCC2020: <a href="https://www.open-bio.org/2020/08/13/lessons-learned/">Lessons learned from organizing a virtual conference</a>; <a href="https://www.open-bio.org/2020/09/01/planning-an-online-conference-is-hard/">Why planning an online conference is hard.</a></h4> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/BOSC2020-party-attendees.png" alt="Bioinformatics Community Conference 2020 July 19-21, 2020"></p> <h1 id="bosc-2020">BOSC 2020</h1> <p><a href="https://bcc2020.github.io/">BCC2020</a>, the first Bioinformatics Community Conference, brought together the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in a joint ONLINE meeting in July 2020. Participants from 62 countries joined us for sessions scheduled twice a day to accommodate both western and eastern hemispheres. <a href="https://bcc2020.github.io/keynotes/">Keynote speakers</a> were Abigail Cabunoc Mayes, Lincoln Stein, and Prashanth Suravajhala. Check out the conference schedule <a href="https://www.open-bio.org/events/bosc/schedule/">here</a>.</p> <p>The Bioinformatics Open Source Conference (BOSC) has been <a href="https://www.open-bio.org/events/bosc/about/">held annually since 2000</a>. <a href="https://www.open-bio.org/events/bosc-2019/">BOSC 2019</a> was part of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB</a> in Basel.</p> <h2 id="key-dates">Key Dates</h2> <ul> <li>April 21: <a href="https://bcc2020.github.io/Registration/">BCC registration</a> opens</li> <li>May 8: <a href="https://www.open-bio.org/events/bosc/submit/">Abstract submission</a> deadline</li> <li>July 10: <a href="https://bcc2020.github.io/Registration/">Early registration</a> ends</li> <li>July 15: <a href="https://bcc2020.github.io/Registration/">Late registration</a> ends</li> <li>July 16 (July 17 in eastern hemisphere): <a href="https://www.open-bio.org/2020/07/08/bcc2020-pre-conference-open-house/">pre-BCC open house</a> for registered attendees</li> <li>July 17-18 (July 18-19 in eastern hemisphere): BCC2020 optional <a href="https://bcc2020.sched.com/overview/subject/Training">training sessions</a></li> <li><strong>July 19-21 (July 20-22 in eastern hemisphere): <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2020</a></strong>, part of <a href="https://bcc2020.github.io/">BCC2020</a> (online)</li> <li>July 22-23 and 24-25: <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CoFest</a> and CoFest Encore</li> </ul> <h2 id="session-topics">Session Topics</h2> <p>BOSC covers all aspects of bioinformatics software and open science,  including (but not limited to) these topics:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Open Approaches to Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Inclusion, Outreach and Training</li> </ul> <h1 id="overview">Overview</h1> <p>BOSC is organized by the <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.</p> <p>Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <p>BOSC is usually preceded or followed by what we now call <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest (CoFest</a> for short), a two-day community development session. This is an opportunity for anyone interested in open science, biology and programming to meet, talk and work collaboratively. All are welcome to attend CoFest, whether or not you attend BOSC!</p> <p><a href="https://www.open-bio.org/events/bosc/about/">More about BOSC&hellip;</a></p> <h2 id="registration">Registration</h2> <p><a href="https://bcc2020.github.io/blog/registration-open">Registration for BCC2020 is now open</a>! Save by registering before July 10. Prices for the online meeting and optional <a href="https://bcc2020.sched.com/overview/subject/Training">training sessions</a> are very affordable (with discounts for students and postdocs and those from developing countries). The <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CoFest</a> is free, but you must register to participate.</p> <h2 id="sponsoring-bosc">Sponsoring BOSC</h2> <p><a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsorships</a> from private companies and organizations help to defray some of our costs. This year, BOSC will be part of <a href="https://bcc2020.github.io/">BCC2020</a>.</p> <p>See the BCC <a href="https://bcc2020.github.io/partners/">Partners</a> page for information about the BCC sponsors and how you can become one!</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/BOSC2019-audience1-1.jpg" alt=""></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/09/BOSC2020-org-committee.png" alt="">Members of the BOSC 2020 organizing committee</p> <h2 id="organizing-committee">Organizing Committee</h2> <p><strong>Chair: Nomi L. Harris</strong> (Lawrence Berkeley National Laboratory)</p> <ul> <li> <p>Technology Chair: Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)</p> </li> <li> <p><strong>Program Chair: Chris Fields</strong> ( <a href="http://bioperl.org/">Bioperl developer</a>; <a href="https://hpcbio.illinois.edu/">HPCBio</a>, University of Illinois)</p> </li> <li> <p><a href="http://www.scri.ac.uk/staff/petercock">Peter Cock</a> ( <a href="http://biopython.org/">Biopython developer</a>; <a href="http://www.hutton.ac.uk/">James Hutton Institute</a>)</p> </li> <li> <p>Jessica Maia (BD)</p> </li> <li> <p>Monica Munoz-Torres (Oregon State University)</p> </li> <li> <p><a href="http://yo-yehudi.com/">Yo Yehudi</a>(University of Cambridge)</p> </li> </ul> <h3 id="review-committee-affiliations-listed-"><strong>Review Committee (affiliations listed <a href="https://bcc2020.github.io/about/">here</a>)</strong>:</h3> <p>Kai Blin, Kai Blumberg, Christian Brueffer, J. Harry Caufield, Peter Cock, Arun Decano, Gianluca Della Vedova, James Eddy, Scott Edmunds, Chris Fields, Bastian Greshake Tzovaras, Nomi Harris, Michael Heuer, Karsten Hokamp, Aziz Khan, Aleix Lafita-Masip, Jessica Maia, Nico Matentzoglu, Hervé Ménager, Ruchi Munshi, Tazro Ohta, Konstantin Okonechnikov, Lorena Pantano, Luis Pedro Coelho, Surya Saha, Sonika Tyagi, Deepak Unni, Nicole Vasilevsky, Jason Williams, Yo Yehudi</p> <h2 id="previous-boscs">Previous BOSCs</h2> <p>BOSC has been held yearly since 2000. See <a href="https://www.open-bio.org/events/bosc/about#Past_BOSCs">information about the first 19 BOSC conferences.</a></p> <p><a href="https://www.open-bio.org/events/bosc-2019/">BOSC 2019</a> was part of <a href="https://www.iscb.org/ismbeccb2019">ISMB/ECCB 2019</a> in Basel, Switzerland. See the full <a href="https://www.open-bio.org/events/bosc/schedule/">BOSC 2019 schedule of talks, posters</a> and <a href="https://www.open-bio.org/events/bosc/bofs/">Birds of a Feather</a> meetups.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2018">BOSC 2018</a> was held June 26-27, 2018 (with training days June 24-25 and a CollaborationFest June 28-29) at Reed College in Portland, Oregon as part of <a href="https://gccbosc2018.sched.com/">the GCCBOSC 2018 bioinformatics community conference</a> co-hosted with the Galaxy Community Conference.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/03/farah-yo-angel-GCCBOSC-1024x683.jpg" alt=""></p> <h1 id="code-of-conduct">Code of Conduct</h1> <p>As part of BCC2020, BOSC 2020 will be covered by <a href="https://bcc2020.github.io/cod/">the BCC Code of Conduct.</a></p>https://www.open-bio.org/code-of-conduct/Tue, 05 Feb 2019 16:19:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/code-of-conduct/<p>The <a href="https://github.com/OBF/obf-docs/tree/master/code-of-conduct">OBF Code of Conduct</a> was adopted after being <a href="https://www.open-bio.org/2022/01/27/approved-by-obf-membership-vote/">voted on by our members in January 2022</a>, following the OBF Public Board meeting in September 2021.</p> <p>Our annual conference, <a href="https://www.open-bio.org/events/bosc/">BOSC</a>, is normally run as part of the ISMB meeting, where it therefore follows the <a href="https://www.iscb.org/about-iscb/policy-statements-bylaws-and-legal-documents/iscb-a-safe-space-code-of-conduct">ISCB code of conduct</a>.</p>https://www.open-bio.org/donate/Tue, 05 Feb 2019 15:45:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/donate/<h1 id="support-the-obf">Support the OBF</h1> <h3 id="sponsorship-opportunities">Sponsorship opportunities</h3> <p>Our annual meetings, <a href="https://www.open-bio.org/events/bosc/">BOSC</a> and the <a href="https://www.open-bio.org/events/bosc/collaborationfest/">CollaborationFest</a>, are supported in part by sponsorships. Please see the <a href="https://www.open-bio.org/events/bosc/sponsors/">Sponsors</a> page for more information.</p> <h3 id="tax-free-donations">Tax-free donations</h3> <p>Through our fiscal sponsor, <a href="http://spi-inc.org/donations">Software in the Public Interest, Inc.</a>, you can donate to the OBF via <a href="http://spi-inc.org/projects/obf/">PayPal</a> or <a href="https://co.clickandpledge.com/advanced/default.aspx?wid=66788#">online by credit card</a>. Donations made through SPI are 501(c)3 tax-exempt in the US. Your contribution helps fund a growing community of people committed to developing reusable open-source software for advancing biological research.</p> <p><a href="https://co.clickandpledge.com/advanced/default.aspx?wid=66788#">Donate! </a></p>https://www.open-bio.org/get-involved/Mon, 04 Feb 2019 19:04:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/get-involved/<h1 id="join-the-obf-community">Join the OBF community</h1> <p>The OBF welcomes anyone who is involved or plans to become involved in biology-related <a href="https://opensource.org/osd">open source</a> or <a href="https://plos.org/open-science/">open science</a> to join our community. There are many ways you can become part of our growing community, regardless of your career stage and experience with open source and open science.</p> <h2 id="join-our-online-spaces">Join our online spaces</h2> <p>The OBF community has a number of different online spaces that are open to everyone and can be used to network and discuss anything related to open bioinformatics. You can:</p> <ul> <li>Follow our <a href="https://www.open-bio.org/blog/">blog</a></li> <li><a href="https://mailman.open-bio.org/mailman/listinfo/open-bio-l/">Subscribe to our OBF newsletter</a> (and if you have news to share, you can <a href="https://github.com/OBF/newsletter/issues">also suggest topics</a>).</li> <li><a href="https://join.slack.com/t/open-bio/shared_invite/zt-1pnswao9y-8igcckVxBXhQHCMweHt_NA">Join our community <em>Slack</em></a>, where you will find fellow open bioinformatics folks to chat with.</li> <li>We also have an open <a href="https://www.linkedin.com/groups/9539620/"><em>LinkedIn</em> group</a>, where you can hear about open bioinformatics events, job opportunities and more.</li> <li>We also have active presences on social media, including <a href="https://bsky.app/profile/openbio.bsky.social">BlueSky</a> and <a href="https://genomic.social/@openbio">Mastodon</a>.</li> <li>Last but not least, our <a href="https://www.open-bio.org/projects">member projects</a> like BioPython also have their own communication channels.</li> </ul> <h2 id="come-to-our-in-person-and-virtual-events">Come to our in-person and virtual events</h2> <p>We organize an annual conference, the <a href="https://www.open-bio.org/events/bosc"><em>Bioinformatics Open Source Conference</em></a> (BOSC), and the associated <a href="https://www.open-bio.org/events/bosc/collaborationfest/"><em>CollaborationFest</em></a>. These events are a great way to meet others engaged in open source/science around biology. BOSC features talks, posters and panel discussions on the latest research in open bioinformatics, while CollaborationFest offers the chance to work together with others on improving open bioinformatics tools, by coding but also writing documentation and other non-coding tasks.</p> <h1 id="applying-to-become-a-voting-member-of-obf">Applying to become a voting member of OBF</h1> <p>You can also apply to become a voting member of the Open Bioinformatics Foundation, which allows voting on larger OBF issues, including changes to the OBF&rsquo;s governing document, the <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.pdf">bylaws</a>. To be considered as a voting member, you must already be actively and demonstrably engaged in biology-related open science or open source in some form. Examples of such engagement could include contributing to existing open bioinformatics projects, publishing in the field, or attending open source bioinformatics conferences such as BOSC. The reason for this requirement is that we expect voting members to have a long-term engagement with both the field and the OBF itself. The OBF requires a quorum for voting, so we want OBF members to remain actively involved.</p> <p>The best time and place to join is at the annual <a href="https://www.open-bio.org/events/bosc/">BOSC</a> conference, because attendees are automatically deemed eligible based on the fact that they attended BOSC, but you can apply for membership at any time.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/obf_membership.jpg" alt=""></p> <h2 id="history-and-bylaws">History and Bylaws</h2> <p>The OBF membership body was formally established at the 2005 Board of Directors meeting. As laid out in the <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">OBF Bylaws</a>, the Board of Directors elects new Directors when terms expire or new seats are added. The membership of the OBF can nominate candidates for these elections.</p> <p>Voting members are invited to attend the annual public Board meetings, which are announced via the (low-traffic) OBF members mailing list, as well as on our blog and via our social media channels.</p> <h2 id="participation">Participation</h2> <p>The Board established the membership body as the platform from which major future changes to the OBF&rsquo;s mission, agenda, and scope will originate</p> <ul> <li>through active participation and discussion</li> <li>through providing the future leadership of the OBF.</li> </ul> <p>If you are actively engaged in bioinformatics, have ideas and the energy to advocate them then we encourage you to apply to become a voting member, and perhaps to nominate yourself for future elections to the Board. The bylaws define terms for Directors as well as Officers. Elections are typically held yearly or when needed.</p> <p><a href="https://docs.google.com/forms/d/e/1FAIpQLSflxafcgc7BOLEgppy3h_yMWCIkV_9lJB3Z0a0Y2cJ63sRK-Q/viewform">Apply to become a voting member of the OBF</a></p>https://www.open-bio.org/events/gsoc/gsoc-guide/Thu, 31 Jan 2019 15:36:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/gsoc/gsoc-guide/<h1 id="guide-for-prospective-gsoc-contributors">Guide for Prospective GSoC Contributors</h1> <h3 id="before-you-apply">Before you apply</h3> <ul> <li>Proposals should extend one of affiliated toolkits, not start a new project.</li> <li>If you want to apply with your own idea, it’s best to <a href="https://www.open-bio.org/wp/events/gsoc/gsoc-contact">contact</a> the OBF subproject you’re interested in well before the application deadline, so we can work with you to find a mentor and solidify your project idea and application.</li> <li><a href="https://www.open-bio.org/wp/events/gsoc/gsoc-contact">Ask us questions</a> on the subproject mailing lists about the project idea you have in mind.</li> <li>Write a project proposal draft, include a project plan (see below), and <a href="https://www.open-bio.org/wp/events/gsoc/gsoc-contact">send it to a project mailing list</a> for comments before submitting it.</li> </ul> <p>Again, GSoC contributors are strongly encouraged to contact us as early as possible. Frequent and early communication is extremely valuable for putting together successful projects.</p> <h3 id="when-you-apply">When you apply</h3> <p>When applying, (aside from the information requested by Google) please provide the following in your application material.</p> <ol> <li>Your complete contact information, including full name, physical address, preferred email address, and telephone number, plus other pertinent contact information such as IRC handles, etc.</li> <li>Why you are interested in the project you are proposing and are well-suited to undertake it.</li> <li>A summary of your programming experience and skills.</li> <li>Programs or projects you have previously authored or contributed to, in particular those available as open-source, including, if applicable, any past Summer of Code involvement.</li> <li>A project plan for the project you are proposing, even if your proposed project is directly based on one of the proposed project ideas for member projects. <ul> <li>A project plan in principle divides up the whole project into a series of manageable milestones and time-lines that, when all accomplished, logically lead to the end goal(s) of the project. Put in another way, a project plan explains what you expect you will need to be doing, and what you expect you need to have accomplished, at which time, so that at the end you reach the goals of the project.</li> <li>Do not take this part lightly. A compelling plan takes a significant amount of work. Empirically, applications with no or a hastily composed project plan have not been competitive, and a more thorough project plan can easily make an applicant out compete another with more advanced skills.</li> <li>A good plan will require you to thoroughly think about the project itself and how one might want to go about the work.</li> <li>We don’t expect you to have all the experience, background, and knowledge to come up with the final, real work plan on your own at the time you apply. We do expect your plan to demonstrate, however, that you have made the effort and thoroughly dissected the goals into tasks and successive accomplishments that make sense.</li> <li>We strongly recommend that you bounce your proposed project and your project plan draft off of us, using either the pertinent developers mailing list or the IRC channel(s). Through the project plan exercise you will inevitably discover that you are missing a lot of the pieces - we are there to help you fill those in as best as we can.</li> </ul> </li> <li>Any obligations, vacations, or plans for the summer that may require scheduling during the GSoC work period. <ul> <li>We expect the your GSoC project to be your primary focus over the summer. It should not be regarded as a part-time occupation.</li> <li>If you feel that you can manage other work obligations concurrently with your Summer of Code project, make your case and support it with evidence.</li> <li>Be honest and open. If it turns out later that you weren’t clear about other obligations, at best (i.e., if your accomplishment record at that point is spotless) our trust in you will be severely degraded. Also, if you are accepted, discuss with your GSoC mentor before taking on additional obligations.</li> <li>One of the most common reasons for GSoC contributors to struggle or fail is being overcommitted Do not set yourself up for failure! GSoC summers should be fun and rewarding!</li> </ul> </li> </ol>https://www.open-bio.org/events/gsoc/gsoc-overview/Wed, 30 Jan 2019 20:21:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/gsoc/gsoc-overview/<h1 id="what-is-the-google-summer-of-code">What is the Google Summer of code?</h1> <p>Google Summer of Code (GSoC) is an internship program for open-source projects. The program offers eligible GSoC contributors stipends to write code for open source projects over a period of 3 summer months (&ldquo;flip bits, not burgers&rdquo;). See the <a href="http://code.google.com/soc">Google Summer of Code Main Site</a> for general information about the Google Summer of Code program, how to apply, frequently asked general questions, and more.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/GSoC-icon-192.png" alt=""></p> <h1 id="gsoc-2022">GSoC 2022</h1> <p>After yet another successful year as a GSoC organisation in 2021, OBF was once again a GSoC mentoring organisation in 2022. Interested mentors and GSoC contributors should subscribe to the OBF and GSoC mailing lists (see more on the <a href="https://www.open-bio.org/wp/events/gsoc/gsoc-contact/">Contact page</a>). Please announce yourself, so we know who you are! The details of each of our project ideas are listed <a href="https://www.open-bio.org/wp/events/gsoc/gsoc-project-ideas/">in this page</a>, including potential mentors.</p> <h2 id="facts-and-links">Facts and links</h2> <p>Info from Google:</p> <ul> <li><a href="https://developers.google.com/open-source/gsoc/timeline">GSoC Timeline</a></li> <li>For questions of eligibility or others, see the <a href="https://developers.google.com/open-source/gsoc/faq">GSoC FAQ.</a></li> <li>There is a Google group for posting GSoC questions (and receiving answers; note that you will need to sign up for the group) that relate to the program itself (and are not specific to our organization).</li> <li>Development is done entirely remotely and online; there is no requirement or expectation for either GSoC contributors or mentors to travel.</li> </ul> <h1 id="why-apply">Why apply?</h1> <ul> <li>One of the most important features of the program is that GSoC contributor are paired with mentors, who are typically experienced developers from the project to which the person is contributing. The mentor guides the contributor to work productively within the community, and helps them avoid obstacles and pitfalls.</li> <li>The program is global - GSoC contributors and mentors may be located anywhere where they have an internet connection (except for countries affected by US trade restrictions), and no travel is required.</li> <li>Aside from the stipend and mentorship aspects, the GSoC contributor&rsquo;s experience in the internship closely mirrors normal work on distributed development projects. Effective work habits for distributed development are typically not taught as part of computer science curricula, yet are highly desired in the increasingly global and distributed software, IT, and biotechnology industries.</li> <li>From the viewpoint of each open-source project, the program not only offers to pay GSoC contributors for their participation, but more importantly, offers an opportunity to recruit new developers who will hopefully go on to become regular, sustaining contributors.</li> </ul> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/01/mentorship-300x300.png" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2019/01/global-300x300.png" alt=""><img src="https://www.open-bio.org/wp-content/uploads/2019/01/dev-experience-300x300.png" alt=""></p> <h1 id="gsoc-contributor-progress-reports">GSoC Contributor Progress Reports</h1> <p>In addition to writing code, accepted GSoC contributors send weekly updates to the OBF community on their project&rsquo;s progress. These updates allow us to keep aware of how GSoC contributors are doing, give them a forum to ask any questions, and promote overall community bonding.</p> <p>At the beginning of the summer, we ask that you set up a blog for the GSoC project (or a category/tag on your existing blog) which you will use to summarize your progress every week, as well as longer posts about your work if you&rsquo;d like. ( <a href="http://biojs.github.io">See these examples from 2018 and 2019</a>)</p> <p>Then, at the start of each week: Post an update on your blog: What did you do last week? What do you plan to do this week? Do you have any unanswered questions, any unsolved problems from the last week, interesting observations or anything else you&rsquo;d like to mention? Email the URL and text of the post (or a short summary) to the host project&rsquo;s mailing list (your mentors will confirm which one to use).</p> <p>You will be writing under your own name, but with a clear association with your mentors, the OBF and its projects, so please take this seriously and be professional. Remember that your blog will be one of the first things found by anyone interested in the project you&rsquo;re working on, and can be a valuable resource to them — as well as a significant part of your online presence.</p> <h1 id="previous-years">Previous Years</h1> <p>This section contains links to content related to OBF&rsquo;s participation in GSoC in previous years.</p> <ul> <li>2022 - 7 student projects</li> <li>2021 - 8 student projects</li> <li>2020 - 8 student projects</li> <li>2019 - 5 student projects</li> <li>2018 - 5 student projects</li> <li>2017 – 7 student projects</li> <li>2016 – 8 student projects</li> <li>2015 – OBF not accepted, some Bio* projects partnered with other organisations</li> <li>2014 - 6 student projects</li> <li>2013 – OBF not accepted, some Bio* projects partnered with other organisations</li> <li>2012 – 5 student projects</li> <li>2011 – 6 student projects</li> <li>2010 – 6 student projects</li> </ul>https://www.open-bio.org/events/gsoc/Wed, 30 Jan 2019 20:09:31 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/gsoc/<h1 id="open-bioinformatics-foundation-in-gsoc">Open Bioinformatics Foundation in GSoC</h1> <p><a href="https://www.open-bio.org/wp/events/gsoc/gsoc-overview/"><img src="https://www.open-bio.org/wp-content/uploads/2019/01/GSoC-icon-192-1.png" alt=""></a></p> <h3 id="overview"><a href="https://www.open-bio.org/wp/events/gsoc/gsoc-overview/">Overview</a></h3> <p>Here you will find a general outline of what Google Summer of Code is.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/01/idea.png" alt=""></p> <h3 id="project-ideas"><a href="https://www.open-bio.org/wp/events/gsoc/gsoc-project-ideas/">Project Ideas</a></h3> <p>All the OBF/GSoC projects are listed here complete with details, including potential mentors.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/01/guide.png" alt=""></p> <h3 id="guide-for-prospective-gsoc-contributors"><a href="https://www.open-bio.org/wp/events/gsoc/gsoc-guide/">Guide for Prospective GSoC Contributors</a></h3> <p>Consult this guide for rules about applications.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/01/contact.png" alt=""></p> <h3 id="contact"><a href="https://www.open-bio.org/wp/events/gsoc/gsoc-contact/">Contact</a></h3> <p>The contact links for OBF/GSoC admins and mentors are listed here.</p>https://www.open-bio.org/2019/01/09/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan/Wed, 09 Jan 2019 13:09:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/01/09/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/farah-presentation.jpg" alt="">Farah presents <em>CWLProv</em> at GCCBOSC 2018</p> <p>The <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">next round of our OBF Travel Fellowships just ended</a> on the 15th of December! This round we have introduced a Review Chair coming from the midst of our community that will help us in reviewing the applications. The role will be filled by Farah Zaib Khan, one of our OBF Travel Fellowship alumni. Farah has successfully applied for the Fellowship twice before. Thanks in part to this support, she has become a central community member both of the Bioinformatics Open Source Conference and the Open Bioinformatics Foundation itself.</p> <p>Farah recently completed her PhD at The University of Melbourne, Australia. The OBF travel fellowship helped her interact with the Bioinformatics community during BOSC 2017 and GCCBOSC 2018 where she actively participated in the Codefests and other activities to shape her PhD work. Her PhD research is about the provenance and interoperability of bioinformatics workflows. The funding and support provided by OBF is acknowledged in the article recently <a href="http://dx.doi.org/10.5281/zenodo.1966881">submitted by her for publication</a>.</p> <p>We are happy to see that the Travel Fellowships help students and Early Career Researchers to participate and grow within the Open Bioinformatics community, as well as helping to increase the diversity of participants in Open Bioinformatics events.</p>https://www.open-bio.org/board/meeting-minutes/Tue, 01 Jan 2019 06:41:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/board/meeting-minutes/<p>Starting in July 2019, OBF Board public meeting minutes can be found in <a href="https://github.com/OBF/obf-docs/tree/master/minutes">https://github.com/OBF/obf-docs/tree/master/minutes</a>.</p>https://www.open-bio.org/blog/Tue, 25 Dec 2018 09:13:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/blog/https://www.open-bio.org/2018/12/18/biopython-1-73-released/Tue, 18 Dec 2018 16:58:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/12/18/biopython-1-73-released/<p>Dear Biopythoneers,</p> <p>Biopython 1.73 has been released and is available from our <a href="https://biopython.org/wiki/Download">website</a> and <a href="https://pypi.python.org/pypi/biopython/1.73">PyPI</a>.</p> <p>This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.</p> <p>As in recent releases, more of our code is now explicitly available under either our original &quot; <em>Biopython License Agreement&quot;</em>, or the very similar but more commonly used <em>&ldquo;3-Clause BSD License&rdquo;</em>.  See the <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst">LICENSE.rst</a> file for more details.</p> <p>The dictionary-like indexing in <code>Bio.SeqIO</code> and <code>Bio.SearchIO</code> will now explicitly preserve record order to match a behaviour change in the Python standard dict object. This means looping over the index will load the records in the on-disk order, which will be much faster (previously it would be effectively at random, based on the key hash sorting).</p> <p>The &ldquo;grant&rdquo; matrix in Bio.SubsMat.MatrixInfo has been replaced as our original values taken from Gerhard Vogt&rsquo;s old webpages at EMBL Heidelberg were discovered to be in error. The new values have been transformed following Vogt&rsquo;s approach, taking the global maximum 215 minus the similarity scores from the original paper Grantham (1974), to give a distance measure.</p> <p>Double-quote characters in GenBank feature qualifier values in <code>Bio.SeqIO</code> are now escaped as per the NCBI standard. Improperly escaped values trigger a warning on parsing.</p> <p>There is a new command line wrapper for the BWA-MEM sequence mapper.</p> <p>The string-based FASTA parsers in <code>Bio.SeqIO.FastaIO</code> have been optimised, which also speeds up parsing FASTA files using <code>Bio.SeqIO.parse()</code>.</p> <p>Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alona Levy-Jurgenson (first contribution)</li> <li>Ariel Aptekmann</li> <li>Brandon Invergo</li> <li>Catherine Lesuisse</li> <li>Chris Rands</li> <li>Darcy Mason (first contribution)</li> <li>Devang Thakkar (first contribution)</li> <li>Ivan Antonov (first contribution)</li> <li>Jeremy LaBarage (first contribution)</li> <li>Juraj Szász (first contribution)</li> <li>Kai Blin</li> <li>Konstantin Vdovkin (first contribution)</li> <li>Manuel Nuno Melo (first contribution)</li> <li>Maximilian Greil</li> <li>Nick Negretti (first contribution)</li> <li>Peter Cock</li> <li>Rona Costello (first contribution)</li> <li>Spencer Bliven</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Yi Hsiao (first contribution)</li> </ul> <p>For reference, checksums:</p> <p><code>$ md5sum biopython-1.73* 9bab1776b3f63cb2a81715e78abfb6e0 biopython-1.73-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl a531f656ecae854adf1fc6021735c2a9 biopython-1.73-cp27-cp27m-manylinux1_i686.whl 27f5179f2493408d33e5322690f1bb7a biopython-1.73-cp27-cp27m-manylinux1_x86_64.whl 41fdb1f257cdcd030a468e7339a6c6ab biopython-1.73-cp27-cp27mu-manylinux1_i686.whl bf23d2daae5c72c2d84058bce3acd7a2 biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl d3cab98752b83cef121b7a1e8b81853c 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href="mailto:board@open-bio.org">board@open-bio.org</a> (or, in case of mailing list problems, try <a href="mailto:obf-board@googlegroups.com">obf-board@googlegroups.com</a> as a fallback) You can also find us on <a href="https://www.linkedin.com/groups/9539620/">LinkedIn</a>. The minutes of the previous public Board meetings can be found on our <a href="https://github.com/OBF/obf-docs/tree/master/minutes">GitHub repository</a> (<a href="https://open-bio.org/board/meeting-minutes/">pre-2019 meeting minutes are linked here</a>).</p> <div class="gallery gallery-cols-&#39;2&#39;"><div class="box"> <figure><img src="https://www.open-bio.org/img/Friedberg_Iddo_0817_square.jpg" alt="Image of Iddo Friedberg"><figcaption> <h4>Iddo Friedberg</h4><p><em>At-large Member</em> Associate Professor at Iowa State University. Chair, Function COSI. Early contributor to the Biopython project.</p> </figcaption> </figure> </div> <div class="box"> <figure><a href="https://www.linkedin.com/in/hilyatuz-zahroh-6671ab100"><img src="https://www.open-bio.org/img/Hilya.jpg" alt="Image of Hilyatuz Zahroh"></a><figcaption> <h4><a href="https://www.linkedin.com/in/hilyatuz-zahroh-6671ab100/">Hilyatuz Zahroh</a></h4><p><em>At-large Member</em> <a href="https://www.apbionet.org/current-exco-officers-2020-2022/">APBioNET</a> ExCo</p> </figcaption> </figure> </div> <div class="box"> <figure><a href="https://kipkurui.github.io"><img src="https://www.open-bio.org/img/Caleb_Kibet_pic.jpg" alt="Image of Caleb Kibet"></a><figcaption> <h4><a href="https://kipkurui.github.io/">Caleb Kibet</a></h4><p><em>At-large Member</em> Bioinformatician at the <a href="http://www.icipe.org/research/research-support-units/molecular-biology-bioinformatics-and-biostatistics">International Center of Insect Physiology and Ecology, Kenya</a>; Founder <a href="https://medium.com/openscienceke">OpenScienceKE</a>.</p> </figcaption> </figure> </div> <div class="box"> <figure><a href="https://lappland.io"><img src="https://www.open-bio.org/img/Hilmar-Lapp-1.jpg" alt="Image of Hilmar Lapp"></a><figcaption> <h4><a href="https://orcid.org/0000-0001-9107-0714">Hilmar Lapp</a></h4><p><em>At-large Member</em> Representing <a href="http://www.bioperl.org/">BioPerl</a>, Open Research Faculty at <a href="https://neuromatch.io/">Neuromatch</a>. Former OBF President.</p> </figcaption> </figure> </div> <div class="box"> <figure><img src="https://www.open-bio.org/img/Peter-Cock-1.jpg" alt="Image of Peter Cock"><figcaption> <h4><a href="#">Peter Cock</a></h4><p><em>President</em> <a href="https://biopython.org/">Biopython</a> core developer, bioinformatician at the James Hutton Institute for 16 years, currently at the University of Strathclyde. <a href="https://open-bio.org/wiki/BOSC_2016">BOSC 2016 co-chair</a>.</p> </figcaption> </figure> </div> <div class="box"> <figure><img src="https://www.open-bio.org/img/Chris-Fields.jpg" alt="Image of Chris Fields"><figcaption> <h4><a href="#">Chris Fields</a></h4><p><em>At-large Member</em> <a href="http://bioperl.org/">BioPerl</a> core developer, Assoc. Dir. of HPCBio, Carver Biotechnology Center and <a href="http://www.igb.illinois.edu/">The Institute for Genomic Biology</a> at the <a href="http://www.uiuc.edu/">University of Illinois at Urbana-Champaign</a>.</p> </figcaption> </figure> </div> <div class="box"> <figure><a href="https://www.linkedin.com/in/nomiharris"><img src="https://www.open-bio.org/img/NH-Sept2022-square-1.png" alt="Image of Nomi Harris"></a><figcaption> <h4><a href="https://www.linkedin.com/in/nomiharris">Nomi Harris</a></h4><p><em>Secretary</em> Program Manager at the Lawrence Berkeley National Laboratory; <a href="https://open-bio.org/events/bosc/">BOSC chair</a>.</p> </figcaption> </figure> </div> <div class="box"> <figure><a href="https://twitter.com/hlwiencko"><img src="https://www.open-bio.org/img/Heather-Wiencko-1.jpg" alt="Image of Heather Wiencko"></a><figcaption> <h4><a href="https://twitter.com/hlwiencko">Heather Wiencko</a></h4><p><em>Treasurer</em> Software engineer at Hosted Graphite.</p> </figcaption> </figure> </div> <div class="box"> <figure><a href="https://tzovar.as"><img src="https://www.open-bio.org/img/BastianGreshakeTzovaras.jpg" alt="Image of Bastian Greshake Tzovaras"></a><figcaption> <h4><a href="https://tzovar.as">Bastian Greshake Tzovaras</a></h4><p><em>At-large Member</em> Co-founder of <a href="https://opensnp.org">openSNP</a> and Director of Research at <a href="https://www.openhumans.org">Open Humans</a>.</p> </figcaption> </figure> </div> </div> <h1 id="past-board-members">Past board members</h1> <ul> <li><a href="https://malvikasharan.github.io/">Malvika Sharan</a> - Former at-large member</li> <li><a href="https://www.ebi.ac.uk/about/people/ewan-birney">Ewan Birney</a> - Former OBF President</li> <li><a href="http://www.dalkescientific.com/">Andrew Dalke</a> - Former Secretary</li> <li><a href="http://plantandmicrobiology.berkeley.edu/profile/brenner">Steven E. Brenner</a> - Former At-large member</li> <li><a href="http://kdahlquist.github.io/DahlquistLab/">Kam Dahlquist</a> - Former At-large member</li> <li><a href="https://bioteam.net/bio/chris-dagdigian/">Chris Dagdigian</a> - Former Treasurer</li> <li><a href="http://stajichlab.fungalgenomes.org/">Jason Stajich</a> - Former OBF President</li> <li><a href="https://github.com/kcranston">Karen Cranston</a> - Former At-large member</li> <li><a href="https://twitter.com/yoyehudi">Yo Yehudi</a> - Former At-large member</li> </ul> <h1 id="joining-the-board">Joining the Board</h1> <p>Nominations for the Board of Directors may be made by the general membership at any time throughout the year by contacting any Board Member. The Board tries on an ongoing basis to create opportunities for members of the community to serve, while also ensuring stability of the Board, through expansion of the Board, by replacing a Board member whose term expires, or by volunteers from the community interested in serving.</p> <h2 id="board-expectations">Board Expectations</h2> <ul> <li>Participate in the (informal) <strong>regular meetings</strong> of Board members. Meetings are currently about 1 hour, <strong>once a month</strong>, held by Google Hangout. These meetings are for communicating and discussing <strong>current OBF operations and issues</strong>, as well as brainstorming strategic <strong>directions and initiatives</strong>.</li> <li>Participate in <strong>public Board meetings</strong>, including <strong>voting in elections</strong> and on matters brought before the OBF Board for approval. Public Board meetings take place about <strong>once a year</strong> via conference call, are about 1 hour in duration, and are usually scheduled in place of a Board hangout.</li> <li>Help <strong>promote the causes and objectives</strong> of the OBF, as set and approved by the Board, such as <strong>lobbying funders, employers, and other decision makers</strong> in your network about these objectives and ways to achieve them, as well as promoting the causes of the OBF at community gatherings you attend.</li> <li>Contribute to identifying strategies, opportunities, and mechanisms to better <strong>sustain the OBF</strong>, to <strong>grow its member communities</strong>, and to increase its overall <strong>diversity</strong>, including demographic diversity.</li> </ul> <p>You can <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">find more information in the bylaws of the OBF</a>.</p>https://www.open-bio.org/projects/Tue, 11 Dec 2018 19:11:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/projects/<p>The OBF has <a href="https://www.open-bio.org/adding-projects/">a process for projects in the open bioinformatics realm to become members or affiliated members</a>. Here you can find the existing member projects, affiliated projects and other related open bioinformatics projects.</p> <h1 id="member-projects">Member Projects</h1> <ul> <li><strong><a href="http://biojava.org/">BioJava</a></strong> is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of biological sequences and 3D structures. The main goal of the project is to facilitate rapid application development for bioinformatics.</li> <li>The <strong><a href="http://bioperl.org/">Bioperl Project</a></strong> is an international association of users &amp; developers of open source <a href="https://en.wikipedia.org/wiki/Perl">Perl</a> tools for bioinformatics, genomics and life science BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the <a href="https://en.wikipedia.org/wiki/Human_Genome_Project">Human Genome Project</a>.</li> <li><a href="https://biopython.org/"><strong>BioPython</strong></a> is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst">Biopython License</a>, which is extremely liberal and compatible with almost every license in the world.</li> <li><a href="http://www.bioruby.org/"><strong>BioRuby</strong></a> is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence alignment, biological database parsing, structural biology and other bioinformatics tasks.</li> <li><a href="https://biosql.org/wiki/Main_Page"><strong>BioSQL</strong></a> is a generic unifying schema for storing sequences from different sources, for instance Genbank or Swissprot. BioSQL is meant to be a common data storage layer supported by all the different Bio* projects, Bioperl, Biojava, Biopython, and Bioruby. Entries stored through an application written in, say, Bioperl could be retrieved by another written in Biojava.</li> </ul> <h1 id="affiliated-projects">Affiliated Projects</h1> <ul> <li><a href="https://gmod.org/"><strong>GBrowse</strong></a> (Generic Genome Browser), part of GMOD, is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.</li> <li><a href="https://gmod.org/wiki/Chado"><strong>Chado</strong></a> is a relational database schema that underlies many GMOD installations.</li> </ul> <h1 id="other-related-projects">Other Related Projects</h1> <ul> <li><a href="http://biojs.net/">BioJS</a>: An open-source library of JavaScript components to visualise biological data.</li> <li><a href="http://biohaskell.org/">BioHaskell</a>: Bioinformatics libraries in Haskell.</li> <li><a href="http://biocaml.org/">Biocaml</a>: Bioinformatics library in the functional programming language OCaml.</li> <li><a href="http://biophp.org/">BioPHP</a>: Collection of open-source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools.</li> <li><a href="https://biosmalltalk.github.io/">BioSmallTalk</a>: Bioinformatics in a pure objects environment.</li> <li><a href="https://www.yandell-lab.org/software/cgl.html">CGL</a>: Comparative Genomics Library.</li> <li><a href="https://skam.sourceforge.net/">BioMake &amp; Skam</a>: Task management tool, similar to makefiles.</li> </ul> <h1 id="retired-projects">Retired Projects</h1> <ul> <li>BioSOAP: Aimed to support biological analysis pipelines remotely via SOAP from BioPerl, BioJava and Ensembl initially.</li> <li>BioCORBA: Aimed to support biological analysis pipelines remotely via CORBA and a choice of programming languages.</li> <li><a href="http://biomoby.open-bio.org/">MOBY</a>: A system for interoperability between biological data hosts and analytical services.</li> <li><a href="http://obda.open-bio.org/">OBDA</a>: Standardization of access to sequence data resources.</li> <li>Wikiomics: Bioinformatics Wiki.</li> <li><a href="https://pubmed.ncbi.nlm.nih.gov/12511068/">Pise</a>: A tool to generate Web interfaces software for submitting jobs to these interfaces.</li> <li>OpenBQS: Bibliographic query system.</li> <li>BioClipse: Visual platform based on Eclipse.</li> <li><a href="https://sourceforge.net/projects/bioweka/">BioWeka</a>: Adds bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.</li> <li><a href="https://github.com/cmungall/blipkit">BlipKit</a>: Chris Mungall’s Prolog toolkit for Bioinformatics and BioMedical Informatics.</li> <li><a href="https://github.com/biolib/obf-biolib">Biolib</a>: Cross-project/language C bindings for a shared codebase across the different Bio* projects (Pjotr Prins).</li> <li>DAS / BioDAS: The Distributed Annotation System defines a communication protocol used to exchange annotations on genomic or protein sequences.</li> <li><a href="https://emboss.sourceforge.net/">EMBOSS</a>: An analysis package developed for the needs of the molecular biology (e.g. EMBnet) user community.</li> </ul>https://www.open-bio.org/events/Tue, 11 Dec 2018 19:11:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/events/https://www.open-bio.org/event-awards/Tue, 11 Dec 2018 19:10:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/event-awards/<h2 id="obf-event-fellowships">OBF Event Fellowships</h2> <p>The Open Bioinformatics Foundation (<a href="https://open-bio.org">OBF</a>) promotes open source bioinformatics software development and open science in the biological research community. The OBF Event Fellowship program is aimed at increasing diverse participation at events promoting open science practices such as resource development and dissemination in the bioinformatics and biological research community.</p> <p>These fellowships are available to support both in-person and remote (virtual) participation at events such as conferences, workshops, training courses or collaborative development sprints.</p> <p>This page is a summary of the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">official rules and procedures</a>, which includes the rubric used to evaluate applications.</p> <p><em>The OBF Event Fellowship was previously offered under the title OBF Travel Fellowship.</em></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/02/anisha-keshavan-conf-1024x755.jpg" alt=""></p> <h1 id="what-are-the-selection-criteria">WHAT ARE THE SELECTION CRITERIA?</h1> <h2 id="1-does-the-event-qualify">1. Does the event qualify?</h2> <p><div class="splitbox"><div class="left"> Does the event you want to attend promote open source bioinformatics software development or open science in the biological research community? </div><div class="right"> <img src="https://www.open-bio.org/wp-content/uploads/2019/01/deadline.png" alt=""> </div><div style="clear:both"></div></div> </p> <p>Events can include (but are not limited to) conferences, workshops, code fests, and hackathons. The event can occur anytime in a one-year window starting one month after the application deadline. For example, if you are applying for the April 1 deadline, the event you are hoping to attend should take place between May 1 and the following May 1.</p> <h2 id="2-what-is-your-participation">2 What is your participation?</h2> <div class="splitbox"><div class="left"> <p>We look at your role at the event, your past participation in the project that you are representing, and also your general involvement in open source development or open science.</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/01/filter.png" alt=""></p> </div><div style="clear:both"></div></div> <p>We give a slight preference to OBF events and member projects.</p> <h2 id="3-increasing-diversity">3 Increasing diversity</h2> <div class="splitbox"><div class="left"> <p>Does your attendance increase diversity at the event and/or in the overall open source bioinformatics community?</p> </div><div class="right"> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/01/select-diversity.png" alt=""></p> <p></div><div style="clear:both"></div></div> We understand increasing diversity as increasing participation from groups otherwise underrepresented in the community or at the event, including but not limited to underrepresented demographic groups, ethnic origins, career stages, and disabilities.</p> <h1 id="what-does-the-fellowship-cover">What does the fellowship cover?</h1> <div class="splitbox"><div class="left"> <h3 id="items-covered-for-in-person-participation">Items covered for in-person participation</h3> <ul> <li>The fellowship can be used to cover <strong>direct travel costs</strong> (such as airfare, train, metro, bus and taxi), <strong>hotel, childcare and/or conference registration fees</strong> up to a value of <strong>USD 1,500</strong>.</li> <li>Note that rental car expenses and personal car mileage are <strong>not eligible for reimbursement.</strong> We anticipate that these awards will supplement travel costs, <strong>not cover all expenses.</strong></li> <li>If you anticipate that <strong>you would require more than USD 1,500</strong> in order to attend the event, please <strong>include that information on the application form.</strong></li> </ul> </div><div class="right"> <h3 id="items-covered-for-remote-participation">Items covered for remote participation</h3> <ul> <li>The fellowship can be used to cover conference <strong>registration fees</strong> and the <strong>costs of small hardware</strong> (such as a microphone, speaker and webcam), <strong>childcare for the duration of the event</strong> and/or other supporting materials up to a value of <strong>USD 1,500.</strong></li> <li>Applicants are eligible to apply for the cost of a communication platform only if they are <strong>hosting a virtual event</strong> and will require a paid subscription to access the necessary premium features of the software used in their event.</li> <li>The cost of remote participation will be evaluated on a case-by-case basis. Please note that this fellowship will not cover the cost of buying laptops and computers. However, the rental cost of hardware that is needed in order to participate in the event may be covered.</li> </ul> </div><div style="clear:both"></div></div> <h3 id="reimbursement">Reimbursement</h3> <ul> <li>The OBF will reimburse the recipient <strong>after the event</strong> based on <strong>receipts</strong> provided and <strong>proof of attendance</strong>. There is no cash value beyond eligible and documented expenses.</li> </ul> <h1 id="requirements">Requirements</h1> <p>We expect that your participation in the event will</p> <ul> <li>promote open source software development and/or open science in the biological research community</li> <li>promote diversity in this community.</li> </ul> <p>Awardees are required to write a <a href="https://www.open-bio.org/category/event-fellowship/">post on the OBF blog</a> about their experience attending the event. This should be completed within three weeks after the event ends, and is a prerequisite before the awardee can receive payment.</p> <h1 id="applications">Applications</h1> <h2 id="who-will-review-the-applications">Who will review the applications?</h2> <p>The review panel is drawn from the OBF Board of Directors and OBF members.</p> <p>Any panelist with a clear conflict of interest will recuse themselves from deliberation.</p> <h2 id="how-to-apply">How to apply?</h2> <p>Fill out the <a href="https://forms.gle/L96UvgCGMDgye7su9">application form</a>. Applicants will be notified of the outcome about three weeks after the application deadline.</p> <p>We have created <a href="https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing">a word template</a> of the form, which can be used for creating a draft of your application. Please make a copy or download this document as a ‘.docx’ file. If Google Docs and Forms are not accessible from your geographical location, please email the fellowship chair to receive a template document by email.</p> <p><strong>Application Deadlines:</strong></p> <ul> <li>Round 1: <strong>1 April</strong></li> <li>Round 2: <strong>1 August</strong></li> <li>Round 3: <strong>1 December</strong></li> </ul>https://www.open-bio.org/sample-page/Tue, 11 Dec 2018 16:07:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/sample-page/<p>This is an example page. It&rsquo;s different from a blog post because it will stay in one place and will show up in your site navigation (in most themes). Most people start with an About page that introduces them to potential site visitors. It might say something like this:</p> <blockquote> <p>Hi there! I&rsquo;m a bike messenger by day, aspiring actor by night, and this is my website. I live in Los Angeles, have a great dog named Jack, and I like piña coladas. (And gettin&rsquo; caught in the rain.)</p> </blockquote> <p>&hellip;or something like this:</p> <blockquote> <p>The XYZ Doohickey Company was founded in 1971, and has been providing quality doohickeys to the public ever since. Located in Gotham City, XYZ employs over 2,000 people and does all kinds of awesome things for the Gotham community.</p> </blockquote> <p>As a new WordPress user, you should go to <a href="https://www.open-bio.org/wp/wp-admin/">your dashboard</a> to delete this page and create new pages for your content. Have fun!</p>https://www.open-bio.org/2018/11/19/updates-are-coming/Mon, 19 Nov 2018 21:44:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/11/19/updates-are-coming/<p><img src="https://news.open-bio.org/wp-content/uploads/2018/11/brace-yourself-updates-are-coming-obf.jpg" alt="Brace yourselves - updates are coming"></p> <p>About a year ago, the OBF shared <a href="https://news.open-bio.org/2017/11/14/obf-visioning-2017/">plans to get more involved with the open science community</a>, and followed up by <a href="https://news.open-bio.org/2018/03/20/welcome-to-our-new-board-members/">recruiting two board members</a> for this purpose. Since then, we’ve tried to keep up momentum and community engagement - during GCCBOSC, we held an <a href="https://news.open-bio.org/2018/07/09/following-up-from-boscs-obf-birds-of-a-feather-meeting/">OBF Birds of Feather meeting</a>, allowing members of the board to meet with attendees and discuss their needs and interests. As a result of this meeting, we ended up with our new <a href="https://news.open-bio.org/2018/11/05/new-obf-logo/">community-designed logo</a> and launched a <a href="https://github.com/OBF/newsletter">community newsletter</a> (incidentally, issue 2 of the newsletter is going to be released within the next few days - <a href="https://github.com/OBF/newsletter/issues/3">feel free to suggest a news item</a>).</p> <h2 id="obf--outreachy-intern--site-redesign">OBF + Outreachy Intern = Site Redesign</h2> <p>Our next step is the exciting announcement of a complete site redesign. Over the period of December 2018 - March 2019, <a href="https://github.com/kushinauwu/">Deepashree Deshmukh</a> will be working as an <a href="https://www.outreachy.org/alums/">Outreachy</a> Intern, creating a purpose-built CMS powered website for the OBF.  We’d also like to thank all of the other fantastic applicants to this project. Contributors from around the world spent time, effort, and did some genuinely great work prototyping their designs during the application phase.</p> <p>Currently, the OBF site is comprised of <a href="https://news.open-bio.org/">our blog</a>, where you’re probably reading this, a <a href="https://obf.github.io/GSoC/">GSoC mini-site</a>, and <a href="https://www.open-bio.org/wiki/Main_Page">our main MediaWiki-powered site</a>. We’re looking forward to combining and refreshing these, hopefully resulting in an attractive and easily-updatable site that can function as a community-oriented hub. We’ll be sharing drafts as they evolve. If you have any thoughts or comments on what you’d like to see in the new site, feel free to leave a comment on this post.</p>https://www.open-bio.org/2018/11/05/new-obf-logo/Mon, 05 Nov 2018 22:00:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/11/05/new-obf-logo/<p><img src="https://news.open-bio.org/wp-content/uploads/2018/08/OBF-2018-300x98.png" alt=""></p> <p>We have successfully crowd-sourced a new OBF logo! The process started at the <a href="https://news.open-bio.org/2018/07/09/following-up-from-boscs-obf-birds-of-a-feather-meeting/">OBF Birds of a Feather meeting</a> at <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a> when the OBF leaders announced that we were seeking a new logo design. Two BoF participants immediately started sketching ideas, as well as a third community member who was not at the BoF but saw our tweet. The designs (which you can see <a href="https://github.com/OBF/obf-docs/issues/43">here</a>) were put up for a public vote. <a href="https://github.com/lafita">Aleix Lafita</a>&rsquo;s narrowly won and was adopted as our new OBF logo! We are currently working on possible variations on the logo for special events or causes (for example, a rainbow version).</p> <p>The OBF is delighted that community members responded to our request for new logo designs with creativity and focus&ndash;attributes that are valuable in the open source community.</p> <p>If you&rsquo;re interested in joining the OBF and getting on our (low-traffic) mailing list, please fill out a membership application <a href="https://www.open-bio.org/wiki/Membership">here</a>!</p>https://www.open-bio.org/2018/10/26/obf-membership-form-fixed/Fri, 26 Oct 2018 17:24:19 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/10/26/obf-membership-form-fixed/<p>We recently discovered that the application to join the OBF (linked from the <a href="https://www.open-bio.org/wiki/Membership">OBF membership page</a>) was not working. It broke some time after August 31. We have now replaced it and it is working once again.</p> <p>If you applied for OBF membership between September 1 and yesterday, please go to the new form (<a href="https://goo.gl/x9KYWL">https://goo.gl/x9KYWL</a>) and resubmit your application. We apologize for the inconvenience!</p>https://www.open-bio.org/2018/08/29/the-color-of-bioinformatics/Wed, 29 Aug 2018 10:33:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/08/29/the-color-of-bioinformatics/<p><em>This is a guest blog post from Tendai Mutangadura, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship</a> program to attend the <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a> meeting in Portland, June 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of <a href="https://news.open-bio.org/2018/05/25/travel-fellowships-april-2018/">three awards from our April 2018 travel fellowships call</a>. Our August call recently closed, the current call closes 15 December 2018, you might want to apply?</em></p> <p>When I was selected as one of 3 recipients of the April 2018 OBF Travel Fellowships, I wanted this to signify a turning point in my career. I expected to meet and interact with many great minds in open science and bioinformatics, and the <a href="https://gccbosc2018.sched.com/">GCC-BOSC 2018</a> meeting in beautiful Portland exceeded my expectations. Because I was travelling light and had been to Portland once before, I chose to use public transport from PDX to get to Reed College, the meeting venue. This afforded me a mini tour of Portland before getting to the serious but fun business of the meeting. When I stepped off the Reed College bus stop, I flagged down the first person I saw to ask for directions to the registration venue, and this person was none other than Anton, one of the scientists instrumental in the development of the <a href="https://usegalaxy.org/">Galaxy project</a>. Great start. As we chatted en route to the registration place, I took the opportunity to brag to him that I had recently figured out the causal mutation associated with a neurodegenerative disease in one of our whole-genome-sequenced dogs using the web-based <a href="https://usegalaxy.org/">Galaxy platform</a>.</p> <p>I attended as many training sessions related to Galaxy on Day 1 of training as I could. I have been a Galaxy platform user for &gt;3 years and had previously attended the GCC 2016, so it was great to meet new and old acquaintances this time round. I even had the opportunity to get help with aspects of my <a href="https://jetstream-cloud.org/support/index.php">Jetstream</a> account virtual machines during one of the two CollaborationFest days that I attended. I found the CollaborationFest very useful in making new contacts and discussing potential future collaborations.</p> <p>On Day 2 of Training, the highlights of my training, based my bioinformatics needs, included a 2.5 hour <a href="https://software.broadinstitute.org/gatk/">GATK</a> training session and the <a href="https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html">bcbio</a> workshop. In the latter, Brad Chapman, <a href="https://www.youtube.com/watch?v=ukWhAetvNKE">starring here</a>, talked about and demonstrated how communities can work together to make giant strides in developing robust open source software pipelines and making these freely accessible to anyone, everyone, anywhere. For someone like me, for whom having access to computing resources and setting aside the time to focus on developing or tweaking code as part of my day job can sometimes be an uphill struggle, the bcbio workshop was a godsend. Bcbio allows me to do my day job duties and do bioinformatics too. After the meeting, I immediately contacted one of my XSEDE Extended Collaborative Support Services ( <a href="https://portal.xsede.org/ecss">ECSS</a>) team members, Phil Blood, to discuss the possibility of putting together a species agnostic variant-calling pipeline. I have already started this project using my <a href="https://www.xsede.org/">XSEDE</a> start-up grant computing resources allocation on <a href="https://www.psc.edu/bridges">Bridges</a>, at the Pittsburgh Supercomputing Center ( <a href="https://www.psc.edu/">PSC</a>). So far, I have been off to a good start. For those who may not be aware of the many great free computing resources out there, such resources exist, as I have alluded to above, for anyone to take advantage of.</p> <p>Now, a light-hearted reference to a serious (according to me), but common observation at conferences such as but definitely not limited to GCC-BOSC: the lack of diversity of attendees. This is what prompted me to title my blog post the way I did. My first answer was (metaphorically speaking) that the color of bioinformatics <em>should</em> be ‘rainbow’. But when I googled ‘rainbow colors’ it occurred to me that the colors black and white are not part of the rainbow. I also refreshed my rusty optical physics and got explanations why this is the case. Now, to get back on track, would it not be wonderful if more people of color were involved in this bioinformatics revolution? What can be done to redress this current state of affairs? Thumbs up to the OBF for recognizing and doing something about this lack of diversity by creating the OBF Travel Fellowship! For my part, when and if I complete any pipeline(s) based on bcbio code, I plan to publish a collection of such pipelines online as self-paced tutorials (the website will go live soon) in a very user-friendly format targeted to those who are command line challenged, from any community, to encourage them to get started in bioinformatics analyses, or at least analyze their own data without buying expensive commercial packages. This would be my way, albeit at very small scale, of democratizing bioinformatics. One of the advantages of involving people with as diverse backgrounds as possible with basic training in bioinformatics and genomics is that this may help <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354806/">reduce mistrusts</a> linked to unfortunate historical incidents such as the Tuskegee experiments, not only for countries like the US but anywhere around the world where similar types of mistrust may exist.</p>https://www.open-bio.org/2018/08/18/city-of-roses-they-call-it-portland-oregon-usa/Sat, 18 Aug 2018 15:27:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/08/18/city-of-roses-they-call-it-portland-oregon-usa/<p>How should I start describing the fruitful experience in this amazing city&hellip; First time ever in Portland, second time attending BOSC&hellip; I knew I was signing up for a great time but did not know much about the uncanny beauty of this picturesque city.</p> <p>First of all, I would like to thank the Open Bioinformatics Foundation (OBF) for providing partial funding to support my travel expenses (though an <a href="https://www.open-bio.org/2018/05/25/travel-fellowships-april-2018/">OBF Travel Fellowship award</a>). I would also like to thank my PhD supervisors Andrew Lonie and Richard O. Sinnott for the remaining expenditure.</p> <p>I had written a very detailed blog post of my experience in <a href="https://news.open-bio.org/2017/11/21/bosc-2017-prague-land-of-stories/">BOSC 2017</a>. The experience was a bit different this time as BOSC was organised in conjunction with Galaxy Community Conference(GCC) this year, unlike previous all times when BOSC was held with ISMB. On a lighter note, the most positive difference (as compared to last year) was the unlimited supply of coffee/tea in the <a href="https://en.wikipedia.org/wiki/Coffee_in_Portland,_Oregon">coffee town</a> throughout the conference to keep the morale high.  The other difference was the budget-friendly registration costs of the conference this year. The cheaper accommodation options were available in the hostels of <a href="https://www.reed.edu/">Reed College</a>, the beautiful and lush green venue for the conference.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2018/08/WhatsApp-Image-2018-08-18-at-9.02.55-PM1-300x169.jpeg" alt=""></p> <p>The conference was divided into three cores:</p> <ul> <li><strong>Training days:</strong> The first two days June 25th and June 26th were focused on training sessions running in parallel covering various bioinformatics topics such as Galaxy introduction, RNA-seq data analysis (Galaxy and bcbio), Data carpentry workshop, Conda-Containers, Workflow Definition Language( WDL) and Common Workflow Language (CWL) introduction.</li> <li><strong>Conference days:</strong> The next two days June 27th and June 28th were dedicated to parallel sessions of Galaxy and BOSC talks taking place in two different venues with combined keynote speeches.</li> <li><strong>Core Cofest days:</strong> Unlike last year, the intense collaborative hacking sessions were after the conference on June 29th and 30th.</li> <li><strong>Encore Cofest days:</strong> July 1st and 2nd also part of cofest but on a smaller scale with fewer participants.</li> </ul> <p>This year was special in one more aspect that I contributed in the reviewing process as part of the BOSC program committee.</p> <p><a href="https://twitter.com/farahzk03/status/1011658076900823040">https://twitter.com/farahzk03/status/1011658076900823040</a></p> <p>I have attended all 8 days of the conference beginning from the training all the way to end of the Encore cofest. My <a href="https://f1000research.com/posters/7-916">abstract</a> was accepted for a long talk (and by default for a poster) in BOSC so there was a bit of anxiety until I was done with my presentation on June 28th :). There were so many interesting parallel training sessions and it was quite a tough decision to choose which one to attend. I managed to attend few such as Conda and Containers, Common Workflow Language and Snakemake and Nextflow. During the CWL training session on June 26th, I volunteered to help with the session to answer questions during the training.</p> <p><a href="https://twitter.com/rvmngr/status/1011701337719857152">https://twitter.com/rvmngr/status/1011701337719857152</a></p> <p>Like last year, I decided to print my poster at the venue to save myself from the hassle of carrying it from one continent to the other. Keeping that in mind, I did the same this year. I got the poster printed from a local printing press <a href="https://www.minutemanteam.com/">Minuteman Press</a>. The staff was highly professional, talking over the phone, placing the order over the phone, sending poster via email and paying online saved me from having to visit the shop twice. They checked the poster, called again clarified few things to make sure things are appearing the way they should be. I would say overall the experience was pretty smooth and the print quality was also up to the mark. There were in total two poster sessions, each in the evening of the conference days. My poster was scheduled for the evening session on June 27th. I received the printed copy on the morning of 27th which I arranged on the assigned slot.</p> <p><a href="https://twitter.com/farahzk03/status/1012073266599489537">https://twitter.com/farahzk03/status/1012073266599489537</a></p> <p>The conference on June 27th  started with very informative and interesting keynote speech by Fernando Perez on &ldquo;Sustainable development of scientific open source tools: a view from Jupyter&rdquo;.</p> <p><a href="https://twitter.com/farahzk03/status/1012002955053027328">https://twitter.com/farahzk03/status/1012002955053027328</a></p> <p>I must admit I was not aware of the functionality of <a href="http://jupyter.org/">Jupyter notebooks</a> before this and how interactive these are supporting many scripting languages as including Python, R, Julia, and Scala. Fernando was of the view that computational hygiene should be a day to day practice.</p> <p><a href="https://twitter.com/farahzk03/status/1012013507942891522">https://twitter.com/farahzk03/status/1012013507942891522</a></p> <p>Followed by keynote was an interesting talk where four engineers collaborating remotely for the project &ldquo;FROG&rdquo;,  shared their experiences with the packaging technologies. One of the many lessons emphasized in the talk is <em>&quot;</em> The first <em>step to learn packaging technologies: read the manuals.&quot;</em></p> <p><a href="https://twitter.com/farahzk03/status/1012019611741577216">https://twitter.com/farahzk03/status/1012019611741577216</a></p> <p>An interesting talk in the evening session was given by Ravi K. Madduri on &ldquo;Reproducible big data science: A case study in continuous FAIRness in which he explained how they demonstrated reproducibility of real-life workflows using Galaxy, minids and BDBags to achieve interoperability in naming and identifier conventions. He emphasized that reproducibility requires patience and discipline but <em>&ldquo;Reproducibility is like brushing your teeth. Once you learnt it, it becomes</em> a habit <em>.&rdquo;</em></p> <p><a href="https://twitter.com/farahzk03/status/1012079639890546688">https://twitter.com/farahzk03/status/1012079639890546688</a></p> <p>Some other talks in this session were  Intermine 2.0 by Yo Yohudi,  NIH Data Commons Introduction by David Siedzik and Snakemake by Johannas Koster. I rushed from Vollum hall where BOSC talks were organized for the Poster presentation In Performing Arts Building. The poster session was very interactive and the audience enjoyed the tea/coffee walking around and asking the presenters about their work. I think the time went by very fast and we had to rush back for the Panel discussion in Vollum hall which I missed a bit because of the ongoing conversations at the poster venue,</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2018/07/lots-of-people-at-poster-session-1-300x231.jpg" alt="Presenters and attendees mingle at the GCCBOSC 2018 poster/demo session"></p> <p>As I arrived late so could attend half of the panel discussion. The panel discussion was on a topic which is of my personal interest as I am working on Provenance of the Bioinformatic workflows. The topic of the discussion was &ldquo;Training and Documentation in Bioinformatics&rdquo; where Fernando Perez, Tracy K. Teal, Jason Williams and Berenice Batut were guests.</p> <p><a href="https://twitter.com/farahzk03/status/1012127092421455872">https://twitter.com/farahzk03/status/1012127092421455872</a></p> <p>Also, GigaScience has the coolest Game of Thrones-themed shirts as always :D I got my hands on one last year but this year I could not get one :(.</p> <p><a href="https://twitter.com/farahzk03/status/1012175720682905605">https://twitter.com/farahzk03/status/1012175720682905605</a></p> <p>After the panel discussion, now the time was to prepare for my talk the next morning. I was very anxious but also excited to present what I am passionate about. Michael R. Crusoe was patient to listen to me, very kind to help me with the preparation of the presentation and encouraging that it will all be good. I don&rsquo;t have a massive public speaking fear but the start is always the hardest.</p> <p>The highlight of June 28th for me was the presentation which was scheduled for the morning session at 11:40 am. It turned out to be better than I expected :). A huge sigh of relief and then I could really enjoy the rest of the talks without thinking about mine.</p> <p><a href="https://twitter.com/biocrusoe/status/1012394197121261568">https://twitter.com/biocrusoe/status/1012394197121261568</a></p> <p>My talk was about <a href="https://zenodo.org/record/1208478">CWLProv,</a> a format for the representation and automatic aggregation of workflow enactment, its results and provenance to promote interoperability and reproducibility of methods. The feedback from the live audience during and after the presentation and on twitter was very helpful and encouraging, one of the most outstanding characteristics of the BOSC community :).</p> <p><a href="https://twitter.com/yoyehudi/status/1012401483776577537">https://twitter.com/yoyehudi/status/1012401483776577537</a></p> <p><a href="https://twitter.com/farahzk03/status/1012479030979747841">https://twitter.com/farahzk03/status/1012479030979747841</a></p> <p>The day got better with many interesting talks such as celebrating that CWL, a project that was founded in 2014 during the discussions in BOSC2014 turned four years old :). It is exciting to see how much the standard has grown and influenced projects all around the globe with more than 20 participating organizations and many individual contributors. CWL is an epitome of &ldquo;Open Source-ness&rdquo; and Community-driven projects designed with continuous interaction with the community itself to build a standard for workflow definition which promotes interoperability, portability and reproducibility and resolves the heterogeneity issue in workflow domain.</p> <p><a href="https://twitter.com/yoyehudi/status/1012395134665703424">https://twitter.com/yoyehudi/status/1012395134665703424</a></p> <p>Another highlight is the provision of affordable daycare for the participants and encouraging participants from all backgrounds to participate. An example was Cristel Thomas presenting in Galaxy session with the youngest participant with her. That’s the example, this amazing event is set for the other conferences. Encouraging participation if you are eager, no matter what the circumstances are.</p> <p><a href="https://twitter.com/crstlthms/status/1012054388347555840">https://twitter.com/crstlthms/status/1012054388347555840</a></p> <p>The day ended with an open door BBQ conference dinner, the weather, the food, the mood everything was on point. The beauty of the lush green campus and artistic architecture is breathtaking, sad that I was not able to explore much beauty but whatever I saw and wherever I went was telling a story.</p> <p><a href="https://twitter.com/farahzk03/status/1012528947836276736">https://twitter.com/farahzk03/status/1012528947836276736</a></p> <p>A big improvement during Cofest was gender balance which was a bit alarming last year during code fest where only 3 female participants joined in total out of &gt;60 participants. This year the situation improved drastically because of the two communities doing it together. The venue was quite spacious and full of resources to accommodate more than 100 participants working on different projects.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2018/07/codefest-big-group-on-steps-300x200.jpg" alt=""></p> <p>Like always the regular updates from groups were spread throughout the day, in the morning, before lunch and at the end of the day. These update sessions keep you going and motivate you to push yourself for tangible outputs. I worked alongside Michael (CWL) and we refactored the implementation of CWLProv, improved the prototype implementation working continuously for four days of cofest.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2018/08/WhatsApp-Image-2018-08-18-at-9.02.53-PM-300x225.jpeg" alt=""></p> <p>I believe in collaborative science without caring about geographical scenarios but with a huge time difference, it does get tricky sometimes to work together on a project. These four days were breath of fresh air discussing long due issues face to face, getting instant help, contributing more efficiently and getting a Pull Request with <a href="https://github.com/common-workflow-language/cwltool/pull/676">338 commits merged into cwltool</a> :). That is the biggest highlight for my participation and I am sure it would have taken much longer if  I did not have this opportunity. I encourage everyone to participate in the code fest as it will increase your productivity 10x.</p> <p><a href="https://twitter.com/farahzk03/status/1016537277160275974">https://twitter.com/farahzk03/status/1016537277160275974</a></p> <p><em>P.S. Some other day, I will write about my experience with food, walks around the city, strolling on the river bank and the non-science talks.</em></p>https://www.open-bio.org/2018/08/02/taking-turns/Thu, 02 Aug 2018 16:55:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/08/02/taking-turns/<p><strong>BOSC 2019 will be part of ISMB 2019</strong> Every year until 2018, BOSC was part of the annual ISMB conference as a community of special interest (COSI, formerly known as a SIG, Special Interest Group). As part of our continuing quest to broaden and deepen the BOSC community, we decided to perform an experiment this year by partnering with the Galaxy Community Conference rather than with ISMB. <a href="https://news.open-bio.org/2018/07/27/gccbosc-2018-post-meeting-report/">As we reported</a>, the experiment was a success&ndash;participants were overwhelmingly positive about the experience, and the conference did attract a somewhat different mix of attendees than in past years. However, we also concluded that there are some advantages to meeting with ISMB&ndash;for example, it attracts more students and postdocs, and the presence of other COSI tracks provides a wider range of scientific topics. Moreover, unlike the GCC 2018 venue, the venue already chosen for <a href="https://galaxyproject.org/galaxy-updates/2018-08/">GCC 2019</a> has a number of drawbacks: we wouldn’t be able to run similarly-sized parallel sessions; registration prices wouldn’t be as affordable as in 2018; and the venue would not be able to accommodate the larger (160 people) and longer (four days) CollaborationFest that was one of the highlights of GCCBOSC 2018.For these and other reasons, the BOSC organizing committee concluded that <strong>the best way to serve the broadest community of potential BOSC attendees will be to partner with ISMB some years and GCC some years.</strong> We therefore plan to hold BOSC 2019 in Basel as part of ISMB. We hope to partner with GCC in 2020 at a North American site to be determined, or in 2021 in Europe.Wherever we hold future BOSCs, you can be sure that they will include a wide range of topics in open science and open source bioinformatics, and we hope that they will draw an ever-diversifying mix of attendees. As always, we welcome your feedback about what you liked in past BOSCs and your suggestions for the future. Feel free to email us ( <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>) or tweet (@OBF_BOSC).</p>https://www.open-bio.org/2018/07/27/gccbosc-2018-post-meeting-report/Fri, 27 Jul 2018 19:52:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/07/27/gccbosc-2018-post-meeting-report/<p>This year, the Galaxy Community Conference (GCC) and the Bioinformatics Community Conference (BOSC) met together to form the first Bioinformatics Community Conference. At <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>, participants were able to meet and collaborate with a broad community of bioinformatics developers and users who focus on open, interoperable software tools and libraries that facilitate scientific research.</p> <p>Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC attracted nearly 300 participants from around the world. The meeting started with two days of training workshops (Figure 1). The main meeting had some parallel sessions and some joint sessions, including well-received keynote talks by <a href="https://gccbosc2018.sched.com/speaker/tkteal">Tracy Teal</a>, <a href="https://gccbosc2018.sched.com/speaker/fperez10">Fernando Pérez</a> and <a href="https://gccbosc2018.sched.com/event/EQFC/closing-keynote-confound-it-reproducible-biology-from-omics-data-analysis">Lucia Peixoto</a>, as well as a <a href="https://gccbosc2018.sched.com/event/Dup7/panel-training-and-documentation-in-bioinformatics">panel discussion about documentation and training</a>. Posters, demos and Birds of a Feather sessions ( <a href="https://gccbosc2018.sched.com/overview/type/B.+Conference/Birds-of-a-Feather">BoFs)</a> gave participants opportunities to engage in discussions about topics of mutual interest. After the main meeting, many attendees stayed for up to four additional collaboration days (the CollaborationFest, or <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">CoFest</a>).<img src="https://news.open-bio.org/wp-content/uploads/2018/07/tutorial-room-rna-seq-1-300x157.jpg" alt=""> Figure 1. Participants at one of the GCCBOSC training workshops. (All GCCBOSC photographs in this post are from <a href="https://www.flickr.com/photos/134305289@N03/albums/72157695693844792/page3">Bérénice Batut’s Flickr album</a>, under a <a href="https://creativecommons.org/licenses/by-sa/2.0/">CC-BY-SA license</a>.) <img src="https://news.open-bio.org/wp-content/uploads/2018/07/lots-of-people-at-poster-session-1-1024x787.jpg" alt=""><img src="https://news.open-bio.org/wp-content/uploads/2018/07/Sehrish-Kanwal-poster-1-1024x1003.jpg" alt=""> Figures 2,3. Attendees and presenters mingled at the poster/demo sessions.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2018/07/codefest-big-group-on-steps-1024x683.jpg" alt=""> Figure 4. CoFest attendees assembled for morning meetings before breaking into smaller groups to work on collaborative projects.</p> <p>There was wide agreement among GCCBOSC participants that the meeting was informative, productive and enjoyable. Comments from participants in the post-meeting <a href="https://docs.google.com/forms/d/e/1FAIpQLSckB5ckoxvXf8UoheO9qOiGuWYsMRXWoOu_HkQ0RATzXmQZQA/viewform">survey</a> included, “Loved the mix of communities!”, “Location was great,” and “Nice conference. Nice atmosphere. Nice people. I really enjoyed it. Thanks!”. The training workshops and extended CoFest were mentioned by participants as great features of the meeting. Most of the survey respondents who had previously attended a GCC or BOSC rated this year’s meeting as similar or better than past meetings (Figure 5). The main complaint was that the parallel GCC and BOSC sessions forced attendees to choose between them&ndash;an embarrassment of riches.Figure 5: Responses to post-GCCBOSC survey questions from those who had been to previous GCCs or previous BOSCs.<img src="https://news.open-bio.org/wp-content/uploads/2018/07/comparison-with-previous-BOSCs-1-300x178.png" alt=""><img src="https://news.open-bio.org/wp-content/uploads/2018/07/comparison-with-previous-GCCs-2-300x182.png" alt="">Although post-meeting feedback was almost entirely positive, we did receive two reports of behavior at GCCBOSC that the reporter perceived as not consistent with the spirit of the <a href="https://galaxyproject.org/events/gccbosc2018/code-of-conduct/">Code of Conduct</a>. These were handled by the GCCBOSC organizing committee, and everyone involved is satisfied with the outcome. The discussions held by the organizers around these issues led us to re-examine the CoC and think about how we might want to revise it for future meetings. Your input on this topic (or anything regarding GCCBOSC) is welcome.We are grateful to all those who helped make GCCBOSC 2018 a success: the organizers, presenters, workshop leaders, participants, and our generous <a href="https://gccbosc2018.sched.com/directory/sponsors">sponsors</a>, including Platinum sponsor Google Cloud and Gold sponsor Lenovo + Intel. Thanks in part to sponsor funding, we were able to offer subsidized child care and an onsite lactation room that enabled a speaker who would otherwise have been unable to attend to bring her four-month-old baby and participate actively in the meeting.Whether or not you attended GCCBOSC 2018, we look forward to interacting with you in the future!</p>https://www.open-bio.org/2018/07/09/following-up-from-boscs-obf-birds-of-a-feather-meeting/Mon, 09 Jul 2018 15:49:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/07/09/following-up-from-boscs-obf-birds-of-a-feather-meeting/<p>It was really great to meet so many of you at GCCBOSC this year! We will soon have a couple of <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Travel Fellowship</a> blog posts talking about the conference, so we won’t provide too much of a general overview at this point, but we <em>would</em> like to share a little more about one of the Bird of Feather (BoF) events we ran - specifically the OBF community BoF. The aim of this BoF was to engage anyone who was:</p> <ul> <li>Curious about the OBF</li> <li>Interested in suggesting ideas</li> <li>Wanting to help or get more involved with the OBF</li> </ul> <p>The OBF BoF started with a pre-dinner round where we all introduced ourselves and why we were interested in the OBF, and a second round after a quick bite and relocating inside - Portland can get chilly fast in the evening! <strong>Motivations for participating in the BoF</strong> included a desire to help people who come from a software background learn more about the biology / bioinformatics side of things. Other participants shared the feeling that they loved the conference but weren’t sure how to take home the “open / good practices make for better software and better research” message we were trying to share. We ended up with lot of brainstorming and helpful discussions - here are some of the topics.</p> <h2 id="obf-logo-and-site">OBF logo and site</h2> <p>The OBF logo is over a decade old now and looks a little… <a href="https://github.com/OBF/obf-docs/issues/43">dated</a>. When we floated the idea of redesigning it at the meeting, we didn’t expect to have sketches roughed out by several attendees before the end of the BoF meeting! We’ve ended up with three different design sets, which you can check out or comment on in <a href="https://github.com/OBF/obf-docs/issues/43">this GitHub issue</a>. We’re also considering updating the entire OBF site, if we can find someone to work on that (possibly a summer intern).</p> <h2 id="increasing-year-round-sense-of-community">Increasing year-round sense of community</h2> <p>For many people, BOSC and the OBF are approximately the same thing - which makes sense, since BOSC is one of the biggest and most noticable things we do. We’d like to support open bioinformatics all year, though. Possible ways we could do this:</p> <ul> <li><strong>Local OBF / bioinformatics meetups or hackathons</strong>. If the OBF created guidelines for this, would you be interested in running a group in your area?</li> <li><strong>Newsletters</strong> with project updates, interesting open / bioinformatics news, events, etc.</li> <li><strong>“How to be open in bioinformatics” webinar</strong> - a sort of “open 101” for projects that are interested in being open but aren’t sure where to start. This would be a nice way to kick-start projects that want to present a poster or talk at BOSC but don’t yet meet the openness requirements. (Note that anyone is allowed to <em>attend</em> BOSC, whether or not they have any open repositories - it’s only presenting that mandates a fully open project.)</li> </ul> <h2 id="joining-the-obf-as-a-project-or-individual">Joining the OBF as a project or individual</h2> <p>A pertinent question asked at the BoF was: why join, as an individual? Many people have attended BOSC multiple times and even been heavily involved in the community without officially being in the rolls of registered members. The primary reason to join is the ability for membership to <strong>vote</strong> on issues pertaining to the OBF. In the next few months, we’re hoping to run a vote on changing OBF bylaws pertaining to how projects join, as well as a plain to adopt a Code of Conduct that may apply to both the OBF and its member projects. If this matters to you because A) you care about a project that might be joining soon (there are a couple!) or B) you’d like to see the OBF adopt a more explicit behaviour standard in the form of a CoC, please join the OBF so you can vote!</p> <h2 id="get-involved">Get involved</h2> <p>After reading all this, if you’re interested in helping out with any of the ideas or initiatives suggested, please follow up by any of these mechanisms:</p> <ul> <li>Open an issue on our <a href="https://github.com/OBF/obf-docs/issues/new">OBF-docs repo</a> - this is our preferred method as it allows others to chime in easily and is less transient than a tweet.</li> <li>Leaving a comment on this post!</li> <li>Tweet to <a href="https://twitter.com/obf_news">@obf_news</a></li> </ul> <p>Also - please don’t forget to <a href="https://www.open-bio.org/wiki/Membership"><strong>join the OBF</strong></a> if you haven’t already. Any BOSC attendee automatically qualifies for membership, and even if you haven’t attended BOSC before, if you’re reading this post there’s a good chance you’ll fulfil the requirements anyway. <a href="https://www.open-bio.org/wiki/Membership">Details are in the form!</a> <div class="gallery gallery-cols-1"><div class="box"> <figure><img src="https://www.open-bio.org/wp-content/uploads/2018/07/OBF-BoF-2018-25.jpg" alt="OBF-BoF-2018 - 25"><figcaption> <h4>OBF-BoF-2018 - 25</h4> </figcaption> </figure> </div> <div class="box"> <figure><img src="https://www.open-bio.org/wp-content/uploads/2018/07/OBF-BoF-2018-31.jpg" alt="OBF-BoF-2018 - 31"><figcaption> <h4>OBF-BoF-2018 - 31</h4> </figcaption> </figure> </div> <div class="box"> <figure><img src="https://www.open-bio.org/wp-content/uploads/2018/07/OBF-BoF-2018-22-e1531151626641.jpg" alt="Hilmar, Peter, and Yo"><figcaption> <h4>Hilmar, Peter, and Yo</h4> </figcaption> </figure> </div> </div> </p>https://www.open-bio.org/2018/06/27/biopython-1-72-released/Wed, 27 Jun 2018 19:06:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/06/27/biopython-1-72-released/<p>Dear Biopythoneers,</p> <p>I&rsquo;m writing this in Portland at the <a href="https://gccbosc2018.sched.com/">GCC BOSC 2018 conference</a>, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI:</p> <p><a href="https://biopython.org/wiki/Download">https://biopython.org/wiki/Download</a> <a href="https://pypi.python.org/pypi/biopython/1.72">https://pypi.python.org/pypi/biopython/1.72</a></p> <p>This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.</p> <p>Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and SeqIO.write (especially when used in a for loop).</p> <p>The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use inclusive end co-ordinates to better handle searches at end points. This will require you to rebuild any existing MAF index files.</p> <p>In this release more of our code is now explicitly available under either our original &ldquo;Biopython License Agreement&rdquo;, or the very similar but more commonly used &ldquo;3-Clause BSD License&rdquo;. See the LICENSE.rst file for more details.</p> <p>The Entrez module now supports the NCBI API key. Also you can now set a custom directory for DTD and XSD files. This allows Entrez to be used in environments like AWS Lambda, which restricts write access to specific directories. Improved support for parsing NCBI Entrez XML files that use XSD schemas.</p> <p>Internal changes to our C code mean that NumPy is no longer required at compile time - only at run time (and only for those modules which use NumPy).</p> <p>Seq, UnknownSeq, MutableSeq and derived classes now support integer multiplication methods, matching native Python string methods.</p> <p>A translate method has been added to Bio.SeqFeature that will extract a feature and translate it using the codon_start and transl_table qualifiers of the feature if they are present.</p> <p>Bio.SearchIO is no longer considered experimental, and so it does not raise warnings anymore when imported.</p> <p>A new pairwise sequence aligner is available in Bio.Align, as an alternative to the existing pairwise sequence aligner in Bio.pairwise2.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Benjamin Vaisvil (first contribution)</li> <li>Blaise Li</li> <li>Chad Parmet</li> <li>Chris Rands</li> <li>Connor T. Skennerton</li> <li>Francesco Gastaldello</li> <li>Michiel de Hoon</li> <li>Pamela Russell (first contribution)</li> <li>Peter Cock</li> <li>Spencer Bliven</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul> <p>Thank you all.</p> <p>Peter</p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a></p> <p>&ndash;</p> <p>Checksums for interest/public record:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.72* </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>abc14a111ed89332c902d239f516cc9ab84ab4458b577c61208dc4c20b74dc83 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>3e8c85d4a3295be598a9e9616adeed8a4f81bd0452326aaea7bf81cca468f7c1 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>f1b4abd90d0c84ab2c5dab704da1d397cf75ee41f72619a1802479c3768ac347 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>b426a2d858414bed0c25fca155fdf27485347ce6f69805db65b8b36ec00a0f41 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27mu-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>71762c193ffc9a1b936dfaa2d456fb172856f0952090483ee4a84635a1aa6fe3 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27mu-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>57a449709df7a47980360ecbd2f195effc56e9b0253fa0e74fb00b10b44778e0 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27m-win32.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>3d3deb59c3f5d04d41aec443db4e89dbbdd0bb7749078f91e797935849c8db48 </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27m-win_amd64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>b76241a55a1ba832c2768733fb113eef1fdfa1d738aa1f84fcdd4ba0b6432394 </span></span><span style="display:flex;"><span>biopython-1.72-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>ad2c72c289561d51f6f7a9ae977e9cd54cd48b575b946421f82ede1ac24198cb </span></span><span style="display:flex;"><span>biopython-1.72-cp34-cp34m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>3a199d469465c4f3c4c238f688d07b9bce4f504be73dead6cdf5d36a47728fcd </span></span><span style="display:flex;"><span>biopython-1.72-cp34-cp34m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>16a99e2462ee5acb6962f3a1d344336db58d7b87acf9d5023beb3efe6ebb47a8 </span></span><span style="display:flex;"><span>biopython-1.72-cp34-cp34m-win32.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>defd163110d698ea534e470995c68c519bd56e4e23043ae9dd8b646f2a803e5b </span></span><span style="display:flex;"><span>biopython-1.72-cp34-cp34m-win_amd64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>5882ba8fb87cbbe36d9e5d87c9b8f3139d503fe7da1023b472760a8122e579e6 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style="display:flex;"><span>biopython-1.72.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.72* </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>661d50514eaa8151192b2127f52a8f5e </span></span><span style="display:flex;"><span>biopython-1.72-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>a66e12a83c44ee50f01888129658eba0  biopython-1.72-cp27-cp27m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>d7eb8003d855b3b425e2d7b5062d390a </span></span><span 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style="display:flex;"><span>biopython-1.72-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>50e8fc0e63ca3ad524ea8c5d237ed6b1  biopython-1.72-cp34-cp34m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>d20e9cfa98ee8991b7008f64a44f6130 </span></span><span style="display:flex;"><span>biopython-1.72-cp34-cp34m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>1ea11554a42996491c847ae0cf36de97  biopython-1.72-cp34-cp34m-win32.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>848d5d53c3a6c60d9e94528e6cc35087  biopython-1.72-cp34-cp34m-win_amd64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>bde20eb5d6abdaa6479113dc96690603 </span></span><span style="display:flex;"><span>biopython-1.72-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>75b83b673997dbae8a8fe1a6fa15d3e3  biopython-1.72-cp35-cp35m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>b883f5439353885224789b9e25107661 </span></span><span style="display:flex;"><span>biopython-1.72-cp35-cp35m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>d76442d3fc18de8953936a6c5ef5a79f  biopython-1.72-cp35-cp35m-win32.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>f043fa59e3fbd5d505599474aaed74b5  biopython-1.72-cp35-cp35m-win_amd64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>dab6b61605938b75eef18fa9cae944da </span></span><span style="display:flex;"><span>biopython-1.72-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>49fd975593798f0d7a293ebe327f800e  biopython-1.72-cp36-cp36m-manylinux1_i686.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>8259fbf571b15dc05f0405b5e99394ce </span></span><span style="display:flex;"><span>biopython-1.72-cp36-cp36m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>4e0d4de83b89d632a5dad9ee417306f2  biopython-1.72-cp36-cp36m-win32.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>acdf4e57da4fc90bf7c52c76c2bf4182  biopython-1.72-cp36-cp36m-win_amd64.whl </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>418fecc41f75353fde30de73586900ac  biopython-1.72.tar.gz </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>e1db4737caf6bd2f7443f7e3c986ebbb  biopython-1.72.zip </span></span></code></pre></div>https://www.open-bio.org/2018/06/14/obf-bof-gccbosc-2018/Thu, 14 Jun 2018 18:11:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/06/14/obf-bof-gccbosc-2018/<p>If you&rsquo;re going to <a href="https://gccbosc2018.sched.com/">GCCBOSC 2018</a>, we invite you to join us at the <a href="https://gccbosc2018.sched.com/event/FCGp">OBF Birds of a Feather</a> on Wednesday, June 27, from 5:40-7:40pm. Come and chat over dinner! Everyone is invited, whether you&rsquo;re a longtime OBF member or someone who&rsquo;s never even heard of the OBF. (By the way, anyone who is involved in open source or open science is welcome to <a href="https://www.open-bio.org/wiki/Membership">join the OBF</a>, and there is no membership fee.) More details at <a href="https://gccbosc2018.sched.com/event/FCGp">https://gccbosc2018.sched.com/event/FCGp</a> We look forward to seeing some of you there!</p>https://www.open-bio.org/2018/05/25/travel-fellowships-april-2018/Fri, 25 May 2018 14:54:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/05/25/travel-fellowships-april-2018/<p>We had another great round of applications for the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF Travel Fellowship</a> this spring. After reviewing the applications, the OBF Board selected three recipients, who have all accepted the award.</p> <p>Congratulations to our spring 2018 recipients:</p> <ul> <li><a href="https://github.com/akeshavan">Anisha Keshavan</a> –  attended the <a href="https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018">eLife Innovation Sprint</a>. Anisha is a postdoctoral fellow at the University of Washington, where she develops open source code, including citizen scientist platforms for <a href="http://braindr.us/">image quality classification</a> and <a href="https://test.medulina.com/">image segmentation</a> ( <em>update</em> - see <a href="https://www.open-bio.org/2018/05/22/saving-science-from-itself-2018-elife-innovation-sprint/">blog post</a>).</li> <li><a href="https://github.com/FarahZKhan">Farah Zaib Khan</a> – attending <a href="https://gccbosc2018.sched.com/">GCCBOSC2018</a> including the CollaborationFest. Farah is a <a href="https://www.commonwl.org/">Common Workflow Language</a> contributor based at the University of Melbourne. She has recently been working on a project to record the <a href="https://github.com/common-workflow-language/cwltool/tree/provenance">provenance of CWL workflows</a>, and <a href="https://news.open-bio.org/2017/11/21/bosc-2017-prague-land-of-stories/">first attended BOSC in 2017</a> ( <em>update</em> - see <a href="https://www.open-bio.org/2018/08/18/city-of-roses-they-call-it-portland-oregon-usa/">blog post</a>).</li> <li>Tendai Mutangadura – attending <a href="https://gccbosc2018.sched.com/">GCCBOSC2018</a> including the CollaborationFest. Tendai is a first-time BOSC attendee who works at the University of Missouri and focuses on studying disease-causing mutations in <a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP049358">canine genomics</a> ( <em>update</em> - see <a href="https://www.open-bio.org/2018/08/29/the-color-of-bioinformatics/">blog post</a>).</li> </ul> <p>Watch this space for blog posts from each of the awardees ( <em>update - links added above</em>).</p> <p>The next deadline for travel awards is August 15. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community.The program is aimed at increasing diverse participation at such events. See the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel award</a> page for details and how to apply.</p>https://www.open-bio.org/2018/05/22/saving-science-from-itself-2018-elife-innovation-sprint/Tue, 22 May 2018 12:54:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/05/22/saving-science-from-itself-2018-elife-innovation-sprint/<p><em>This is a guest blog post from <a href="https://github.com/akeshavan">Anisha Keshavan</a>, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship</a> program to attend the <a href="https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018">2018 eLife Innovation Sprint</a> in Cambridge, May 2018. The OBF&rsquo;s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of <a href="https://news.open-bio.org/2018/05/25/travel-fellowships-april-2018/">three awards from our April 2018 travel fellowships call</a>. The current call closes 15 August 2018, you might want to apply?</em> It is hard for me to put into words the thrill, excitement, and inspiration I’m feeling after attending the 2 day eLife Innovation sprint on May 10th and 11th. The <em><strong>#eLifeSprint</strong></em> ( <a href="https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018">https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018</a>) in Cambridge, UK, brought together software developers, researchers, designers, and anyone who was passionate about leveraging web technology to advance open scientific communication. The goal: to save science from itself!</p> <p>What do I even mean by this? Well, let me explain how the process unfolds:</p> <ol> <li>Get some background knowledge on your topic of interest, read a bunch of publications and about all the experiments and theories up to this point in time <strong><em>#readallthepubs</em></strong></li> <li>Think of a new scientific hypothesis or theory, design an experiment to test it</li> <li>Write up <em>exactly</em> what you did in your experiment, the results, and your interpretation <strong><em>#reproduceit</em></strong></li> <li>Show your write up to your peers and have them review it &ndash; it’s their job to make sure what you did was legit, and that your results and  interpretation makes sense <strong><em>#sanitycheck</em></strong></li> <li>Share it with the scientific community and world, which adds to the growing pile of theories/evidence/background in 1. <em><strong>#sharetheknowledge</strong></em></li> </ol> <p>Sounds great. Why do we need to save science from itself?</p> <p><em><strong>#readallthepubs</strong></em>: Turns out, scientists are publishing SO MUCH that its nearly impossible to read and comprehend all the scientific literature out on the web. This is also called research debt (and here&rsquo;s a great article: <a href="https://distill.pub/2017/research-debt/">https://distill.pub/2017/research-debt/</a> )</p> <p><em><strong>#reproduceit</strong></em>: You&rsquo;d think computers would have made our lives easier because we can  automate data analyses, but actually reproducing an analysis is really difficult. Describing what the analysis code does in the methods section of a paper just doesn&rsquo;t cut it. And if another scientist can&rsquo;t reproduce an experiment, can we trust the original experiment&rsquo;s outcome?</p> <p><strong><em>#sanitycheck</em></strong>: Reviewing a paper well is a lot of work! Peer reviewers do this for free and anonymously, which sucks because they never get recognized for the work they put in. Understandably, its not a high priority to review papers in a timely manner, and this means that important research findings don&rsquo;t get published for a long time.<em><strong>#sharetheknowledge</strong></em>: Now that a scientist has read all the background on their topic of interest, designed and ran a reproducible experiment, and revised their manuscript based on peer review, they submit their article to a journal so that other scientists all over the world can read it. Usually, they <em>pay</em> the journal to publish their paper, and then other scientists also <em>pay</em> the journal to read the paper (Yes, these journals make BANK $$$). If you and your institution can&rsquo;t pay all the fees, that&rsquo;s a bummer. In fact, its a bummer for all of science! Progress is majorly hindered when bright, intelligent scientists with something to contribute to a field don&rsquo;t have access to vital information because they can&rsquo;t pay publishers. For example, <a href="https://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-ebola.html?_r=0">a Liberian physician doesn&rsquo;t have access to Ebola research articles because each article costs half a weeks salary</a>. Information needs to be open to everyone, regardless of how much money you have.</p> <p>Ok, so clearly science needs a major course correction. Enter: the 2018 eLife innovation sprint! In the following sections I&rsquo;ll list the project prototypes and links from the sprint that aim to correct one or more of the the four topics above.</p> <h2 id="readallthepubs">#readallthepubs</h2> <p><a href="https://appstract.pub">https://appstract.pub</a> :My team! We built a citizen science game to collect annotations on publications, so that we can run meta-analyses to summarize a large set of publications. You can compete with friends on the leaderboard, win badges, and contribute to science!<img src="https://pbs.twimg.com/media/Dc7Gw6PWsAA7AQk.jpg" alt="team appstract!"><a href="https://github.com/Samwalton9/WikiCiteVis">WikiCiteViz</a>:  A project to visualize citations, so you can see how a study has influenced other studies in the field.<a href="https://github.com/Bubblbu/zotero-insights">Zotero Insights</a>:  When you read papers, you can take notes in Zotero on a PDF. This project extracts all your notes (or annotations) and puts it into a machine-readable format, and creates reports and analyses of your notes<img src="http://citationgecko.com/" alt="Citation Gecko">: a way to find more relevant papers to read using citation data, and finds papers you may have missed.<a href="https://github.com/nlisgo/abstract-babel">Abstract Babel</a>: what it sounds like! Translate abstracts to different languages . I don&rsquo;t speak any other languages, but they say the translations are solid!</p> <p><a href="https://docs.google.com/presentation/d/1dM_HWimJ0SIfl9D3clhqKpxq04sLCVKOoNcxiHw0Myw/edit#slide=id.p">Funda</a>: a project <a href="https://docs.google.com/document/d/1R8AdItJ6cVivrCm6zWuMykz_rrCoj_o7vSMzNUQ6F7E/edit">roadmap</a> for teaching web literacy in South Africa.</p> <h2 id="reproduceit">#reproduceit</h2> <p>New technology has made our science experiments a little more complicated. We’re collecting a ton of data, and we write a lot of custom programs to crunch the numbers and make inferences. It turns out that sometimes what works on your computer won’t work on someone else’s! It can take a lot of CS skills to get the same analysis running on your computer, and that really slows us down. The following tools can help address this:<a href="https://github.com/popperized/open-comp-rsc-popper">Reproducible computational research</a>:a case study that shows reproducible computational neuroscience research using <a href="http://falsifiable.us/">Popper</a> and <a href="https://pythonhosted.org/Sumatra/">Sumatra</a> .<a href="https://github.com/dat-land/project-trackbook">Project Trackbook</a>:an open lab notebook that &ldquo;gives researchers an interface to securely share and version control files in a <em>decentralized</em> network&rdquo;.<a href="https://github.com/minrk/jupyter-dar/">Jupyter + Stencila</a>: combines some great tools: the <a href="http://stenci.la/">Stencila editor</a>, the <a href="http://jupyter.org/">Jupyter notebook</a>, and <a href="https://mybinder.org/">mybinder</a>, to create &ldquo;interactive, reproducible, and transparent&rdquo; scientific articles!</p> <h2 id="sanitycheck">#sanitycheck</h2> <p><a href="https://octopus-hypothesis.netlify.com/">Project Octopus</a>: This was probably the biggest group at the sprint, and covers both the <em>#sanitycheck</em> and <em>#sharetheknowledge</em>. On the octopus platform, you&rsquo;ll be able to review other scientist&rsquo;s work, and get credit for doing so! You should also checkout the blog on their website, which does <a href="https://octopus-hypothesis.netlify.com/blog/2018/05/13/2018-05-13_fixingscience/">a great job explaining in depth the problems we face in science, and how octopus can help</a>.<a href="https://github.com/SamanthaHindle/preprint_JournalClub">PREreview</a>: &quot; <em>Putting the ‘peer’ back into peer review!&quot;</em> Many scientists have started to upload their manuscripts to preprint servers, so that scientists can access the information before the lengthy peer-review and publication process. And this is really great for authors! For example, <a href="https://arxiv.org/pdf/1805.05238.pdf">here</a> is a preprint on how preprints that are posted before conference submission garner more citations than those posted after. PREreview is a platform for the &ldquo;collaborative writing of preprint reviews&rdquo; :) I found a very useful blog post on their site on <a href="https://prereview.org/users/164141/articles/200820-prereview-guidelines-how-to-write-a-preprint-review">guidelines for writing a preprint review</a>.</p> <h2 id="sharetheknowledge">#sharetheknowledge</h2> <p><a href="https://octopus-hypothesis.netlify.com/">Project Octopus</a>: On the octopus platform, all published work will be open to everython, and as a scientist, you&rsquo;ll be able to &ldquo;publish your hypotheses, methods, results and analyses in Octopus as you produce them, in whatever language you are most comfortable in&rdquo;.<a href="http://sarabosshart.wixsite.com/plauditpub">Plaudit</a>: It would be great if the value of the paper was not dependent on journal status, but instead on the quality of the work! Plaudit lets you publicly endorse an article, so that scientists don&rsquo;t have to worry about whether your article is published in a name brand journal, and it incentivizes open publishing and publishing preprints.</p> <h2 id="conclusions">Conclusions</h2> <p>Sometimes I feel really pessimistic about science, because of how inefficient and unfair it can be. But all the amazing participants at the eLifeSprint showed me that 1) SO many people care about these issues, 2) people have brilliant ideas and prototypes to address these issues, and 3) how many tools already exist, that I just didn&rsquo;t know about until I attended the sprint (I was excited to learn about the amazing <a href="https://openaccessbutton.org">openaccessbutton.org</a> API). Overall I left feeling very optimistic about the future of science! Thanks to Naomi Penfold and eLife for organizing this amazing event, and especially, <a href="https://news.open-bio.org/2018/05/25/travel-fellowships-april-2018/">thanks to OBF for the travel award</a> so that I could attend!</p>https://www.open-bio.org/2018/04/24/welcome-to-our-google-summer-of-code-2018-students/Tue, 24 Apr 2018 16:02:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/04/24/welcome-to-our-google-summer-of-code-2018-students/<p>The Open Bioinformatics Foundation is again participating in the Google Summer of Code program this year. Last Monday the selected students were announced. Congratulations to all of you, and a heartfelt welcome. I also want to use this opportunity to thank all students who applied. Resources were limited, we did not get all the slots that we asked for, and so we had to make some tough choices.  We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one, as you will find out.</p> <p>The Open Bioinformatics Foundation will host <a href="https://summerofcode.withgoogle.com/organizations/5340733272227840/#projects">six student projects</a> this year:</p> <ul> <li>Hitesh Joshi will be working on a Bionode workflow engine for streamed data analysis</li> <li>Synchon Mandal will be improving the constraint-based modeling in COBRApy</li> <li>Sophia Mersmann will improve the posterior error probability estimation for OpenMS peptide search engine results</li> <li>Edgar Garriga Nogales will implement support for Research Object specification into the Nextflow framework</li> <li>Sarthak Sehgal will be rewriting the front-end code powering the BioJS websites</li> <li>Megh Thakkar will be revamping the back-end of the BioJS websites</li> </ul> <p>Please join me in welcoming all of them to the Open  Bioinformatics community and the respective subprojects. I&rsquo;m sure we&rsquo;ll have a great, productive summer together.</p> <p>Kai Blin OBF administrator for GSoC 2018</p> <p>PS: We ask all our students to blog about their summer of code experience and will be updating this post with links to their respective blogs.</p>https://www.open-bio.org/2018/04/09/biojava-5-0-0-is-out/Mon, 09 Apr 2018 17:37:14 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/04/09/biojava-5-0-0-is-out/<p>BioJava 5.0.0 was released on the 23rd of March 2018. This represents a major milestone that brings more consolidation and reorganisation of modules. This is the first release to be based on Java 8, bring in your lambdas and stream API calls!</p> <p>The release represents work done in the last 2 years, alpha releases were available for quite some time and now this makes all the changes officially public.</p> <p>Some major refactoring occurred in the biojava-structure module. The data model to deal with macromolecular structures has been adapted to be closer to the mmCIF data model. Other improvements in biojava-structure are support for MMTF format and improved symmetry detection code.</p> <p>See the <a href="https://github.com/biojava/biojava/releases/tag/biojava-5.0.0">full release notes</a> or browse the official <a href="http://biojava.org/docs/api/">API documentation</a>.</p>https://www.open-bio.org/2018/04/04/biopython-1-71-released/Wed, 04 Apr 2018 15:32:14 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/04/04/biopython-1-71-released/<p>Dear Biopythoneers,</p> <p>Source distributions of Biopython 1.71 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the official <a href="http://biopython.org/">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.71">on the Python Package Index (PyPI)</a> including pre-compiled Wheel Packages for Linux, Mac OS X and Windows.</p> <p>This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now dropped support for Python 3.3). It has also been tested on PyPy2.7 v5.10.0 and PyPy3.5 v5.10.1.</p> <p>Python 3 is the primary development platform for Biopython. We will drop support for Python 2.7 no later than 2020, in line with the end-of-life or sunset date for Python 2.7 itself.</p> <p><em><strong>Setup changes:</strong></em></p> <p>We now explicitly recommend installation using &ldquo;pip install biopython&rdquo;, rather than the classic &ldquo;python setup.py install&rdquo; approach. In a related change, we depend on the Python package setuptools (rather than the older package distutils in the Python standard library) and have made the dependency on NumPy explicit and automatic.</p> <p><em><strong>License changes:</strong></em></p> <p>As of Biopython 1.69, we have started to dual-license Biopython under both our original liberal “Biopython License Agreement”, and the very similar but more commonly used “3-Clause BSD License”. A growing number of the Python files are explicitly available under either license, but most of the code remains under the “Biopython License Agreement” only. See the <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst">LICENSE</a> file for more details.</p> <p><em><strong>Code changes:</strong></em></p> <p>Encoding issues have been fixed in several parsers when reading data files with non-ASCII characters, like accented letters in people&rsquo;s names. This would raise <code>UnicodeDecodeError: 'ascii' codec can't decode byte ...</code> under some system locale settings.</p> <p>Bio.KEGG can now parse Gene files.</p> <p>The multiple-sequence-alignment object used by Bio.AlignIO etc now supports a per-column annotation dictionary, useful for richly annotated alignments in the Stockholm/PFAM format.</p> <p>The SeqRecord object now has a translate method, following the approach used for its existing reverse_complement method etc.</p> <p>The output of function <code>format_alignment</code> in <code>Bio.pairwise2</code> for displaying a pairwise sequence alignment as text now indicates gaps and mis-matches.</p> <p>Bio.SeqIO now supports reading and writing two-line-per-record FASTA files under the format name &ldquo;fasta-2line&rdquo;, useful if you wish to work without line-wrapped sequences.</p> <p>Bio.PDB now contains a writer for the mmCIF file format, which has been the standard PDB archive format since 2014. This allows structural objects to be written out and facilitates conversion between the PDB and mmCIF file formats.</p> <p>Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc wrapper and include a new wrapper for fuzzpro.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the November 2017 release of REBASE.</p> <p>New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2) were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain no dedicated stop codons; the stop codons in these codes have a context dependent encoding as either STOP or as amino acid.</p> <p>IO functions such as <code>SeqIO.parse</code> now accept any objects which can be passed to the builtin <code>open</code> function. Specifically, this allows using <code>pathlib.Path</code> objects under Python 3.6 and newer, as per <a href="https://www.python.org/dev/peps/pep-0519">PEP 519</a>.</p> <p>Bio.SearchIO can now parse InterProScan XML files.</p> <p>For Python 3 compatibility, comparison operators for the entities within a Bio.PDB Structure object were implemented. These allow the comparison of models, chains, residues, and atoms with the common operators (==, !=, &gt;, &hellip;) Comparisons are based on IDs and take the parents of the entity up to the model level into account. For consistent behaviour of all entities the operators for atoms were modified to also consider the parent IDs. NOTE: this represents a change in behaviour in respect to v1.70 for Atom comparisons. In order to mimic the behaviour of previous versions, comparison will have to be done for Atom IDs and alternative locations specifically.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python <a href="https://www.python.org/dev/peps/pep-0008">PEP8</a>, <a href="https://www.python.org/dev/peps/pep-0257">PEP257</a> and best practice standard coding style.</p> <p><em><strong>Acknowledgements:</strong></em></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Adhemar Zerlotini</li> <li>Ariel Aptekmann</li> <li>Chris Rands</li> <li>Christian Brueffer</li> <li>Erik Cederstrand (first contribution)</li> <li>Fei Qi (first contribution)</li> <li>Francesco Gastaldello</li> <li>James Jeffryes (first contribution)</li> <li>Jerven Bolleman (first contribution)</li> <li>Joe Greener (first contribution)</li> <li>Joerg Schaarschmidt (first contribution)</li> <li>João Rodrigues</li> <li>Jeroen Van Goey</li> <li>Jun Aruga (first contribution)</li> <li>Kai Blin</li> <li>Kozo Nishida</li> <li>Lewis A. Marshall (first contribution)</li> <li>Markus Piotrowski</li> <li>Michiel de Hoon</li> <li>Nicolas Fontrodona (first contribution)</li> <li>Peter Cock</li> <li>Philip Bergstrom (first contribution)</li> <li>rht (first contribution)</li> <li>Saket Choudhary</li> <li>Shuichiro MAKIGAKI (first contribution)</li> <li>Shyam Saladi (first contribution)</li> <li>Siong Kong</li> <li>Spencer Bliven</li> <li>Stefans Mezulis</li> <li>Steve Bond</li> <li>Yasar L. Ahmed (first contribution)</li> <li>Zachary Sailer (first contribution)</li> <li>Zaid Ur-Rehman (first contribution)</li> </ul> <p>Thank you all.</p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a> <em><strong>Checksums</strong></em>:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.71* </span></span><span style="display:flex;"><span>b2cd1215bacfb7cb9ee73b6b67695da0 biopython-1.71-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>a85b46133003383e428b05895e5d3613 biopython-1.71-cp27-cp27m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>89e368cbcb6517915ee371f27f459b90 biopython-1.71-cp27-cp27m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>395e12573e9a56130489aafe3617e254 biopython-1.71-cp27-cp27mu-manylinux1_i686.whl </span></span><span style="display:flex;"><span>f80e811aeebf9241e03a6ef3d4c9d9c6 biopython-1.71-cp27-cp27mu-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>b98d04351a94eb94a95e57c4ded460c2 biopython-1.71-cp27-cp27m-win32.whl </span></span><span style="display:flex;"><span>4997d76f075f4840d82f7d596917ba92 biopython-1.71-cp27-cp27m-win_amd64.whl </span></span><span style="display:flex;"><span>47b6e58c03599b4e8a5534efa9171d0c biopython-1.71-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>53df08929d39abda3c0b668d7d06456c biopython-1.71-cp34-cp34m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>d308f83c49dc38395928348628d24238 biopython-1.71-cp34-cp34m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>a2f05c067222c31091ad97c6c394e54d biopython-1.71-cp34-cp34m-win32.whl </span></span><span style="display:flex;"><span>b5f26e1288f5124a2a02ffeab7139650 biopython-1.71-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>0f5e731a17b3d5798347a21b88224583 biopython-1.71-cp35-cp35m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>4f1fa297348d4797acab537b44480aaa biopython-1.71-cp35-cp35m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>cf859db69d1c182f133cd34774ff15ca biopython-1.71-cp35-cp35m-win32.whl </span></span><span style="display:flex;"><span>9eb34690189f4c156157e0991852bb56 biopython-1.71-cp35-cp35m-win_amd64.whl </span></span><span style="display:flex;"><span>80cf17e84f22a4ea61e7394a521500f9 biopython-1.71-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>09fbad06133a8b2b9c3d20faa0d6a156 biopython-1.71-cp36-cp36m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>d7e15723aac481d945289d179a52a9f9 biopython-1.71-cp36-cp36m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>80c03614cb3b4c486793e6e31c62403d biopython-1.71-cp36-cp36m-win32.whl </span></span><span style="display:flex;"><span>dc7149f7297176bf0c8ca80fa176ecb0 biopython-1.71-cp36-cp36m-win_amd64.whl </span></span><span style="display:flex;"><span>966ac542f39809c37852410a95f641fb biopython-1.71.tar.gz </span></span><span style="display:flex;"><span>4c63ec2a2908adf8d3338f8e8b180514 biopython-1.71.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.71* </span></span><span style="display:flex;"><span>f919aa78031c00e44350742331f5a1eed7b447bde7812abe2ca0f6a5165900bb biopython-1.71-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>7449d7df74a298c190fbc9ad60591577acb2e45d5ff788faa8672df460f3dc4d biopython-1.71-cp27-cp27m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>3fdf4c9502404dd62905fd70bce57806cb775e636eede5de13f1abe8f0915158 biopython-1.71-cp27-cp27m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>4960e0ec35de8b02cd0b6a720db623abf30931a5677046ec06c0097b6a565541 biopython-1.71-cp27-cp27mu-manylinux1_i686.whl </span></span><span style="display:flex;"><span>4e4c6fe00e1d49e016634602e8554380ec437b505d8f20132da408a37da560ce biopython-1.71-cp27-cp27mu-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>65f00db00b2f91ba90e5bb61c7dd14d2beacb9f2d3e60c9d4330376b693d8975 biopython-1.71-cp27-cp27m-win32.whl </span></span><span style="display:flex;"><span>6318172b107ad72abf45a03de6a189a3e7cfc2e682d402520c14bbbe8295e335 biopython-1.71-cp27-cp27m-win_amd64.whl </span></span><span style="display:flex;"><span>5b7284947a4b657d7955d0af8c48594be62a4d8dd51b84223fded371e81911d6 biopython-1.71-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>20fbbbc0f1c2f11972ea598191ba2cd8cb7ecb38595fa89031b9c3974ebcbdff biopython-1.71-cp34-cp34m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>9fabcb8cd0a87c5e2514bc959f5504ea5dc58219bc2ff91e6c689279322319c6 biopython-1.71-cp34-cp34m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>038ecb2376cbfd2b42e79f64fe96ffb4921fecacad6f5157b684168933320455 biopython-1.71-cp34-cp34m-win32.whl </span></span><span style="display:flex;"><span>b7782271639fb92ea7fde4ad1caeeed3ca4ba6795de81bde391a4ea21e3870fb biopython-1.71-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>14067b4ae2596979fd82a1e61fafbf2f8acd81f547b09220d8f4d7642a2b3759 biopython-1.71-cp35-cp35m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>1c6190b552c5b9e2b2b7456ecc5258f344b1afee63c1d656b610a5c1a4b52b3f biopython-1.71-cp35-cp35m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>23580bf169d044cc749819465520f33579c62ce06816f87f814e4a78fdd48877 biopython-1.71-cp35-cp35m-win32.whl </span></span><span style="display:flex;"><span>f2603eeb09a7eef41eb81d874901c02e848ad80776f9e80d91b15206e7c4441d biopython-1.71-cp35-cp35m-win_amd64.whl </span></span><span style="display:flex;"><span>9f800d7db93685a73fe244d16ab76dec91e51ddcde20a3f9e8dffa3d05170d96 biopython-1.71-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl </span></span><span style="display:flex;"><span>4b7f6552b4d9162ca90bc0515a93815a7d81b8b0435932ab0aaf2affc53b40f6 biopython-1.71-cp36-cp36m-manylinux1_i686.whl </span></span><span style="display:flex;"><span>6ac8e5c2f6ffa1190a491ccc5f00e004d05107abf9879ebdff202088be31d02a biopython-1.71-cp36-cp36m-manylinux1_x86_64.whl </span></span><span style="display:flex;"><span>693e9f2955393438613a431fe9b308d3d39a30923fe1efd32e0000c83feda6e3 biopython-1.71-cp36-cp36m-win32.whl </span></span><span style="display:flex;"><span>dccb66a68968c4c76a7ec92d82e44abf8721a2f65c9afb7acdc3deb2457b7b4e biopython-1.71-cp36-cp36m-win_amd64.whl </span></span><span style="display:flex;"><span>4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033 biopython-1.71.tar.gz </span></span><span style="display:flex;"><span>08e2123c043cbfc4faf483fd59857b7df95662ac706ad9c3c9ef34d7a41b1d2d biopython-1.71.zip </span></span></code></pre></div>https://www.open-bio.org/2018/03/20/welcome-to-our-new-board-members/Tue, 20 Mar 2018 20:43:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/03/20/welcome-to-our-new-board-members/<p>As mentioned in <a href="https://news.open-bio.org/2018/03/05/march_2018_board_meeting/">our previous blog post</a>, last Friday the OBF had a board of directors meeting. <a href="https://www.open-bio.org/wiki/Minutes:2018_Mar_ConfCall">One of the notable meeting items this time</a> was to elect more board members to help be involved with the community. We’re pleased to announce that both candidates, <a href="https://twitter.com/gedankenstuecke">Bastian Greshake Tzovaras</a> and <a href="https://twitter.com/yoyehudi">Yo Yehudi</a>, were unanimously voted in by the other board members!Logically, one of their first moves as newly minted members was to draft this blog post! Some of the their possible ideas for the future include:</p> <ul> <li>Applying to participate as a mentor organisation in <a href="https://www.outreachy.org/">Outreachy</a> - a program similar to <a href="https://news.open-bio.org/">Google Summer of Code</a>, but specifically dedicated to increasing diversity in open source.</li> <li>Growing our network and connecting more closely with like-minded organizations in the open science-space</li> </ul> <p>If any of these sound of interest and you’d like to be involved, please let us know by leaving a comment on this post, mailing the main <a href="http://mailman.open-bio.org/mailman/listinfo/members">OBF mailing group</a> (membership required), or tweeting <a href="https://twitter.com/obf_news">@obf_news</a>. We’re especially keen to hear if any of you have other suggestions for things you’d like to see to help build the community!</p>https://www.open-bio.org/2018/03/16/minutes2018-mar-confcall/Fri, 16 Mar 2018 05:46:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/03/16/minutes2018-mar-confcall/<h2 id="dial-in-information">Dial-in information</h2> <ul> <li>Dial-in Information: +1-857-216-2939</li> <li>PIN: 62534</li> <li><a href="http://www.uberconference.com/hlapp">http://www.uberconference.com/hlapp</a></li> </ul> <h2 id="agenda">Agenda</h2> <p><strong>Venue:</strong> To be held by conference call on March 16, 2018, 11.00am EDT (15:00 UTC, 16:00 CET, 8.00am PDT). <em>Note that at the time of the meeting, the US will have switched already to DST, whereas Europe will not, so the time zone difference is an hour less than it would normally be.</em> <strong>Dial-in Information:</strong> +1-857-216-2939 PIN: 62534 <a href="http://www.uberconference.com/hlapp">http://www.uberconference.com/hlapp</a></p> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2016_Oct_ConfCall">Oct 2016 BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>Term expirations and Elections for the Board ( <a href="https://vote.heliosvoting.org/helios/e/obf-mar-2018">electronic ballot</a>) <ul> <li>Bastian Greshake Tzovaras, running for Board member at-large</li> <li>Yo Yehudi, running for Board member at-large</li> </ul> </li> <li>Fiscal sponsor - experiences, lessons, possibilities</li> </ol> </li> </ol> <h2 id="minutes">Minutes</h2> <p><strong>Attending:</strong></p> <ul> <li><strong>Directors</strong>: Hilmar Lapp, Peter Cock, Heather Wiencko, Nomi Harris, Chris Field, Karen Cranston</li> <li><strong>Guests</strong>: Bastian Greshake Tzovaras, Yo Yehudi</li> </ul> <p>Meeting called to order at 11.03am EDT, 15:03 UTC.</p> <h3 id="old-business">Old business</h3> <ul> <li>Oct 2016 BoD meeting minutes <ul> <li>Approved - Hilmar raised, Peter second, approved by unanimous consent</li> <li><a href="https://www.open-bio.org/wiki/Minutes:2016_Oct_ConfCall">2016 Oct ConfCall minutes</a> approved unanimously</li> </ul> </li> </ul> <h3 id="new-business">New business</h3> <p>Hilmar welcomed B and Y and asked them to introduce themselves.</p> <ul> <li>Term expirations and Elections for the Board (electronic ballot)</li> <li>Introduction - Bastian Greshake Tzovaras, running for Board member at-large <ul> <li>Many many different open-source/science projects (OpenSNP is only one)</li> <li>Mozilla!</li> <li>Would like to get the OBF name out there, be more</li> </ul> </li> <li>Introduction - Yo Yehudi, running for Board member at-large <ul> <li>Intermine</li> <li>Open Science - increase open source in open science</li> <li>Also involved with Mozilla</li> <li>SSI fellow this year</li> <li>Outreachy - not just GSoC but WiS, increasing diversity</li> </ul> </li> <li>We have quorum for voting <ul> <li>6/6 votes for Bastian and 6/6 votes for Yo!  Congrats to both!</li> <li>Action on Hilmar to add them to the Board mailing list etc.</li> </ul> </li> <li>Fiscal sponsor - experiences, lessons, possibilities <ul> <li>Our fiscal sponsor is SPI (<a href="https://spi-inc.org">https://spi-inc.org</a>). <ul> <li>Dissolved our own incorporation and became an SPI associated project in 2012 (<a href="https://news.open-bio.org/2012/10/12/obf-now-spi-associated/)">https://news.open-bio.org/2012/10/12/obf-now-spi-associated/)</a>.</li> <li>Having a fiscal sponsor allows us to receive tax-exempt donations (501(c)3 in the US), without having to spend the effort of obtaining and maintaining our own 501(c)3 non-profit status.</li> <li>One of the reasons we chose SPI over others was the good cultural fit (SPI is relatively hands-off) and tie-in with Debian-based bioinformatics community efforts (DebianMed).</li> </ul> </li> <li>Encountered a number of pain points over the years <ul> <li>Financial reporting is behind and slow</li> <li>Travel fellowships generally come from BOSC account - pretty quick</li> <li>Other reimbursements from SPI generally take longer</li> <li>Lack of financial reporting sometimes for extended periods of time, which makes it difficult to verify receipt of sponsorship commitments, for example.</li> <li>Transferring some of our domain name assets to SPI did not go smoothly, many delays. Sysadmin side of SPI is too slow and unresponsive to be considered functional.</li> <li>AWS billing on someone’s personal credit card (and reimbursing later) is a high risk for the individual.</li> </ul> </li> <li>There are more alternatives now than there were back in 2012. This might be a good time to consider their pros and cons. <ul> <li>OpenCollective <a href="https://opencollective.com/">https://opencollective.com/</a> <ul> <li><a href="https://opencollective.com/apply">Application form</a></li> <li>Yo came across OpenCollective for a project of her own. Very attractive, but need &gt;100 stars. Several OBF Bio* projects would fit this.</li> </ul> </li> <li>NumFOCUS, Community Initiatives <a href="http://communityin.org/">http://communityin.org/</a> <ul> <li>The joint Carpentries just moved from NumFOCUS to Community Initiatives. See blog post: <a href="https://software-carpentry.org/blog/2018/01/fiscal-sponsor-transition.html">https://software-carpentry.org/blog/2018/01/fiscal-sponsor-transition.html</a></li> <li>We probably don’t fit the annual budget and revenue size that CI is looking for in their fiscally sponsored projects.</li> <li>NumFOCUS fiscally sponsors many projects that tie into our community and mission. Much of what motivated the Carpentries to move probably doesn’t apply to OBF.</li> </ul> </li> </ul> </li> <li>SPI community includes associated projects that are similar to us, and hence should still be a good fit. The challenges seem to be precipitated by SPI not having paid staff, hence little to no accountability for meeting service level standards.</li> </ul> </li> </ul> <p>Any other business?</p> <ul> <li>H3ABionet interaction - promotion of open science and open source across Africa</li> </ul> <p>Hilmar moves to adjourn meeting at 11.51am EDT, 15:51 UTC. Peter seconds, approved by unanimous consent.</p>https://www.open-bio.org/2018/03/05/march_2018_board_meeting/Mon, 05 Mar 2018 16:37:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/03/05/march_2018_board_meeting/<p>The <a href="https://www.open-bio.org/wiki/Board">OBF Board of Directors</a> holds a public meeting about once a year, in accordance with our <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">bylaws</a>. The next such meeting will take place on <strong>March 16, 2018</strong>, at 15:00 UTC (11am EDT / 8am PDT / 16:00 CET). The meeting agenda can be found at <a href="https://www.open-bio.org/wiki/Minutes:2018_Mar_ConfCall">/wiki/Minutes:2018_Mar_ConfCall</a>.</p> <p>At this public Board meeting, we will consider two new candidates running for Board seats: Bastian Greshake Tzovaras and Yo Yehudi. Both are known for their promotional and organizational involvement in open science, open data and open source bioinformatics.</p> <p><a href="https://twitter.com/gedankenstuecke?lang=en">Bastian</a> has been active in the larger field of Open Science since 2010, when he helped to run a successful petition for the German legislative to overhaul their Open Access policies. He is the co-founder of <a href="https://opensnp.org/">openSNP</a> and currently serves as the Director of Research at <a href="https://www.openhumans.org/about/">Open Humans</a>. He mentors open science projects as part of the Mozilla Science Lab mentorship programs. Bastian recently earned a PhD in bioinformatics from the University of Frankfurt. He is on the <a href="https://www.open-bio.org/wiki/BOSC_2018">BOSC</a> organizing committee.</p> <p><a href="https://twitter.com/yoyehudi">Yo</a> works on software and community outreach for <a href="http://intermine.org">Intermine</a> at the University of Cambridge. and is a passionate advocate of open* in research. She runs a project called <a href="http://www.codeisscience.com/">Code is Science</a>, dedicated to increasing the number of publications about scientific software that include Open Source code. Yo tweets about open science and open bioinformatics (for example, at <a href="https://medium.com/plos-comp-biol-field-reports-2016/bosc-2017-day-1-fbe73f01de2e">BOSC 2017</a>). She hopes to apply her scientific communication and outreach skills to help the OBF grow and deepen its community impact.</p> <p>During the March 16 public Board meeting, the two candidates will introduce themselves, and the current board members will vote via secret (though verifiable) electronic ballots. Additionally, the minutes from the previous BoD meeting and the financial reports for previous years will be presented and approved.</p> <p>All members of OBF are invited to join us for this meeting. Membership in OBF is free and open to anyone who is interested in and aligned with the objectives of the organization. If you would like to apply for membership, please visit <a href="https://www.open-bio.org/wiki/Membership">/wiki/Membership</a>.</p> <p>Meeting time: March 16, 2018, 11.00am EDT (15:00 UTC, 16:00 CET, 8.00am PDT). Note that at the time of the meeting, the US will have switched already to DST, whereas Europe will not, so the time zone difference is an hour less than it would normally be. Dial-in Information: +1-857-216-2939 PIN: 62534 <a href="http://www.uberconference.com/hlapp">http://www.uberconference.com/hlapp</a></p>https://www.open-bio.org/2018/02/23/obf-accepted-as-a-mentoring-organisation-for-google-summer-of-code-2018/Fri, 23 Feb 2018 10:51:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/02/23/obf-accepted-as-a-mentoring-organisation-for-google-summer-of-code-2018/<p>The Open Bioinformatics Foundation has been accepted as a <a href="https://summerofcode.withgoogle.com/organizations/5340733272227840/">mentoring organisation</a> for the <a href="https://opensource.googleblog.com/2018/02/gsoc-2018-organizations.html">2018 instance of the Google Summer of Code</a>. OBF is acting as an umbrella for ten bioinformatics Open Source projects, making it possible to offer a <a href="http://obf.github.io/GSoC/ideas/">very diverse set of student projects</a>.</p> <p>Are you a student and interested in applying for any of the projects? The student application period is open from March 12th through 27th from the <a href="https://summerofcode.withgoogle.com/">official GSoC website</a>. See the full <a href="https://summerofcode.withgoogle.com/how-it-works/#timeline">timeline</a> for details. Feel free to contact the mentors of projects you are interested in already, though.</p>https://www.open-bio.org/2018/02/21/gccbosc-2018-a-bioinformatics-community-conference-call-for-abstracts/Wed, 21 Feb 2018 10:07:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/02/21/gccbosc-2018-a-bioinformatics-community-conference-call-for-abstracts/<p><a href="https://gccbosc2018.sched.com/"><img src="https://news.open-bio.org/wp-content/uploads/2018/02/gcc-bosc-2018-logo-boxed-150.png" alt="Logo"></a></p> <p>We are pleased to announce that abstract submission and early registration for <a href="https://gccbosc2018.sched.com/">GCCBOSC2018</a> are now open. This event brings our annual <strong>Bioinformatics Open Source Conference</strong> and the <strong>Galaxy Community Conference</strong> together into a unified week-long event. If you work in open source life science or data-intensive biomedical research, then there is no better place than <strong>GCCBOSC 2018</strong> to present your work and to learn from others.</p> <p><strong>Dates</strong>: June 25-30, 2018 <strong>Location</strong>: Reed College, Portland, OR <strong>GCCBOSC website</strong>: <a href="https://gccbosc2018.sched.com/">https://gccbosc2018.sched.com/</a> <strong>BOSC website:</strong> <a href="https://www.open-bio.org/wiki/BOSC_2018">/wiki/BOSC_2018</a> <strong>Email BOSC organizers</strong> <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> <strong>BOSC announcements mailing list</strong>: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a> <strong>Twitter</strong>: <a href="https://twitter.com/OBF_BOSC">@OBF_BOSC</a>, <a href="https://twitter.com/search?q=%23GCCBOSC">#GCCBOSC</a></p> <h1 id="important-dates">Important Dates</h1> <ul> <li><strong><a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">Abstract submission</a> deadline: March 16, 2018</strong></li> <li>Authors notified: April 10, 2018</li> <li><a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Travel fellowship</a> application deadline: April 15, 2017</li> <li>GCCBOSC 2018 Training: June 25-26, 2018</li> <li>GCCBOSC 2018 Talks: June 27-28</li> <li>GCCBOSC CollaborationFest: June 29-30</li> </ul> <h1 id="about-bosc">About BOSC</h1> <p>Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.</p> <h1 id="why-is-bosc-partnering-with-gcc-in-2018">Why is BOSC partnering with GCC in 2018?</h1> <p>In past years, BOSC has been part of the ISMB conference. Because of our continuing focus on broadening and deepening the BOSC community, we&rsquo;ve been exploring ways to reach those in the bioinformatics community who aren’t already part of the audience attracted by ISMB. As part of that exploration, we have looked at other organizations and conferences that have been successful at establishing a strong and growing community of participants, such as the Galaxy Community Conference (GCC).</p> <p>After much discussion and planning, we decided to hold BOSC in conjunction with GCC in 2018. We hope that this will be an enjoyable and productive experience for all participants, and we welcome your feedback before, during and after the event.</p> <p>As always, BOSC 2018 will include two days of talks and posters, two <a href="https://galaxyproject.org/events/gccbosc2018/keynotes/">keynote speakers</a>, a panel discussion, Birds of a Feather, and more. BOSC sessions will run in parallel with GCC 2018 sessions, with some sessions shared. The two days of talks will be preceded by two days of <a href="https://galaxyproject.org/events/gccbosc2018/training/">training</a> on topics nominated by the community, and will be followed by a two-day CollaborationFest that merges BOSC&rsquo;s Codefest and Galaxy&rsquo;s Developer and User Hackathon Days.</p> <h1 id="abstract-submission">Abstract submission</h1> <p>We encourage you to submit one-page abstracts (due March 16) on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, demos and/or posters. Abstract submission instructions and a link to the EasyChair submission portal can be found on <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">/wiki/BOSC_Abstract_Submission</a> <strong>BOSC session topics include</strong> (but are not limited to):</p> <ul> <li>Open Science and Reproducible Research</li> <li>Open Biomedical Data</li> <li>Citizen/Participatory Science</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Workflows</li> <li>Visualization</li> <li>Medical and Translational Bioinformatics</li> <li>Developer Tools and Libraries</li> <li>Bioinformatics Open Source Project Progress Reports</li> </ul> <p>We look forward to receiving your abstract and meeting you at GCCBOSC 2018!</p> <p>Sincerely,</p> <p>BOSC 2018 Organizing Committee: Nomi Harris (chair), Heather Wiencko (co-chair), Brad Chapman (co-chair), Peter Cock, Christopher Fields, Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres</p> <p>P.S. Don&rsquo;t forget to submit your BOSC abstract by March 16 at <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">/wiki/BOSC_Abstract_Submission</a>! Please share this announcement with your colleagues!</p>https://www.open-bio.org/2018/02/11/obf-travel-fellowship-coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/Mon, 12 Feb 2018 00:59:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/02/11/obf-travel-fellowship-coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/<p><em>This blog post is syndicated from a <a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/">post on Arun Decano&rsquo;s blog</a>, originally published Feb 1, 2018. Arun was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship program</a> to attend a Galaxy Admin Workshop held in Oslo, Norway Jan 7-14, 2018.</em> <em>The OBF&rsquo;s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 April 2018.</em></p> <p>Sharing highlights of my unforgettable experience in the snowy white city of Oslo, Norway from the 7th to the 14th of January, 2018.</p> <p>I submitted a last-minute application for the <a href="https://www.elixir-europe.org/events/european-galaxy-administrator-workshop">Galaxy Admin workshop</a> in the University of Oslo so I was extremely delighted when Dr. Nygard dropped me a message confirming my place for the training. I was thrilled with both the thought of learning how to customize my own Galaxy server and traveling to the <a href="http://www.oslobusinessregion.no/oslo-world-winter-capital/">winter capital of the world</a>!</p> <p>I had a limited understanding about how Galaxy servers work as we have have our own server in the lab. But I knew that Galaxy offers various <a href="https://galaxyproject.github.io/training-material/">efficient pipelines</a> for large genomic data analysis so I was  curious how to get started with it.</p> <p>The facilitators of the training were very prompt in setting our expectations for the event. They constantly sent e-mails with tips on how to get around Oslo and which hotel offers the best yet affordable accommodation. I booked a place in Airbnb for mine so not only did I get trained with Galaxy server administration but I also had a first-hand information about the city from a local. I stayed in 2 different places: somewhere in Blindern during the entire workshop and another one in Rosenborg (close to the city center) for the weekend before my flight back to Dublin. <img src="https://arundecano.files.wordpress.com/2018/02/img-20180112-wa0005.jpg?w=1024&amp;h=768" alt="">View from my Airbnb flat in Blindern The sky was clear and the sun was out on our first day of training. Our instructors, who came from different parts of the world were also the main code contributors to the <a href="https://galaxyproject.github.io/">Galaxy project</a> so everyone was enthusiastic to learn from them.</p> <p>Our training jumpstarted with modules on how to install and deploy Galaxy program via PostgreSQL and nginx databases and basic pre-requisites or dependencies for running the server. We were also taught how to further extend Galaxy installation and customize our “brand” to what we need the server for.</p> <p><a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/mvdoslopic/"><img src="https://arundecano.files.wordpress.com/2018/02/mvdoslopic.jpg?w=150&amp;h=113" alt=""></a><a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/img_20180108_190035_851/"><img src="https://arundecano.files.wordpress.com/2018/02/img_20180108_190035_851.jpg?w=150&amp;h=102" alt=""></a></p> <p>The event organizers arranged a get-together dinner for us the next day. We went to <a href="http://www.cafeelias.no/nb/">Cafe Elias Mat &amp; Sant</a> in the city center and had traditional Norwegian dishes: my favorite was the sautéed reindeer! I can’t stop thinking about the poor <em>Rudolph the red-nosed reindeer</em> though the entire time I was eating dinner. <img src="https://s1.wp.com/wp-content/mu-plugins/wpcom-smileys/uneasy.svg" alt=":/"><a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/#gallery-404-1-slideshow">Click to view slideshow.</a></p> <p>The snow started falling hard come Wednesday yet we continued on with our training about the specifics of Galaxy server administration. <img src="https://arundecano.files.wordpress.com/2018/02/img_20180111_210420_640.jpg?w=240&amp;h=300" alt="">Snow-proof. Even though we had to debug the scripts real-time and as we went along with the workshop, I have to say that our instructors were very keen with time and were very efficient in handling technical challenges. We discussed how to tailor fit the Galaxy configuration file and how to use Ansible to deploy the server.</p> <p>Thursday was scheduled for us participants to deliver lightning talks. Some presented how to link a customized Galaxy server to a larger local (i.e. university) server and others talked about issues they encountered when uploading tools from different providers other than <a href="https://toolshed.g2.bx.psu.edu/">Tool Shed</a>. Everyone had interesting new ideas and expressed their willingness to help address the difficulties raised. It was a very engaging day! <img src="https://arundecano.files.wordpress.com/2018/02/oslo-admin-class.jpg?w=1075" alt="">Taken from Galaxy Project news site: <a href="https://galaxyproject.org/galaxy-updates/2018-02/">https://galaxyproject.org/galaxy-updates/2018-02/</a> Fast-forward to the last day of our workshop: we covered all the topics as scheduled and more! The instructors gave us additional tips and workarounds (that were not listed in the syllabus) on how to create and manage our own Galaxy server. Dr. Björn Grüning of Galaxy-Frieburg and Dr. Marius van den Beek of Curie Institute, Paris also demonstrated several ways to troubleshoot installation failures, Tool errors and non-running jobs in Galaxy. For all the modules presented, we always had a prepared exercise so the training was indeed hands-on.</p> <p>We capped our very productive workshop by going to a bar and restaurant for a celebratory dinner by the harbor. People were playing BINGO when I got there which added to the already-celebrating atmosphere. One of my classmates won a box of essential oils for completing a round! Myself and one of the instructors almost won as well but we failed to shout “BINGO!” as soon as our last missing number was called so the prize was given to someone else! Ahh but it was fun! We all had a great time. <img src="https://s0.wp.com/wp-content/mu-plugins/wpcom-smileys/twemoji/2/72x72/1f642.png" alt="🙂"><a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/img_20180112_235636_778/"><img src="https://arundecano.files.wordpress.com/2018/02/img_20180112_235636_778.jpg?w=150&amp;h=84" alt=""></a><a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/img_20180112_235636_781/"><img src="https://arundecano.files.wordpress.com/2018/02/img_20180112_235636_781.jpg?w=150&amp;h=84" alt=""></a></p> <p>We all then took a walk and went back to our own quarters. Many of us had to fly back home the next day but I stayed for the weekend and visited some historical spots in the city. I also took Metro #1 and went all the way to the last station to spend a little time in the Winter Park before the sky turned pitch black again in the afternoon.</p> <p><a href="https://arundecano.wordpress.com/2018/02/01/coding-in-the-winter-wonderland-galaxy-admin-training-in-oslo-2018/#gallery-404-2-slideshow">Click to view slideshow.</a></p> <p>I flew back to Ireland the next day full of these exciting memories and new knowledge about Galaxy server administration.</p> <p>I especially want to thank the Open Bioinformatics Foundation (OBF) Board for choosing me for their <a href="https://news.open-bio.org/2018/01/30/arun-decano-awarded-obf-travel-fellowship/">Travel Award</a> and offering to defray the cost of this wonderful trip! More power to OBF!</p>https://www.open-bio.org/2018/01/30/arun-decano-awarded-obf-travel-fellowship/Wed, 31 Jan 2018 00:40:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/01/30/arun-decano-awarded-obf-travel-fellowship/<p><img src="https://news.open-bio.org/wp-content/uploads/2018/01/ArunDecano_profile-300x300.jpg" alt="Arun Decano"> Arun Decano is a PhD research fellow in the Infection Genomics Group at Dublin City University in Dublin, Ireland. Her research, with advisor <a href="https://www.dcu.ie/biotechnology/people/tim-downing.shtml">Dr. Tim Downing</a>, focuses on the phylogenomic study of a multidrug-resistant bacterial population and aims to develop novel infection control strategies using whole genome sequence data.</p> <p>The Open Bioinformatics Foundation awarded Ms. Decano a <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">travel fellowship</a> to help defray the cost of attending the European Galaxy Administrator Workshop ( <a href="https://www.elixir-europe.org/events/european-galaxy-administrator-workshop">https://www.elixir-europe.org/events/european-galaxy-administrator-workshop</a>) in January 2018.</p> <p>The <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship</a> program was launched in 2016 to help increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The next application deadline will be April 15, 2018—see <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md</a> for information and to apply.</p>https://www.open-bio.org/2017/12/15/mailing-list-consolidation/Fri, 15 Dec 2017 19:52:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/12/15/mailing-list-consolidation/<p>The OBF&rsquo;s self-hosted <a href="https://news.open-bio.org/2017/11/12/mailing-list-outage-and-public-board-meeting-update/">mailman server is still struggling</a> right now, so we are looking at migrating the active mailing lists to paid hosting, and as part of this consolidating down to ideally about a dozen mailing lists. Currently we have a <em>lot</em> of mailing lists, but many are dormant or redundant.</p> <p>Some were announcement specific, where nowadays blogs and Twitter work quite well. Others were development specific (including automatic commit logs from central source code repositories), but now most OBF Project discussions are on GitHub. While the main project mailing lists used to have a lot of user support traffic, much of that has moved to external Q&amp;A style sites like BioStars, StackExchange, or StackOverflow. What this means is that the OBF software projects probably only need a single mailing list each.</p> <p>Based on <a href="http://mailman.open-bio.org/mailman/listinfo">http://mailman.open-bio.org/mailman/listinfo</a> here are the current publicly listed OBF hosted mailing lists.</p> <p>Miscellaneous active public lists (propose to retain in some form):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bosc-announce/">Bosc-announce</a> - BOSC meeting announcements and updates ( <a href="http://mailman.open-bio.org/pipermail/bosc-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/gsoc/">GSoC</a> - OBF mentors and students for Google Summer of Code ( <a href="http://mailman.open-bio.org/pipermail/gsoc/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/open-bio-l/">Open-Bio-l</a> - Open Bioinformatics Foundation cross-project dev discussion ( <a href="http://mailman.open-bio.org/pipermail/open-bio-l/">archive</a>)</li> </ul> <p>Miscellaneous active but non-public lists (propose to retain in some form):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioinfo-core/">bioinfo-core</a> - Managers, Staff, and Scientists of Bioinformatics, Data Science and Research IT core facilities ( <a href="http://mailman.open-bio.org/mailman/private/bioinfo-core/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/gsoc-mentors/">Gsoc-mentors</a> - GSoC - mentors only ( <a href="http://mailman.open-bio.org/mailman/private/gsoc-mentors/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/members/">Members</a> - Communication channel to OBF members ( <a href="http://mailman.open-bio.org/mailman/private/members/">private archive</a>)</li> </ul> <p>BioPerl (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bio-phylo-l/">Bio-phylo-l</a> - BioPerl Phylogenetics modules ( <a href="http://mailman.open-bio.org/pipermail/bio-phylo-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-announce-l/">BioPerl-announce-l</a> - Bioperl Project Announcements ( <a href="http://mailman.open-bio.org/pipermail/bioperl-announce-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-dev/">bioperl-dev</a> - BioPerl Developer Core ( <a href="http://mailman.open-bio.org/pipermail/bioperl-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-guts-l/">BioPerl-guts-l</a> - BioPerl internals &amp; bug reports ( <a href="http://mailman.open-bio.org/mailman/private/bioperl-guts-l/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l/">BioPerl-l</a> - Bioperl Project Discussion List ( <a href="http://mailman.open-bio.org/pipermail/bioperl-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-microarray/">bioperl-microarray</a> - Microarrays in BioPerl ( <a href="http://mailman.open-bio.org/pipermail/bioperl-microarray/">archive</a>)</li> </ul> <p>BioJava (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev/">BioJava-dev</a> - BioJava developers list ( <a href="http://mailman.open-bio.org/pipermail/biojava-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l/">BioJava-l</a> - Biojava discussion list ( <a href="http://mailman.open-bio.org/pipermail/biojava-l/">archive</a>)</li> </ul> <p>Biopython (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biopython/">Biopython</a> - Biopython discussion list ( <a href="http://mailman.open-bio.org/pipermail/biopython/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-announce/">Biopython-announce</a> - Biopython announcements and news ( <a href="http://mailman.open-bio.org/pipermail/biopython-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev/">Biopython-dev</a> - Biopython Developers List ( <a href="http://mailman.open-bio.org/pipermail/biopython-dev/">archive</a>)</li> </ul> <p>BioRuby (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioRuby/">BioRuby</a> - BioRuby Project Discussion List ( <a href="http://mailman.open-bio.org/pipermail/bioruby/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioruby-cvs/">BioRuby-cvs</a> - BioRuby CVS commit notices ( <a href="http://mailman.open-bio.org/pipermail/bioruby-cvs/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioruby-ja/">BioRuby-ja</a> - BioRuby Project Discussion List (in Japanese) ( <a href="http://mailman.open-bio.org/pipermail/bioruby-ja/">archive</a>)</li> </ul> <p>BioSQL (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biosql-guts-l/">BioSQL-guts-l</a> - Commit and Bugzilla messages for BioSQL ( <a href="http://mailman.open-bio.org/pipermail/biosql-guts-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biosql-l/">BioSQL-l</a> - BioSQL Discussion List ( <a href="http://mailman.open-bio.org/pipermail/biosql-l/">archive</a>)</li> </ul> <p>EMBOSS (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss/">EMBOSS</a> - EMBOSS mailing list ( <a href="http://mailman.open-bio.org/pipermail/emboss/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss-announce/">emboss-announce</a> - EMBOSS Announcements (Releases, etc.) ( <a href="http://mailman.open-bio.org/pipermail/emboss-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss-bug/">emboss-bug</a> - EMBOSS Bug Reports and Support Requests ( <a href="http://mailman.open-bio.org/mailman/private/emboss-bug/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss-dev/">emboss-dev</a> - EMBOSS Development Discussion (Open to all) ( <a href="http://mailman.open-bio.org/pipermail/emboss-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/private/emboss-submit/">emboss-submit</a> - EMBOSS submissions - new packages and apps ( <a href="http://mailman.open-bio.org/pipermail/emboss-submit/">private archive</a>)</li> </ul> <p>DAS (propose to merge to a single list, or close and archive):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/das/">DAS</a> - DAS discussion list ( <a href="http://mailman.open-bio.org/pipermail/das/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/das-announce/">DAS-announce</a> - DAS announcement list ( <a href="http://mailman.open-bio.org/pipermail/das-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/das2/">DAS2</a> - DAS2 Discussion List ( <a href="http://mailman.open-bio.org/pipermail/das2/">archive</a>)</li> </ul> <p>Dormant lists, including legacy projects (propose to close and archive):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biobiz/">BioBiz</a> - Commercial aspects of open source life science code ( <a href="http://mailman.open-bio.org/pipermail/biobiz/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biocorba-announce-l/">Biocorba-announce-l</a> - BioCorba Announcements ( <a href="http://mailman.open-bio.org/pipermail/biocorba-announce-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biogroovy-l/">biogroovy-l</a> - biogroovy general discussion list ( <a href="http://mailman.open-bio.org/pipermail/biogroovy-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biolib-dev/">BioLib-dev</a> - BioLib Developers List ( <a href="http://mailman.open-bio.org/pipermail/biolib-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biosoap-l/">Biosoap-l</a> - BioSOAP project ( <a href="http://mailman.open-bio.org/pipermail/biosoap-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bP-announce/">bp-announce</a> - BioPathways Consortium Announcements ( <a href="http://mailman.open-bio.org/pipermail/bp-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-announce/">Moby-announce</a> - MOBY annoucements ( <a href="http://mailman.open-bio.org/pipermail/moby-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-dev/">MOBY-dev</a> - Core developer announcements ( <a href="http://mailman.open-bio.org/pipermail/moby-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-guts/">MOBY-guts</a> - MOBY CVS Commits Log ( <a href="http://mailman.open-bio.org/pipermail/moby-guts/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-l/">moby-l</a> - MOBY discussion list ( <a href="http://mailman.open-bio.org/pipermail/moby-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/obf-developers/">obf-developers</a> - Open-Bio.org members with developer access ( <a href="http://mailman.open-bio.org/pipermail/obf-developers/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/ontologies/">Ontologies</a> - Open Bio Ontologies list ( <a href="http://mailman.open-bio.org/mailman/private/ontologies/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/open-bio-announce/">Open-Bio-Announce</a> - OBF announcements ( <a href="http://mailman.open-bio.org/pipermail/open-bio-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/open-bioinformatics-foundation/">Open-Bioinformatics-Foundation</a> - OBF broadcast list ( <a href="http://mailman.open-bio.org/pipermail/open-bioinformatics-foundation/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/Volunteer/">Volunteer</a> - Open-Bio volunteer coordinator ( <a href="http://mailman.open-bio.org/mailman/private/volunteer/">private archive</a>)</li> </ul> <p>If this affects you directly (e.g. any project leaders we have not been able to contact yet), please write to the OBF board. Since mailman is currently unreliable, board at open-bio.org might not work. Please CC our fall back address of obf-board at Google Groups.</p> <p><strong>Update</strong>: Projects can also get in touch via this <a href="https://github.com/OBF/obf-docs/issues/42">GitHub issue</a>.</p>https://www.open-bio.org/2017/12/07/travel-fellowship-deadline-dec-15/Fri, 08 Dec 2017 00:25:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/12/07/travel-fellowship-deadline-dec-15/<p>The <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> was launched in 2016 to help increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. There are four application deadlines per year; the next will be <strong>December 15, 2017</strong>. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships. More information, including a link to the application form, can be found at <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md</a>.</p>https://www.open-bio.org/2017/11/21/bosc-2017-prague-land-of-stories/Tue, 21 Nov 2017 14:02:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/11/21/bosc-2017-prague-land-of-stories/<p><em>This is a guest blog post from Farah Zaib Khan, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> to attend our annual conference BOSC 2017 and its preceding Codefest in Prague, July 2017. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 December 2017, you might want to apply?</em></p> <p>So the journey started back in May 2017 when I met <a href="http://www.commonwl.org/">Common Workflow Language (CWL)</a> co-founder,  <a href="https://orcid.org/0000-0002-2961-9670">Michael R. Crusoe</a> during his visit to our University ( <em>University of Melbourne</em>). I have been working with CWL team since 2015 but it was only then we met in person and discussed various aspects of the CWL standard and how we can collaborate to incorporate principles of Provenance modelling to capture retrospective provenance of CWL workflow enactments. We started working on an idea which led to <a href="https://f1000research.com/posters/6-1547">poster submission</a> and acceptance at <a href="https://www.open-bio.org/wiki/BOSC_2017">Bioinformatics Open Source Conference (BOSC) 2017</a>. I was excited as well as nervous (will explain how this changed later :) ). Excited because this was my very first time attending any BOSC and ISMB conference and nervous because of the feeling that the names that you see at the top of high quality research articles will be there and you get to meet and talk to world class scientists doing wonders.</p> <p>Nervous and excited I prepared for all the travelling which involved applying for a visa of course (going to Sydney for that) and arranging accommodation, conference registration, booking plane ticket and finally receiving the visa 7 days before my flight. The Czech Consulate was very professional and kind to process the visa in just 7 working days. I left Melbourne to attend 2-Day OBF Codefest followed by 2-Day BOSC and remaining ISMB conference. My Airbnb host was waiting for me when I reached and welcomed me warmly. She had the whole day planned for us as I reached at 9 am July 19th and the codefest had to commence on July 20th. She was keen to learn about my culture, home country, language and research too :). During the day we roamed around the City, had lunch and she shared information about the Czech history and how late 80&rsquo;s Velvet Revolution changed the economic conditions of the country.</p> <p>In the evening of my first day, I had a dinner with few members of Seven Bridges team and CWL working group (thanks to Michael for arranging this) at an amazing vegan restaurant in the  Old town. We kick started discussion of our work informally during dinner where SevenBridges team introduced their super cool open source toolkit, <a href="http://rabix.io/launch">Rabix</a> for describing the CWL tools workflows. I presented the idea of CWL provenance module which we had planned to work on during the OBF Codefest the very next day. Mostly it was getting to know the teams and getting ready for the next day while enjoying delicious dinner in the heart of Prague Old town.</p> <p>All geared up, next morning I took a subway from the station right next to Congress center to reach <a href="https://brmlab.cz/">Brmlab</a> which is a non-profit hackerspace self supported by community. The transport system of Prague is commendable as despite the signs written Czech, it was quite straight forward to follow Google maps and take the right subways, trams or buses. When I reached, <a href="https://twitter.com/chapmanb">Brad Chapman</a>, <a href="https://twitter.com/matuskalas">Matúš Kalaš</a> and others were already there making arrangements, providing enough extension cables, arranging food (with many vegan friendly options) and making sure everything is in place. There were more than 60 participants for this open collaborative event to build things and discuss future prospects of research together. The day kick started with introductions and organization into groups to work on related projects. This was followed by coffee and local produce (fruits, bread and pastries) break where people carried on with individual introductions and conversations.</p> <p>[caption id=&ldquo;attachment_1782&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;378&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2017/11/DSC_0553-300x169.jpg" alt=""> &ldquo;Breakfasting&rdquo; in open air outside the lab. Image was originally shared <a href="https://photos.google.com/share/AF1QipNQrGZitpC7yhTozyeX6dWnV5IZzhx1G-fJgkQWfvNpZiwj49qGmPN6azx5gJ7eLg?key=ZTJwdmtGdkV3dGlZWXlZYlg5a2hqaTNkMXRUWkVR">here</a>.[/caption]</p> <p>Various groups started working on different projects from 10 am to 1 pm. These projects include <a href="http://multiqc.info/">MultiQC</a>, <a href="http://biopython.org/">biopython</a>, <a href="https://www.nextflow.io/">nextflow</a>,  <a href="https://github.com/johnfonner/cwltool/tree/feature-singularity">Singularity support in CWL</a>,  <a href="https://github.com/common-workflow-language/cwltool/tree/provenance">Provenance support in CWL</a>,  <a href="https://github.com/common-workflow-language/python-cwlmodel">CWL SDK</a> and <a href="http://rabix.io/launch">Rabix</a>. Our group led by <a href="https://twitter.com/soilandreyes">Stian Soiland-Reyes</a> started working on Provenance analysis and had a very useful discussion about what to capture from a workflow run retrospectively and how to structure the Provenance of a CWL workflow run. To start with, we decided to include a provenance module in reference implementation <a href="https://github.com/common-workflow-language/cwltool/tree/master/cwltool">cwltool</a> developed by CWL team. Nervously I started but now it felt like home and we got to work during 10am-1pm work window. I had guidance through out this time by people around me and I would like to thank them once more :) .</p> <p>[caption id=&ldquo;attachment_1784&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;446&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2017/11/DSC_0582-300x169.jpg" alt=""> Work in Progress for 10am-1pm session[/caption]</p> <p>At 1 pm, we took a lunch break but before going for lunch break all the groups gathered and presented their progress so far. A round of applause for the organizers and sponsors who kept the supply of coffee running through out the day. The lunch was delicious pizza with local flavored soft drinks. Again all dietary requirements were accounted for and everyone seemed to enjoy &quot; <em>across-group</em>&quot; discussion and food. After lunch break the group gathered again and started working from 2 pm to 6 pm before leaving for the group dinner. We kept working on our project idea and all the groups reported at 6 pm presenting their progress and headed out for the group dinner. Our group stayed back as Brad graciously offered to stay back if someone wants to continue working. Luckily brmlab was also open 24/7 so we kept working till 9 pm. Late night dinner and headed to the apartment taking the same subway. The city was awake and happening even later in the night. At last the first very productive day came to an end.</p> <p>July 21st was the second and last day of the Codefest. On my way to brmlab, I stopped at <a href="https://www.copygeneral.cz/">Copy General</a> to get the print of my poster which was required to be displayed the next day. I must admit the staff at this shop was very professional and helpful. They made sure I get the right size of my poster (as it was in landscape orientation) and were quite flexible about the pick up time. Getting done with this important task, I was relaxed and headed to the lab for second day of codefest. The day followed the same pattern as July 20th starting with projects&rsquo; updates, plans to be followed for the day followed by coffee and breakfast. Our organizers collected some best quality local produce from a farmer&rsquo;s market and kept everything organized efficiently.</p> <p>We further worked on the implementation of a basic Research Object generation as a result of CWL workflow run. By the lunch time we were able to complete the set goals and presented out progress. Everyone was excited and engaged in working with their groups and contributing in every way they could. At 6 pm every group leader wrapped up their progress through out these two days and everyone participated in cleaning the space as it is a community-run space shared by everyone. At the end of these two amazing days, I looked back and realized I was nervous for nothing. As Brad Chapman says and  I quote <strong>&quot; <em>BOSC is all about getting people together and learning from each other&quot; .</em></strong></p> <p>I don&rsquo;t think anyone can disagree with this statement and the idea of community led projects and open source bioinformatic software feels real and in practice when one interacts and participates in events like OBF-Codefest and BOSC. The codefest ended with dinner at Zly cafe near the Congress center where the next four days are scheduled.</p> <p>[caption id=&ldquo;attachment_1787&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;482&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2017/11/DSC_0614-300x169.jpg" alt=""> Dinner at Zly Cafe[/caption]</p> <p>New day, new tasks.. July 22nd was the first day of BOSC 2017 and at the same time all the posters were required to be hanged in the morning. I rushed to the copy general to collect my poster which was ready the same day. On my way to the shop I met loving and most friendly <a href="https://twitter.com/monimunozto">Monica Munoz-Torres</a> from UC Berkeley who was volunteering as part of organizing committee (presenting Apollo later as well) and was headed to the same copy center. We had good conversation about open source bioinformatics initiatives and her work as volunteer organizing BOSC which she calls her favorite conference :) .</p> <p>Rushed back to the Congress center, arranged the poster on its designated location along with 100s of amazing posters and headed to attend BOSC opening talks. I was impressed by OBF progression and their support for researchers by providing <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">OBF Travel scholarship</a> and participation in organizing Google summer code camps. Brad presented the summary of Codefest afterwards which had a slide we prepared for our part of work [Provenance Support in CWL]. There were many talks related to CWL application and usage during the whole day. Rabix composer, Rabix Executor, CWL Viewer, bcbio and many more CWL oriented work was presented. We organized a Birds of a feather session during lunch time to discuss <em>what should be captured in a Research Object when a CWL workflow is enacted</em>. This session initiated interesting discussion about different levels and views of Provenance.</p> <p>In the afternoon Björn Grüning&rsquo;s talk was very interesting where he empathized on <strong>Findability, Accessibility, Interoperability, and Reusability (FAIR)</strong> principles for tool deployment and resolving tool dependencies using package managers as Conda and BioConda. Later during this and next day <a href="https://twitter.com/search?q=%23BOSC2017%20FAIR%20bingo&amp;src=typd">FAIR bingo</a> became a real thing as part of most of the talks. The highlight of the day was indeed the key note speech <em>&ldquo;Open Sourcing Ourselves&rdquo;</em> by <a href="http://www.madeleineball.net/">Madeleine Ball</a> who is working on the project <a href="https://www.openhumans.org/">Open Humans</a>. She discussed inspiring Dana Lewis&rsquo;s story who is creator of &ldquo;Do-It-Yourself Pancreas System&rdquo; and made her own continuous glucose monitor alarms louder further leading to the foundation of OpenAPS.</p> <p>On the second day of BOSC, we had more talks and updates  starting with the key note speech &quot; <em>Bioinformatics for Personalized Medicine: Looking Beyond the Genome</em>&quot; by <a href="http://epigenomics.cemm.oeaw.ac.at/meg/">Christoph Bock</a>. He presented few examples from cancer research explaining how epigenomic mutations can be mapped to identify the various aspects of cancer. The topic was of my personal interest and indeed very informative. The ultimate goal is to make the dream of personalized medicine a reality using the available technologies including use of CRISPR for modelling epigenomic factors.</p> <p>After the key note speech I attended Monica Munoz-Torres&rsquo;s talk about <em><a href="http://apollo.berkeleybop.org/">Apollo</a></em>, collaborative genomic annotation editor that automatically synchronizes the work of geographically separated research community and establishes a network between the researchers, more like a social network for curators according to Monica. The huge user base working on different genomes interact using Apollo and share the curated genomes. The next talk by  Pjotr Prins was about <em>Journal of Open Source Software (JOSS)</em> , an initiative all available on <a href="https://github.com/openjournals/joss">GitHub</a> for accrediting academic software equipped with documentation.  In this way, software engineers can publish their software without getting to write a paper about it. It will facilitate the users as the software will be better documented when intended to be published.</p> <p>Another impressive talk was about &quot; <em>Distance-based, online bioinformatics training in Africa: the H3ABioNet experience&quot;</em> by Nocola Mulder from University of Cape Town. She described the efforts made to bring bioinformatics training to all the places in Africa using a distributed classroom model. Due to internet connectivity issues and other factors, the lectures were recorded beforehand. The lectures were delivered live (online) as well but if there is a connectivity issue, the recordings were available. In addition, various practical assignments were designed to enhance the learning experience. The combination of live lectures, online classes, recordings and practical exercises together results in connectivity and highly interactive environment. Another highlight from the session was release of open source variant calling toolkit <a href="https://software.broadinstitute.org/gatk/download/beta">GATK4</a> coupled with <a href="https://software.broadinstitute.org/wdl/">WDL</a> and Cromwell.</p> <p>There were many more talks that I attended and enjoyed such as talk by Ted Liefeld about <a href="http://www.genomespace.org/">GenomeSpace</a>, Kai Blin about <a href="https://bitbucket.org/antismash/antismash">anitSMASH</a> and Kenzo-Hugo Hillion about <a href="http://docs.biothings.io/en/latest/">BioThings SDK</a>. Oh and during lunch time I attended the BoF session organized by JOSS (was intrigued after listening to the presentation earlier). Later in the day, the panel discussion was worth attending chaired Madeleine Ball, Prof. <a href="http://www.manchester.ac.uk/research/Carole.goble/">Carole Goble</a>, <a href="http://sulab.org/">Andrew Su</a> and <a href="http://lab.loman.net/">Nick Loman</a>. Carole Goble&rsquo;s point made perfect sense that the young scientists although are willing to share the data and are open to collaborations where as senior scientists (PIs) consider it more effort  with less rewarding results.</p> <p>Day 2 ended with an amazing closing key note speech by <a href="http://lab.loman.net/">Nick Loman</a> who discussed  virus outburst surveillance using the Oxford nanopore minION sequencing technology, using two examples, namely Ebola outburst in Africa in 2015 and the Zika virus in Brazil. &ldquo;If you can&rsquo;t move the subjects and samples to the sequencer, bring the sequencer to the subject&rdquo;.</p> <p>Oh wait the day actually ended with an end of BOSC dinner ..</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/11/DFcPys3WsAIhebp-169x300.jpg" alt=""></p> <p>but before that we stopped at <a href="https://academic.oup.com/gigascience">GigaScience</a>&rsquo;s 5th birthday for cake and free GOT themed <em>&ldquo;Data is coming&rdquo;</em> T shirt which they graciously saved ^_^  (because I reached late). Why did I reach late?</p> <p>Yes I was there for a poster presentation :) . The poster presentation was from 6-7 pm and was a terrific experience talking about my work and progress we made during code fest earlier.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/11/21294979_893002990907345_5610908708142841856_n-300x300.jpg" alt=""></p> <p>All in all, everything was amazing, the people, the venue, the city, the knowledge gain, the help you get from peers, the encouragement from fellow researchers. Remember the  nervousness I mentioned at the beginning of this post ? ALL GONE after this fruitful experience. Few things that might be helpful in future: We should work towards resolving the issue of gender imbalance that was seen (and usually seen in conferences), discussed and acknowledged during Code fest and BOSC.  I think we can advertise the Codefest and the objectives in more detail so people can attend even if they don&rsquo;t have a group there to start with. This is by no means a complaint or criticism, just something I observed and felt as there were 3 female participants out of &gt;60 total participants of Codefest. I think in future we can make this better and advertise about the welcoming environment of Codefest and BOSC.</p> <p>Thanks to <a href="https://www.open-bio.org/wiki/Main_Page"><strong>OBF</strong></a> for covering my air fare by refunding through OBF travel funding. I would also like to thank <a href="http://daspos.org/">Data and Software Preservation for Open Science</a> ( <strong>DASPOS</strong>) (working in developing workflow and provenance tracking for high energy physics) for covering the rest of conference related expenses . In the end, this post will be incomplete if I don&rsquo;t thank <em>Michael Crusoe</em> for the mentoring, encouragement, guidance, all the support, connecting me with DASPOS and providing prompt feedback whenever I ask :) .</p> <p><strong><em>Need a shorter version and more pictures</em></strong>?? &ndash;&gt; <a href="//storify.com/farahzk03/bosc-2017-in-the-land-of-stories">View the story &ldquo;BOSC-2017 in the Land of stories&rdquo; on Storify</a></p> <p>P.S. Some other day, I might write about wandering experience in Prague Castle, Old Town, Charles Bridge, local wooden sovereigns, amazing food especially Goats cheese and of course&hellip; lemonades :) .</p>https://www.open-bio.org/2017/11/14/obf-visioning-2017/Tue, 14 Nov 2017 17:08:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/11/14/obf-visioning-2017/<p>TL;DR: The OBF isn&rsquo;t doing enough in public policy and advocacy around Open Science, and we are looking to recruit a new board member who is interested in this role. Is that you? If yes, then <a href="mailto:obf-board@googlegroups.com">contact us</a>.</p> <hr> <p>At our October meeting, the OBF board took some time to think broadly about the OBF, current and future. We tried to answer the questions: What do we say we do? What do we actually do? What more do we wish we could do? We re-read our mission statement and list of public activities from the <a href="https://www.open-bio.org/wiki/Main_Page">OBF main page</a>, listed the current efforts of the board members and affiliates, and assessed how our actual work aligned with the stated goals of the organization. This was motivated by having board members who are new-ish to the OBF, as well as upcoming board elections.</p> <p>Our general mission is fairly broad (&ldquo;promoting the practice and philosophy of Open Source software development and Open Science within the biological research community&rdquo;). We aim to do this through running / sponsoring BOSC and other open source events (codefests and Google Summer of Code); running a travel fellowship program; managing servers, mailing lists, domain names and other assets for our member projects; and by advocacy through policy and public statements.</p> <p>With BOSC being our flagship event, it is not surprising that about 50% of our board time is spent on organizing this meeting, with our remaining effort about equally focused on the travel fellowship, server / domain management, and financials.</p> <p>What more could we be doing? OBF could help facilitate other events, as we do for Google Summer of Code (GSoC). In this model, the board does not directly run the event, but instead provides support with financial management (e.g., reimbursements and payments) and advertising, while the hands-on organization is done by non-board members. In the case of GSoC, Kai Bin has been the OBF GSoC administrator for the past couple of years (thanks, Kai!). So, even though the board members don&rsquo;t have bandwidth to organize other events, we could certainly help in a &lsquo;producer&rsquo; role.</p> <p>The big area where we aren&rsquo;t doing enough is advocacy and communication. There is huge interest in Open Science, reproducibility, software sustainability and other similar topics, but the OBF is surprisingly silent. This doesn&rsquo;t reflect a lack of interest (or opinion!) among the board members, but rather the difficulty in carving out time from other OBF jobs.</p> <p>So, we are looking to recruit a new board member who is interested in policy and advocacy around Open Science. Does that sound like you? If you want to put your name forward, please <a href="mailto:obf-board@googlegroups.com">email the board</a>. The election will be held at the upcoming public board meeting in January. If you want more information, or want to contact one of us to talk about being on the board, see the <a href="https://www.open-bio.org/wiki/Board">OBF Board page</a>.</p>https://www.open-bio.org/2017/11/12/mailing-list-outage-and-public-board-meeting-update/Sun, 12 Nov 2017 09:50:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/11/12/mailing-list-outage-and-public-board-meeting-update/<p>This time of year we&rsquo;d normally be having a public board meeting as part of our commitment to communication with our member projects and the wider OBF community. As per our bylaws we notify the community at least 10 days in advance, and we&rsquo;d also handle election of new board members and leadership changes where appropriate. For a couple of reasons, we&rsquo;re going to postpone that until early 2018.</p> <p>Our mailing list server (which hosts many of our member project lists) has been overwhelmed in the past few days, leading to delayed or blocked communication not just to our members but for our member projects who rely on it. We&rsquo;re looking into options for solving this problem, which might include migrating to a hosted solution.</p> <p>This comes at the same time that the OBF board has been taking a look at how best to direct the organisation as we move forward. We&rsquo;d like to have that conversation with our members <em>after</em> we&rsquo;ve crystallised our thoughts a bit, and we&rsquo;re still in the process of doing that.</p> <p>As we&rsquo;re sorting this out, we decided to push the public meeting back to early 2018 so everyone involved can get the most out of it. We hope you understand, and we&rsquo;re looking forward to hearing from as many of you as we can at that meeting.</p>https://www.open-bio.org/2017/10/28/bosc-2017-report/Sat, 28 Oct 2017 23:01:19 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/10/28/bosc-2017-report/<p>BOSC 2017 ( <a href="https://www.open-bio.org/wiki/BOSC_2017">/wiki/BOSC_2017</a>) was held in Prague in July 2017 as part of the annual ISMB conference. Nearly 250 people, half of whom were first-time attendees, participated in the meeting. Over 50 talks and a similar number of posters covered topics ranging from workflow tools to a crowd-funded &ldquo;tree of beers.&rdquo; This year&rsquo;s Open Data theme was reflected in the keynote talks by Madeleine Ball and Nick Loman and the panel discussion about the opportunities and challenges of open data.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/10/bosc-crowd-nh-at-podium-by-berenice-batut-1-300x114.jpg" alt=""></p> <p>A report about BOSC 2017 is now available on F1000 ( <a href="https://f1000research.com/articles/6-1858/v1">https://f1000research.com/articles/6-1858/v1</a>), and most of the talk and poster abstracts and talk videos are linked from the schedule page ( <a href="https://www.open-bio.org/wiki/BOSC_2017_Schedule">/wiki/BOSC_2017_Schedule</a>).</p> <p>In 2018, BOSC will be partnering with the Galaxy Community Conference (GCC) as an experiment in broadening the BOSC community. We invite anyone who has an interest in open source bioinformatics or open science to join us in Portland, Oregon, June 25-30&ndash;see <a href="https://gccbosc2018.sched.com/">https://gccbosc2018.sched.com/</a> for more information.</p>https://www.open-bio.org/2017/09/05/biopython-on-podcastinit/Tue, 05 Sep 2017 16:17:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/09/05/biopython-on-podcastinit/<p><a href="https://www.podcastinit.com/">Podcast.__init__</a> describes itself as <em>&ldquo;The Podcast About Python and the People Who Make It Great&rdquo;</em>, and the most recent episode is &quot; <a href="https://www.podcastinit.com/biopython-with-peter-cock-wibowo-andrarto-and-tiago-antao-episode-125/">Biopython with Peter Cock, Wibowo Arindrarto, and Tiago Antão (Episode 125)</a>&quot;.</p> <p>Listening to the finished podcast, interviewer Tobias Macey did a great job. There are things I would have liked to have said - but it turned out pretty well. I hope you&rsquo;ll agree:</p> <p>Its worth looking back over the podcast archives, here are a few that caught my eye:</p> <ul> <li><a href="https://www.podcastinit.com/coverage-py-with-ned-batchelder-episode-121/">Coverage.py with Ned Batchelder (Episode 121)</a></li> <li><a href="https://www.podcastinit.com/episode-105-scikit-image-with-stefan-van-der-walt-and-juan-nunez-iglesias/">Scikit-Image with Stefan van der Walt and Juan Nunez-Iglesias (Episode 105)</a></li> <li><a href="https://www.podcastinit.com/episode-98-pandas-with-jeff-reback/">Pandas with Jeff Reback (Episode 98)</a></li> </ul>https://www.open-bio.org/2017/08/28/obf-travel-fellowship-jonathan-sobel/Mon, 28 Aug 2017 14:43:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/08/28/obf-travel-fellowship-jonathan-sobel/<p><em>This blog post is syndicated from a <a href="https://jonathansobel1.wordpress.com/2017/07/27/bosc-session-of-the-eccbismb-2017/">post on Jonathan Sobel&rsquo;s blog</a>, originally published July 27, 2017. Jonathan was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship program</a> to attend the 2017 Bioinformatics Open Source Conference (BOSC), held as part of the 2017 ISMB/ECCB meeting in Prague, Czech Republic, in July 2017.</em> <em>The OBF&rsquo;s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 December 2017.</em></p> <p>As the lucky recipient of an <a href="https://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (OBF)</a> travel grant, I had the chance to attend to my first <a href="https://www.open-bio.org/wiki/BOSC_2017">Bio-informatics Open Source Conference (BOSC)</a> in Prague the 21 and 22 July 2017.</p> <p><img src="https://jonathansobel1.files.wordpress.com/2017/07/pear.png?w=164&amp;h=117" alt="Pear"></p> <p>During the event, I discovered an amazing community of scientists and developers involved in the field of bioinformatics, with a strong open source mindset. “Sharing is caring” and I can tell these guys care a lot! The first day was quite technical with several talks about projects developed during the <a href="https://www.open-bio.org/wiki/Codefest_2017">code fest</a> that happen just prior to the conference. I had the opportunity to discover the <a href="https://www.nature.com/articles/sdata201618">FAIR principles</a> (Findability, Accessibility, Interoperability, and Reproducibility) of open data, and several tools aimed at simplifying bioinformatics workflow sharing, visualizing and production. These teams triggered my curiosity towards the <a href="http://www.commonwl.org/draft-3/UserGuide.html">Common Workflow Language</a> (CWL) and data standards, notably <a href="http://rabix.io/">RABIX</a>, <a href="http://ga4gh.org/#/">GA4GH</a> and <a href="https://www.nextflow.io/index.html">nextflow</a>. Several talks presented very useful tools such as <a href="https://github.com/alesssia/YAMP">YAMP</a> (Yet Another Metagenomic Pipline!) or <a href="http://multiqc.info/">MiltiQC</a> for next generation sequencing quality control, and <a href="https://www.openms.de/">Open MS 2.0</a> for mass-spectrometry data analysis. One important topic of the day was the reproducibility of bioinformatics piplines and several talks were addressing this question with various approaches, such as containers (Dockers, <a href="https://biocontainers.pro/">BioContainers</a>), <a href="https://www.gnu.org/software/guix/">GNU Guix</a> or package repository such as <a href="https://bioconda.github.io/">BioConda</a>.</p> <p><img src="https://jonathansobel1.files.wordpress.com/2017/07/logo.png?w=339&amp;h=168" alt="logo"></p> <p>On the second day, I had the chance to present our <a href="http://www.genome.beer/">BeerDeCoded</a> project in the Citizen Science session of the BOSC. I had the first slot in the morning with an audience of nearly 250 attendees. The beer topic is kind of holy in a geek environment. I had the pleasure to share several important message regarding science conducted outside of academia or industry, in a community laboratory space like <a href="http://www.hackuarium.ch/en/">Hackuarium</a>. I put some emphasis about science communication between fields and outside of our institutional scientific community. As experts, we have the responsibility to make our knowledge and our researches accessible to a wide audience, and this is exactly our goal with BeerDeCoded and Hackuarium. In addition, I could announce <a href="https://github.com/beerdecoded/Beer_ITS_analysis">the official release</a> of our first results based on the metagenomic analysis of <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA388541/">39 beer samples</a>. I was able to show our preliminary analysis. The BOSC community was really enthusiastic about the project and attendees tweeted quite a lot about it.</p> <blockquote> <p>Some background material for <a href="https://twitter.com/JonathanSobel1">@JonathanSobel1</a>&rsquo;s &ldquo;BeerDeCoded&rdquo; talk at <a href="https://twitter.com/hashtag/BOSC2017?src=hash">#BOSC2017</a><img src="https://s0.wp.com/wp-content/mu-plugins/wpcom-smileys/twemoji/2/72x72/1f37a.png" alt="🍺"> <a href="https://t.co/O52PI6k1hT">pic.twitter.com/O52PI6k1hT</a></p> <p>— Madeleine Price Ball (@madprime) <a href="https://twitter.com/madprime/status/889038522836975616">July 23, 2017</a></p> </blockquote> <blockquote> <p>The scientific method reloaded: Analyse data, think, drink, repeat. <a href="https://twitter.com/hashtag/BOSC2017?src=hash">#BOSC2017</a> <a href="https://t.co/JY0sLuXtzw">pic.twitter.com/JY0sLuXtzw</a></p> <p>— Bastian Greshake (@gedankenstuecke) <a href="https://twitter.com/gedankenstuecke/status/889038120691392513">July 23, 2017</a></p> </blockquote> <blockquote> <p>Work in progress for <a href="https://twitter.com/beerdecoded">@beerdecoded</a> – really really want <a href="https://twitter.com/nanopore">@nanopore</a> (so do we!) <a href="https://twitter.com/hashtag/BOSC2017?src=hash">#BOSC2017</a> <a href="https://twitter.com/hashtag/ISMBECCB?src=hash">#ISMBECCB</a> <a href="https://t.co/FplOglIpb0">pic.twitter.com/FplOglIpb0</a></p> <p>— BauhiniaGenome (@BauhiniaGenome) <a href="https://twitter.com/BauhiniaGenome/status/889039041215303680">July 23, 2017</a></p> </blockquote> <p>In addition, I had some very interesting questions about the interest of breweries in BeerDeCoded, the potential fear of companies that citizen scientist decode their proprietary yeast strain or about the data integration of sequencing with GC/MS in order to study small molecules present in our beer data-set. Moreover, this talk will potentially trigger new collaborations with with Bérénice Batut from the <a href="https://galaxyproject.org/teach/gtn/">Galaxy training network</a>.  <a href="https://usegalaxy.org/">Galaxy</a> is an open source, web-based platform for data intensive biomedical research. The Galaxy platform regroups a collection of bioinformatics tools and workflow that can be run without coding knowledge. This program is widely used by biologists to analyze their next generation sequencing data. BeerDeCoded will benefit from this collaboration with a specific instance of Galaxy to make the beer metagenomics accessible to anyone.</p> <p>Later during this second day, I was impressed by several other talks. One of the greatest initiative is the work of the <a href="http://www.h3abionet.org/">H3ABioNet</a>, which aim at training bioinformaticians in Africa. I discovered the <a href="http://joss.theoj.org/about">Journal of open source software</a> (JOSS) that facilitate the publication of bioinformatics software. Then, <a href="http://biothings.io/#">BioThings</a> SDK and <a href="https://www.wikidata.org/wiki/Wikidata:Main_Page">Wikidata</a> presented their API and their knowledge base that allows retrieving efficiently some annotations of biological data. This day was as well the occasion to discuss about data sharing of human data (wearable, clinical, etc.) in order to improve precision medicine and the ethical implication. In addition, second-hand data usage and the problem of re-digitalization of published data in a non-machine readable format was evoked. Finally, Nick Loman gave the closing keynote presentation at BOSC. He gave a great talk about virus outburst surveillance using the Oxford nanopore minION sequencing technology, using two examples, namely Ebola outburst in Africa in 2015 and the Zika virus in Brazil.</p> <p>In summary my first BOSC experience was very intense and highly interesting. I met with great scientists and developers and I learned about the newest open source software/library/API and practices in this field. I would like to thank once again the BOF committee for allowing me to join this great event and to give me the opportunity to present Hackuarium and the BeerDeCoded project.</p> <blockquote> <p><a href="https://twitter.com/hashtag/bosc2017?src=hash">#bosc2017</a> cheers! Thanks for this great conference <a href="https://t.co/m6oO8Wbbky">pic.twitter.com/m6oO8Wbbky</a></p> <p>— Jonathan Sobel (@JonathanSobel1) <a href="https://twitter.com/JonathanSobel1/status/889229547102666752">July 23, 2017</a></p> </blockquote> <p><a href="http://feeds.wordpress.com/1.0/gocomments/jonathansobel1.wordpress.com/73/"><img src="http://feeds.wordpress.com/1.0/comments/jonathansobel1.wordpress.com/73/" alt=""></a></p>https://www.open-bio.org/2017/08/27/obf-travel-fellowship-vitalina-kirgizova/Mon, 28 Aug 2017 02:21:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/08/27/obf-travel-fellowship-vitalina-kirgizova/<p><em>This blog post is syndicated from a <a href="https://vitalinabiology.com/2017/06/06/bioinformatics-training-course/">post on Vitalina Kirgizova&rsquo;s blog</a>, originally published June 6, 2017. Vitalina was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship program</a> to attend bioinformatics training course held at the Instituto Gulbenkian de Ciência, Oeiras, Portugal, in November 2016.</em> <em>The OBF&rsquo;s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 December 2017.</em></p> <p>Better late than never. On November 2016 I participated at the training course- <a href="ftp://gtpb.igc.gulbenkian.pt/bicourses/2016/AAIRR16/index.html">Analysis of Adaptive Immune Receptor Repertoires using high throughput sequencing data (NGS)</a>. Many thanks for invitation for <a href="http://gtpb.igc.gulbenkian.pt/bicourses/index.html">Pedro Fernandes</a>, who organizes bioinformatic training courses during 20 years! On the basis of the Instituto Gulbenkian de Ciência, Oeiras, Portugal we could go deep into the jungle of algorithms for the analysis of antibody and TCR genes. Our instructor Dr <a href="http://www.vet.cam.ac.uk/directory/sdf22@cam.ac.uk">Simon Frost</a> from University of Cambridge, U.K., made journey exciting and interesting.</p> <p>And I specially want to thank <a href="https://news.open-bio.org/about/">Open Bioinformatics Foundation</a> for supporting my participation!</p> <p><img src="https://vitalinabiology.files.wordpress.com/2016/12/img_0184.jpg?w=700" alt="img_0184"></p> <p>At the IGC bioinformatic class. (Ph Pedro Fernandes)</p> <p>Antibodies, also called immunoglobulins, are large Y-shaped proteins. They are produced by B -cells which function to identify and help remove foreign targets such as viruses, bacteria without damaging the rest of the body.</p> <p>The T-cell receptor, or TCR, is a molecule found on the surface of T cells, that is responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules. T-lymphocytes protect our body from cancer invasions and viruse infections.</p> <p>Each antibody or TCR binds one unique molecule, just as the key fits into the lock. A human can probably make more than 1 000 billion different adaptive immune receptors molecules – it is adaptive immune receptor repertoire.</p> <p><img src="https://vitalinabiology.files.wordpress.com/2016/12/04-t-limfocit-i-kljuch.png?w=700" alt="04-t-limfocit-i-kljuch"></p> <p>Cute T-lymphocyte holds key – T-Cell Receptor (TCR). (Illustration- me)</p> <p>Immunoglobulins are proteins, and proteins are encoded by genes. Randomized combination inherited gene segments – V(D)J recombination of DNA and somatic hypermutation are the primary mechanisms diversification of the human antibody repertoire. High-throughput sequencing (HTS) enables thorough investigation of the diverse immune receptors that determine the specificity of adaptive immunity responses.</p> <p><img src="https://vitalinabiology.files.wordpress.com/2017/06/14947862_1110768205708694_5847757213665972751_n.jpg?w=700" alt="14947862_1110768205708694_5847757213665972751_n"></p> <p>Sweet immuno- bioinformatic November</p> <p>I had an experience in repertoire analysis before. I use software developed at the laboratory where I’m currently working <a href="https://milaboratory.com">MiLaboratory</a>. Also I coauthored a paper reporting the software for immune receptor analysis <a href="https://vitalinabiology.com/publications/">VDJtools</a>.</p> <p><img src="https://vitalinabiology.files.wordpress.com/2016/12/img_0185-1.jpg?w=700" alt="img_0185-1"></p> <p>Our international team. Dr Simon Frost (course instructor) at the left. (Ph Pedro Fernandes)</p> <p>Nevertheless practical course give me an opportunity to develop my knowledge, try different solutions and protocols: IgBLAST, pRESTO, Change-O, etc.,  Also this was the first time when I worked with very useful software tool <a href="http://jupyter.org">Jupyter Notebook</a>. It helps to manage the code and looks very attractive for bioinformatician who grew up from a wet-laboratory (i.e. for me).</p> <p>I have a great time at Portugal. The community of the researchers whom use the immune receptor repertoire analysis in daily routine is not very large. This is very specific and complicate topic because of peculiar nature of the lymphocyte receptor rearrangement. So bioinformatic course was a perfect opportunity for me to accumulate knowledge directly from highly skilled professionals.</p> <p><img src="https://vitalinabiology.files.wordpress.com/2017/06/snapseed-1.jpg?w=700" alt="Snapseed (1)"></p> <p>After another one hard day at the bioinformatic course. With Simon Frost and Pedro Fernandes, bioinformatics training coordinator, at the left)</p> <p><a href="http://feeds.wordpress.com/1.0/gocomments/vitalinabiology.wordpress.com/868/"><img src="http://feeds.wordpress.com/1.0/comments/vitalinabiology.wordpress.com/868/" alt=""></a><img src="https://pixel.wp.com/b.gif?host=vitalinabiology.com&amp;blog=121300637&amp;post=868&amp;subd=vitalinabiology&amp;ref=&amp;feed=1" alt=""></p>https://www.open-bio.org/2017/07/29/travel-fellowships-deadline-august-15/Sat, 29 Jul 2017 13:17:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/07/29/travel-fellowships-deadline-august-15/<p>The next deadline for the OBF travel fellowship is coming up soon on August 15, 2017. If you are attending any event that develops / promotes open source software or open science, and you are willing to write a blog post about the event, we welcome your application. See the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">travel fellowship</a> page for more details and link to the application form.</p>https://www.open-bio.org/2017/07/11/biopython-1-70-released/Tue, 11 Jul 2017 10:45:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/07/11/biopython-1-70-released/<p>Dear Biopythoneers,</p> <p>Source distributions of Biopython 1.70 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the official <a href="http://biopython.org/">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.70">on the Python Package Index (PyPI)</a>. Windows installers and/or wheels should be available later. ( <em>Update: Compiled wheel packages now available for Linux, Mac OS X and Windows</em>).</p> <p>This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now dropped support for Python 3.3). It has also been tested on PyPy v5.7, PyPy3.5 v5.8 beta, and Jython 2.7 (although we are deprecating support for Jython).</p> <p><em><strong>New Logo:</strong></em></p> <p>Biopython now has a new <a href="http://biopython.org/wiki/Logo">logo</a>, contributed by Patrick Kunzmann. Drawing on our original logo (with two yellow snakes) and the current Python logo, this shows a yellow and blue snake forming a double helix.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/07/biopython_logo_l-300x200.png" alt=""><img src="https://news.open-bio.org/wp-content/uploads/2013/12/biopython-300x84.jpg" alt="[Biopython Logo]"> <em><strong>Setup changes:</strong></em></p> <p>We now explicitly recommend installation using pip, rather than the classic &ldquo;python setup.py install&rdquo; approach. In a related change, we now depend on the Python package setuptools (rather than the older package distutils in the Python standard library) and have made the dependency on NumPy explicit and automatic (except on Jython).</p> <p><em><strong>License changes:</strong></em></p> <p>As of Biopython 1.69, we have started to dual-license Biopython under both our original liberal “Biopython License Agreement”, and the very similar but more commonly used “3-Clause BSD License”. A growing number of the Python files are explicitly available under either license, but most of the code remains under the “Biopython License Agreement” only. See the <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst">LICENSE</a> file for more details.</p> <p><em><strong>Code changes:</strong></em> <code>Bio.AlignIO</code> now supports Mauve&rsquo;s eXtended Multi-FastA (XMFA) file format under the format name &ldquo;mauve&rdquo; (contributed by Eric Rasche).</p> <p><code>Bio.ExPASy</code> was updated to fix fetching PROSITE and PRODOC records, and return text-mode handles for use under Python 3.</p> <p>Two new arguments for reading and writing blast-xml files have been added to the Bio.SearchIO functions (read/parse and write, respectively). They are <code>use_raw_hit_ids</code> and <code>use_raw_query_ids</code>. Check out the relevant SearchIO.BlastIO documentation for a complete description of what these arguments do.</p> <p><code>Bio.motifs</code> was updated to support changes in MEME v4.11.4 output.</p> <p>The <code>Bio.Seq</code> sequence objects now have a <code>.count_overlap()</code> method to supplement the Python string like non-overlap based <code>.count()</code> method.</p> <p>The <code>Bio.SeqFeature</code> location objects can now be compared for equality.</p> <p>In <code>Bio.Phylo.TreeConstruction</code>, the <code>DistanceMatrix</code> class (previously <code>_DistanceMatrix</code>) has a new method <code>.format_phylip()</code> to write Phylip-compatible distance matrix files (contributed by Jordan Willis).</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.</p> <p><em><strong>Acknowledgements:</strong></em></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Kitzmiller (first contribution)</li> <li>Adil Iqbal (first contribution)</li> <li>Allis Tauri</li> <li>Andrew Guy</li> <li>Ariel Aptekmann (first contribution)</li> <li>Ben Fulton</li> <li>Bertrand Caron (first contribution)</li> <li>Chris Rands</li> <li>Connor T. Skennerton</li> <li>Eric Rasche</li> <li>Eric Talevich</li> <li>Francesco Gastaldello</li> <li>François Coste (first contribution)</li> <li>Frederic Sapet (first contribution)</li> <li>Jimmy O&rsquo;Donnell (first contribution)</li> <li>Jared Andrews (first contribution)</li> <li>John Kern (first contribution)</li> <li>Jordan Willis (first contribution)</li> <li>João Rodrigues</li> <li>Kai Blin</li> <li>Markus Piotrowski</li> <li>Mateusz Korycinski (first contribution)</li> <li>Maximilian Greil</li> <li>Michiel de Hoon</li> <li>morrme (first contribution)</li> <li>Noam Kremen (first contribution)</li> <li>Patrick Kunzmann</li> <li>Peter Cock</li> <li>Rasmus Fonseca (first contribution)</li> <li>Rodrigo Dorantes-Gilardi (first contribution)</li> <li>Sacha Laurent (first contribution)</li> <li>Sourav Singh</li> <li>Ted Cybulski (first contribution)</li> <li>Tiago Antao</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Zheng Ruan</li> </ul> <p>Thank you all.</p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a> <em><strong>Checksums</strong></em>:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.70.* </span></span><span style="display:flex;"><span>feff7a3e2777e43f9b13039b344e06ff biopython-1.70.tar.gz </span></span><span style="display:flex;"><span>6307ab27c257fe69b9dae4bfc3052f49 biopython-1.70.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.70.* </span></span><span style="display:flex;"><span>4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b biopython-1.70.tar.gz </span></span><span style="display:flex;"><span>34312ce899f6c3fc9dea77ca997f9a8c228043d05284a0653577594aeb119d4f biopython-1.70.zip </span></span></code></pre></div>https://www.open-bio.org/2017/06/05/travel-award-recipients-for-april-2017/Mon, 05 Jun 2017 14:36:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/06/05/travel-award-recipients-for-april-2017/<p>We had a huge response to this round of the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel award</a>. After reviewing the applications, the OBF board selected four recipients. Three applicants accepted awards, and all plan to use the funds to attend <a href="https://www.open-bio.org/wiki/BOSC_2017">this year&rsquo;s BOSC</a>, to take place July 22-23 in Prague.</p> <p>Congratulations to our spring 2017 recipients:</p> <ul> <li>Sourav Singh, who will participate in the Codefest and present the <a href="http://biopython.org/">Biopython</a> Project Update 2017 talk</li> <li>Jonathan Sobel, presenting on a citizen science project named <a href="http://www.genome.beer/">BeerDeCoded</a>, carried out by members of the Swiss non-profit called the Hackuarium</li> <li>Jiwen Xin, presenting the <a href="http://biothings.io/">BioThings Explorer</a> project, which integrates genomic data via public APIs</li> </ul> <p>We encourage everyone at BOSC to come out and support our award winners! After BOSC, watch for blog posts from each of the awardees.</p> <p>The next deadline for travel awards is August 15. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. See the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel award</a> page for details and link to application.</p>https://www.open-bio.org/2017/04/13/bosc-2017-keynote-speakers/Thu, 13 Apr 2017 10:28:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/04/13/bosc-2017-keynote-speakers/<p>We’re delighted to announce the keynote speakers for the <a href="https://www.open-bio.org/wiki/BOSC_2017">Bioinformatics Open Source Conference, BOSC 2017</a>, and our first sponsors.</p> <p>But first a final reminder - today (Thursday 13 April 2017) is our deadline for submitting a full length talk abstract to BOSC 2017.</p> <h2 id="dawn-field">Dawn Field</h2> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/04/Dawn_Field-e1492000853658-253x300.jpg" alt="">Dawn Field is a Lamberg International Guest Professor at Göteborg University’s Department of Marine Sciences. Previously she was a senior research fellow at the NERC Centre for Ecology and Hydrology, Head of the Molecular Evolution and Bioinformatics Group at the Centre for Ecology and Hydrology in Wallingford, UK, and a research associate at the Smithsonian Institution. She is also a founder of the Genomic Standards Consortium, the Genomic Observatories Network and Ocean Sampling Day.</p> <p>Dr. Field is credited with introducing the concept of a biological code, or &ldquo;biocode&rdquo; - the sum of all DNA on earth. In their book <a href="https://global.oup.com/academic/product/biocode-9780199687756">Biocode: The New Age of Genomics</a>, she and coauthor Neil Davies describe the rapid rise of genomics, how it is revealing the scale and diversity of life on Earth, and future possibilities and implications.</p> <p>Dr. Field&rsquo;s advocacy for open data and interoperability is epitomized by her past leadership of the Genomics Standards Consortium ( <a href="http://gensc.org/about-gsc/">GSC</a>), which aims to facilitate genomic data integration, discovery and comparison through international community-driven standards.</p> <p>The title of Dr. Field&rsquo;s keynote talk is &ldquo;Understanding the Biocode: Global Sharing of Data.&rdquo;</p> <h2 id="nick-loman">Nick Loman</h2> <p><a href="http://lab.loman.net/about/">Nick Loman</a> <a href="http://lab.loman.net/about/"><img src="https://news.open-bio.org/wp-content/uploads/2017/04/Nick-Loman-199x300.jpg" alt=""></a> is known as a vocal proponent of open genomic data in healthcare. A Professor of Microbial Genomics and Bioinformatics at the University of Birmingham, Dr. Loman explores the use of cutting-edge genomics and metagenomics approaches to human pathogens. He promotes the use of open data to facilitate the surveillance and treatment of infectious disease.</p> <p>Dr. Loman helped establish real-time genomic surveillance of Ebola in Guinea and Zika in Brazil (via the <a href="http://www.zibraproject.org/">ZiBRA project</a>, which states that &ldquo;Data will be subject to open release as it is generated&rdquo;). In another recent project, real-time genomic data was used to analyze a small outbreak of Salmonella enteritidis in the UK. Through this sharing of genomic datasets, researchers were able to confirm that the cases were linked to a larger, national-scale outbreak. Dr. Loman is one of the authors of <a href="https://poretools.readthedocs.io/">Poretools</a>, and he regularly shares cutting-edge Nanopore data and protocols for using it. In collaboration with Lex Nederbragt, Dr. Loman is developing an open-source repository of sequencing and bioinformatics benchmarking datasets called <a href="http://lab.loman.net/high-throughput%20sequencing/e.%20coli%20o104%20h4/genomics/2012/10/09/seqbench-a-useful-meta-resource-of-e-coli-sequence-reads/">Seqbench</a>.</p> <h2 id="bosc-2017-sponsors">BOSC 2017 Sponsors</h2> <p>We are grateful to and welcome <a href="http://thehyve.nl/">The Hyve</a> (open source solutions for bioinformatics) and <a href="https://science.mozilla.org/">Mozilla Science Lab</a> (a community of researchers, developers, and librarians making research open and accessible), as the first sponsors for BOSC 2017.</p> <p><a href="http://thehyve.nl/"><img src="https://news.open-bio.org/wp-content/uploads/2017/04/thehyve-logo01-without-shadow.png" alt=""></a><a href="https://science.mozilla.org/"><img src="https://news.open-bio.org/wp-content/uploads/2017/04/MSLLogo.png" alt=""></a></p> <p>If you would like to be a sponsor of BOSC, please contact us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>.</p>https://www.open-bio.org/2017/04/07/biopython-1-69-released/Fri, 07 Apr 2017 11:03:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/04/07/biopython-1-69-released/<p>Dear Biopythoneers,</p> <p>Source distributions and Windows installers for Biopython 1.69 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the official <a href="http://biopython.org/">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.69">on the Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.7, 3.3, 3.4, 3.5 and 3.6 (we have now dropped support for Python 2.6). It has also been tested on PyPy v5.7, PyPy3.5 v5.7 beta, and Jython 2.7.</p> <p>We have started to dual-license Biopython under both our original liberal &ldquo;Biopython License Agreement&rdquo;, and the very similar but more commonly used &ldquo;3-Clause BSD License&rdquo;. In this release a small number of the Python files are explicitly available under either license, but most of the code remains under the &ldquo;Biopython License Agreement&rdquo; only. See the <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst">LICENSE</a> file for more details.</p> <p>We now expect and take advantage of NumPy under PyPy, and compile most of the Biopython C code modules as well.</p> <p><a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a> now supports the UCSC Multiple Alignment Format (MAF) under the format name &ldquo;maf&rdquo;, using new module Bio.AlignIO.MafIO which also offers indexed access to these potentially large files using SQLite3 (contributed by Andrew Sczesnak, with additional refinements from Adam Novak).</p> <p>Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The underlying format (ABIF) remains the same as AB1 files and so the string &lsquo;abif&rsquo; is the expected format argument in the main SeqIO functions. AbiIO determines whether the file is AB1 or FSA based on the presence of specific tags.</p> <p>The Uniprot parser is now able to parse &ldquo;submittedName&rdquo; elements in XML files.</p> <p>The NEXUS parser handling of internal node comments has been improved, which should help if working with tools like the BEAST TreeAnnotator. Slashes are now also allowed in identifiers.</p> <p>New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue, and cell line ontology (contributed by Steve Marshall).</p> <p>For consistency the Bio.Seq module now offers a complement function (already available as a method on the Seq and MutableSeq objects).</p> <p>The SeqFeature object&rsquo;s qualifiers is now an explicitly ordered dictionary (note that as of Python 3.6 the Python dict is ordered by default anyway). This helps reproduce GenBank/EMBL files on input/output.</p> <p>The Bio.SeqIO UniProt-XML parser was updated to cope with features with unknown locations which can be found in mass spec data.</p> <p>The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type from the LOCUS/ID line explicitly in the record.annotations dictionary. The Bio.SeqIO EMBL parser was updated to cope with more variants seen in patent data files, and the related IMGT parser was updated to cope with IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed. The GenBank output now uses colon space to match current NCBI DBLINK lines.</p> <p>The Bio.Affy package supports Affymetrix version 4 of the CEL file format, in addition to version 3.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the February 2017 release of REBASE.</p> <p>Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default), PDBML/XML and mmtf format protein structures. This is inline with the RCSB recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython already has support for parsing mmCif files.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Rosenfeld</li> <li>Adam Kurkiewicz (first contribution)</li> <li>Adam Novak (first contribution)</li> <li>Adrian Altenhoff (first contribution)</li> <li>Allis Tauri (first contribution)</li> <li>Andrew Dalke</li> <li>Andrew Guy (first contribution)</li> <li>Andrew Sczesnak (first contribution)</li> <li>Ben Fulton</li> <li>Bernhard Thiel (first contribution)</li> <li>Bertrand Néron</li> <li>Blaise Li (first contribution)</li> <li>Brandon Carter (first contribution)</li> <li>Brandon Invergo</li> <li>Carlos Pena</li> <li>Carlos Ríos</li> <li>Chris Warth</li> <li>Emmanuel Noutahi</li> <li>Foen Peng (first contribution)</li> <li>Francesco Gastaldello (first contribution)</li> <li>Francisco Pina-Martins (first contribution)</li> <li>Hector Martinez (first contribution)</li> <li>Jacek Śmietański</li> <li>Jack Twilley (first contribution)</li> <li>Jeroen Van Goey (first contribution)</li> <li>Joshua Meyers (first contribution)</li> <li>Kurt Graff (first contribution)</li> <li>Lenna Peterson</li> <li>Leonhard Heizinger (first contribution)</li> <li>Marcin Magnus (first contribution)</li> <li>Markus Piotrowski</li> <li>Maximilian Greil (first contribution)</li> <li>Michał J. Gajda (first contribution)</li> <li>Michiel de Hoon</li> <li>Milind Luthra (first contribution)</li> <li>Oscar G. Garcia (first contribution)</li> <li>Owen Solberg</li> <li>Peter Cock</li> <li>Richard Neher (first contribution)</li> <li>Sebastian Bassi</li> <li>Sourav Singh (first contribution)</li> <li>Spencer Bliven (first contribution)</li> <li>Stefans Mezulis</li> <li>Steve Bond</li> <li>Steve Marshall (first contribution)</li> <li>Uri Laserson</li> <li>Veronika Berman (first contribution)</li> <li>Vincent Davis</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul> <p>Thank you all.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2013/12/biopython-300x84.jpg" alt="[Biopython Logo]"></p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a></p> <p>Checksums:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.69.* </span></span><span style="display:flex;"><span>18ad299569eea79febf4641cce840db0 biopython-1.69.tar.gz </span></span><span style="display:flex;"><span>1acfa83d7340d82e248261f8344038be biopython-1.69.win32-py2.7.exe </span></span><span style="display:flex;"><span>ff38a7286b455156619c8c2c4cb45a0e biopython-1.69.win32-py2.7.msi </span></span><span style="display:flex;"><span>e03809050cd862226299ba4285b25615 biopython-1.69.win32-py3.3.exe </span></span><span style="display:flex;"><span>f8605d2e76e60353c776f69991067e07 biopython-1.69.win32-py3.3.msi </span></span><span style="display:flex;"><span>6bc7d291b7482f194f66a91d3eb89cb6 biopython-1.69.win32-py3.4.exe </span></span><span style="display:flex;"><span>0bc8e39ca0c3127b531f1998c91c7233 biopython-1.69.win32-py3.4.msi </span></span><span style="display:flex;"><span>0944a254c079869c481c13ac3bfa6c53 biopython-1.69.win32-py3.5.exe </span></span><span style="display:flex;"><span>567ba8c2b5e069cbcda5b13b558e4b1e biopython-1.69.win32-py3.5.msi </span></span><span style="display:flex;"><span>48549d7083f1dcd37f73acfdbb30c100 biopython-1.69.win32-py3.6.exe </span></span><span style="display:flex;"><span>d3e02e227b6db736bc15f3ce4a08c149 biopython-1.69.win32-py3.6.msi </span></span><span style="display:flex;"><span>a134c5b8e35d6515ca4f9e663000bcb3 biopython-1.69.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.69.* </span></span><span style="display:flex;"><span>169ffa90c3d3ec5678c7a5c99501c0cfeb54c40ca51a619ce6cee5026d3403eb biopython-1.69.tar.gz </span></span><span style="display:flex;"><span>6520ac092f52fd35b48d12c5f264d78c4cd20ede841a4755b73376184c1f9c83 biopython-1.69.win32-py2.7.exe </span></span><span style="display:flex;"><span>505aa27537f358129d096c1cb5b761108c6200a11483d25ad83188b11089b45c biopython-1.69.win32-py2.7.msi </span></span><span style="display:flex;"><span>11a5a04da0d8830789d53fed7d631f5a8a6d3926869241d212265b7b9889b987 biopython-1.69.win32-py3.3.exe </span></span><span style="display:flex;"><span>7e3e764236e29f01fe3b346878801ee9f1166269e4ac557d88201e2f1cd85949 biopython-1.69.win32-py3.3.msi </span></span><span style="display:flex;"><span>c9ee5594e5f865fbf4871be8661e4be559dcb599c64e7fa4922e55b771aab249 biopython-1.69.win32-py3.4.exe </span></span><span style="display:flex;"><span>8426e2b548e594d63bfa7584f39513ee906d2de32037c900af9b6625318e051c biopython-1.69.win32-py3.4.msi </span></span><span style="display:flex;"><span>3025f12b7f8cf81b25823223dc17830d4e0eeda8095e59177069d44fa2be9d32 biopython-1.69.win32-py3.5.exe </span></span><span style="display:flex;"><span>853eb6b75ca84ba703e0c8873d673b49f1580b5b1b9372105fbf9735153ad0dd biopython-1.69.win32-py3.5.msi </span></span><span style="display:flex;"><span>7f11960168e335c1581de2e4a90bef905c92e08d42c67482f25a522db5d7b702 biopython-1.69.win32-py3.6.exe </span></span><span style="display:flex;"><span>4cac457773f251c511ede520f3e8701d8f00e22524103e03d0d1f69a040f95bf biopython-1.69.win32-py3.6.msi </span></span><span style="display:flex;"><span>e71ae4c5ba996cbe01002d55d877bf5eafa053c116012d7ace489dfc41959e05 biopython-1.69.zip </span></span></code></pre></div>https://www.open-bio.org/2017/04/05/obf-travel-fellowship-anton-khodak/Wed, 05 Apr 2017 19:01:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/04/05/obf-travel-fellowship-anton-khodak/<p><em>This is a guest blog post from Anton Khodak, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> to attend a week long <a href="http://www.commonwl.org/">Common Workflow Language (CWL)</a> workshop in London, November 2016. This was a natural continuation of Anton&rsquo;s work on <a href="https://anton-khodak.github.io/argparse2cwl-blog/2016/08/11/gentle-introduction.html">porting tools to the CWL</a> as one of the <a href="https://www.open-bio.org/2016/04/25/welcome-gsoc-2016-students/">OBF&rsquo;s Google Summer of Code 2016 students</a>.</em> <em>The OBF&rsquo;s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 April 2017 - if you&rsquo;re planning to attend the OBF&rsquo;s annual <a href="https://www.open-bio.org/wiki/BOSC_2017">Bioinformatics Open Source Conference (BOSC) 2017 in Prague</a>, you might want to apply?</em></p> <h1 id="cwl-week-in-london">CWL week in London</h1> <p>( <a href="https://anton-khodak.github.io/argparse2cwl-blog/2017/03/17/cwl-hackathon.html">Originally published Mar 17, 2017</a>)</p> <p>After the successful completion of my GSoC projects, I had been invited to meet my mentors <a href="https://orcid.org/0000-0002-2961-9670">Michael R. Crusoe</a> and <a href="https://se.linkedin.com/in/romanvg">Roman Valls Guimera</a> for the CWL work session that took place in London from the 1st to the 4th of November, 2016. I was thrilled by this opportunity, and though it took quite a while for me to organize this journey (my first solo voyage abroad), it was undoubtfully worth it.</p> <p>I arrived in London a little earlier to take part in <a href="https://mozillafestival.org/">Mozilla Festival 2016</a> together with Roman. At the festival, I presented my summer projects to people from the bioinformatics community who participated in Mozfest’s <a href="https://app.mozillafestival.org/#_space-open-science">Open Science Fair</a>.</p> <p>The CWL week started a day later. The attendees were Michael (Common Workflow Language project), Roman (the Wolfson Wohl Cancer Research Centre), <a href="https://rs.linkedin.com/in/jsimonovic">Janko Simonovic</a> and <a href="https://rs.linkedin.com/in/ivanbatic">Ivan Batic</a> from Seven Bridges Genomics, <a href="https://orcid.org/0000-0001-9795-7981">Niels Drost</a> from the Netherlands eScience Center, <a href="https://uk.linkedin.com/in/robert-sugar-90b8b941">Robert Sugar</a> from Intel Health and Life Sciences, and myself. During these four days, I worked on polishing the tools I developed ( <a href="https://github.com/erasche/argparse2tool">argparse2tool</a>, <a href="https://github.com/common-workflow-language/pypi2cwl">pypi2cwl</a>, <a href="https://github.com/common-workflow-language/cwl2argparse">cwl2argparse</a>) on the basis of the feedback from all the participants. We explored the question of pip installability, filed a bunch of <a href="https://github.com/common-workflow-language/gxargparse/issues?utf8=%E2%9C%93&amp;q=%20is%3Aissue%20">issues</a>, tried applying argparse2tool to <a href="https://github.com/dib-lab/khmer">khmer</a> scripts. Another thing we tackled was bug fixes for running <a href="https://github.com/BD2KGenomics/toil">Toil</a> workflow engine on SLURM cluster. In addition, I learned about the inner workings of another important open-source implementation for CWL <a href="https://github.com/rabix/bunny">bunny</a> directly from its creator Janko. During the CWL week, it was added to the community run continuous integration server and successfully <a href="https://twitter.com/commonwl/status/793767714049384448">passed</a> the latest conformance tests.</p> <p>Overall, it was a highly intensive and productive hackathon. I was very happy to meet my mentors and other people from the CWL community in person and to work with them for these few days. I could not imagine a better finish of my Google Summer of Code 2016 participation!</p> <div class="box"> <figure><img src="https://news.open-bio.org/wp-content/uploads/2017/04/london%5Fcwl.jpg" width="978"> </figure> </div> <p>P.S. A year after, I became a mentor on a CWL project myself! Check the idea here: <a href="https://obf.github.io/GSoC/ideas/#cwl-reference-implementation-cwltool">CWL reference implementation</a>.</p> <p>P.P.S. Special thanks to <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a> for awarding me with the travel fellowship and reimbursing with that a significant part of my travel expenses.</p> <p><em>(Above post contributed by Anton Khodak, <a href="https://anton-khodak.github.io/argparse2cwl-blog/2017/03/17/cwl-hackathon.html">originally on his blog</a>, with our introduction added.)</em></p>https://www.open-bio.org/2016/10/05/obf-public-board-meeting/Wed, 05 Oct 2016 16:56:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/10/05/obf-public-board-meeting/<p>The OBF has at least one public board meeting per year, in part to vote on important business issues, and in part to publicly discuss items relevant to the OBF community.  The latest public OBF Board of Director&rsquo;s meeting took place October 4, 2016. It was attended by Board members Hilmar Lapp, Peter Cock, Nomi Harris, Chris Fields, and Karen Cranston, as well as guests Heather Wiencko (Board candidate), Michael Crusoe, Spencer Bliven, and Robert Gilmore.</p> <p>The <a href="https://www.open-bio.org/wiki/Minutes:2016_Oct_ConfCall">agenda, and tentative minutes</a> (taken by then-secretary Peter Cock) are available from the OBF wiki.  The following is a summary:</p> <h2 id="old-business">Old Business</h2> <p>This mainly focused on approving minutes from the 2015 BoD meeting as well as approving the 2014 financial report and an amendment to the 2013 financial report.  Citing the continuing need to review SPI-provided records against our own, and the effort it took to compile the financial reports, Hilmar emphasized the need to again fill the Treasurer position on the OBF Board, which had been left vacant for several years due to our fiscal sponsor <a href="http://www.spi-inc.org">Software in the Public Interest</a> (SPI) handling OBF accounting.  The Treasurer would also act as primary liaison with SPI, a role held until now by the President.</p> <h2 id="elections">Elections</h2> <p><a href="https://twitter.com/hlwiencko"><img src="https://news.open-bio.org/wp-content/uploads/2016/10/hatAvatar-1-271x300.jpg" alt="Heather Wiencko"></a></p> <p>Speaking of Treasurer&hellip; Elections for five positions on the Board occurred today, with <a href="https://twitter.com/hlwiencko">Heather Wiencko</a> elected to join the Board as a first-time member!</p> <p>Additionally, Hilmar Lapp was re-elected President, with Peter Cock now elected as Treasurer, Chris Fields elected as Secretary, and Nomi Harris re-elected as a Director-at-Large. Congratulations all!</p> <h2 id="proposed-changes-to-the-obf-bylaws">Proposed changes to the OBF Bylaws</h2> <p><a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.pdf">OBF&rsquo;s Bylaws</a> suggest that they be reviewed every 2 years for stipulations that have become hindering to or inconsistent with OBF&rsquo;s mission or the Board&rsquo;s ability to conduct its business efficiently. The <a href="https://github.com/OBF/obf-docs/pull/8">last (and first) changes to the Bylaws</a> were made in 2012, and hence it was time for another review. As a result, several changes were proposed ( <a href="https://github.com/OBF/obf-docs/pull/28">#28</a> and <a href="https://github.com/OBF/obf-docs/pull/29">#29</a>), and approved at the meeting, including one previously mentioned regarding who acts as the SPI liaison:</p> <ol> <li>Removing the Parliamentarian position, which has largely proven obsolete</li> <li>Assigning the role of primary SPI liaison to the Treasurer</li> <li>Removal of the nominating committee</li> <li>Simplifying the process for future reviews of the bylaws</li> <li>Extension of the term for board members from 2 to 3 years</li> </ol> <h2 id="using-project-branded-swag-to-generate-revenue">Using project-branded swag to generate revenue</h2> <p>Spencer Bliven, one of the Biojava project leads, raised the question of how OBF can enable its projects to generate revenue from selling swag (project-branded merchandise), and to contribute such revenue to the well-being of the OBF community. Doing so would also present opportunities to promote the project&rsquo;s brand, and more generally to improve outreach. However, if individuals from the project collected the payment, it could too easily be considered a conflict of interest in their workplaces, because developers contributing to our open-source projects often do so as part of their employment. If OBF can collect the funds and deposit them into OBF&rsquo;s assets, it would prevent potential conflict of interest issues. Although earmarking funds generated in this way for a particular member project would be difficult due in part to the complexity of accounting, they would benefit the OBF community as a whole, and the programmatic activities sponsored by OBF are available to every member project. This notion received general agreement, and resulted in follow-up tasks for the Board to determine how such point-of-sale payments should best be collected.</p> <p>The discussion then turned to the question whether we should look into trademarking the projects and their respective marks (which allows brand protection) and how other open-source umbrella organizations (such as the Apache Software Foundation) copyright their logos and protect their brands.  Hilmar recommended open-source licensing of the logo with a trademark to allow for additional protection in case projects disagreed with its use.</p> <h2 id="additionaldiscussions">Additional discussions</h2> <p>After the main business, there were several followup questions and conversations:</p> <ul> <li>Michael Crusoe pointed out that having the <a href="https://sfconservancy.org/npoacct/">NPOacct project</a> provide open-source accounting software for non-profits might be useful. SPI has been among the partner organizations that committed funding support early on, and hence through the overhead rate paid to SPI we are contributing to this effort already, if only in a small way.</li> <li>Michael also asked about additional support for imminent GSoC-related travel expenses. These may well be eligible for an OBF Travel Fellowship, and even though by the next deadline for applications the respective event will be in the past, we determined that the Fellowship program rules (at least currently) do not rule out applications for events that have already taken place.</li> <li>Spencer suggested actively inviting members from the various OBF projects to attend the public Board meetings and join the OBF as members. Hilmar reports that membership applications have risen dramatically since we switched to a fully online application process, evidence that the application process is not a significant hurdle anymore. More active outreach to our developer communities should help drive further growth, and promote our community.</li> </ul>https://www.open-bio.org/2016/10/04/minutes2016-oct-confcall/Tue, 04 Oct 2016 05:45:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/10/04/minutes2016-oct-confcall/<h3 id="agenda">Agenda</h3> <p><strong>Venue:</strong> To be held by conference call on Oct 4, 2016, 12.30pm EDT (16:30 UTC, 17:30 BST, 18:30 CEST, 9.30am PDT)  <strong>Dial-in Information:</strong> +1-857-216-2939 PIN: 62534 <a href="http://www.uberconference.com/hlapp">http://www.uberconference.com/hlapp</a></p> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2015_May_ConfCall">May 2015 BoD meeting minutes</a></li> <li><a href="https://github.com/OBF/obf-docs/pull/33">Amendments to the 2013 Financial Report</a></li> <li><a href="https://github.com/OBF/obf-docs/pull/34">2014 Financial Report</a></li> </ul> </li> <li>New business <ol> <li>Term expirations and Elections for the Board ( <a href="https://vote.heliosvoting.org/helios/e/obf-2016">electronic ballot</a>) <ul> <li>Heather Wiencko, running for election to the Board.</li> <li>Hilmar Lapp, President of the Board. Running for re-election.</li> <li>Peter Cock, Secretary. Running for re-election to the Board and as Treasurer.</li> <li>Chris Fields, Board member at-large. Running for re-election to the Board and as Secretary.</li> <li>Nomi Harris, Board member at-large. Running for re-election.</li> </ul> </li> <li>Proposed changes to the OBF Bylaws: <a href="https://github.com/OBF/obf-docs/pull/28">Part 1</a> and <a href="https://github.com/OBF/obf-docs/pull/29">Part 2</a></li> <li>Options for and hurdles to generating revenue from selling swag (OBF project-branded merchandise)</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p>Etherpad for notes: <a href="https://etherpad.wikimedia.org/p/OBF-BoD-Meeting-Oct2016">https://etherpad.wikimedia.org/p/OBF-BoD-Meeting-Oct2016</a></p> <p><strong>Attending:</strong></p> <ul> <li><strong>Directors</strong>: Hilmar Lapp, Peter Cock, Karen Cranston, Chris Fields, Nomi Harris</li> <li><strong>Guests</strong>: Robert Gilmore, Heather Wiencko, Spencer Bliven, Michael Crusoe</li> </ul> <p>Meeting started at 16:34 UTC.</p> <h4 id="old-business">Old business</h4> <ul> <li>2015 BoD meeting minutes approved unanimously</li> <li>2013 Financial Report amendment <a href="https://github.com/OBF/obf-docs/pull/33">https://github.com/OBF/obf-docs/pull/33</a> (originaly approved at 2014 board meeting) to include keynote speaker payment from BOSC escrow, and fixing a $500 error in the ISCB erscow spreadsheet. Approved unanimously, PR merged.</li> <li>2014 Financial Report. Overdue as no serving Treasurer and evolving understanding of how things would work under the SPI umbrella. We now recognise we do need a dedicated treasurer. The drastic drop in the BOSC escrow of circa $7500 is offset by BOSC sponsorship allocated to the SPI account. Approved unanimously.</li> </ul> <h4 id="new-business">New business</h4> <p>1. Elections, with electronic ballots prepared by Hilmar.</p> <p><strong>Heather Wiencko</strong>: (Member at large) Met many of the OBF community via BOSC, having served on the BOSC 2016 organizing committee. Has moved more into open source software as her career has evolved, and welcomes the role of the OBF in encouraging openess in bioinformatics and wishes to help with this. Interested in increasing the visiblity of the OBF (unclear other than backing BOSC). Would like to encourage more membership and activity outside of BOSC.</p> <p><strong>Peter Cock</strong>: (Treasurer) Long-time biopython developer, previous OBF secretary. (Didn&rsquo;t say, but member of the BOSC organising commitee and co-chair for BOSC 2014 and 2015).</p> <p><strong>Chris Fields</strong>: (Secretary) Long-time BioPerl developer, and thus OBF.</p> <p><strong>Nomi Harris</strong>: (Continuing as Member at Large) Long career in Bioinformatics, and involved in the founding of BOSC in 2000 and has served on the committee since - lately as chair or co-chair. Represents BOSC at the OBF board, and is interested in expanding the OBF recognition &amp; community.</p> <p><strong>Hilmar Lapp</strong>: (President) Long-term BioPerl developer &amp; OBF board member, running for a third term with one goal being to enable someone else to take over as president. Most proud of formally launching the OBF Travel Fellowship to improve diversity at relevant events, and would like to expand this with more sponsorship. Has also spent more time than expected keeping OBF infrastructure alive, and would like to reduce this footprint further building on work in the last year.</p> <p>Votes cast electronically by the current board using Helios Voting <a href="https://vote.heliosvoting.org/helios/elections/e1ff4788-89b4-11e6-a3d4-5ed03a4b23b0/view">https://vote.heliosvoting.org/helios/elections/e1ff4788-89b4-11e6-a3d4-5ed03a4b23b0/view</a> all posted accepted with no votes against (unanimous bar abstains).</p> <p>Results (For/Against/Abstain):</p> <ul> <li>Heather Wiencko, Director at-large? 5/0/0</li> <li>Hilmar Lapp, President? 5/0/0</li> <li>Peter Cock, Treasurer? 4/0/1</li> <li>Nomi Harris, Director At-Large? 5/0/0</li> <li>Christopher Fields, Secretary? 4/0/1</li> </ul> <p>2. Proposed changes to the OBF Bylaws:</p> <ul> <li><strong>Part 1</strong> - removing the parliamentatian, altering the treasurer to take on SPI liason role, removing the nominating committee, process for future reviews of the bylaws etc: <a href="https://github.com/OBF/obf-docs/pull/28">https://github.com/OBF/obf-docs/pull/28</a> <ul> <li>Also moves SPI liason role to the treasurer (providing a second opinion of SPI decisions)</li> </ul> </li> <li><strong>Part 2</strong> - extending the terms for board members to 3 years: <a href="https://github.com/OBF/obf-docs/pull/29">https://github.com/OBF/obf-docs/pull/29</a></li> </ul> <p>Approved unamiously by the newly enlarged board.</p> <p>3. Options for and hurdles to generating revenue from selling swag (OBF project-branded merchandise). Raised by BioJava, with Spencer Bliven on the call representing the project. BioJava sees this largely as an outreach opportunity (T-shirts), but because there is money involved there are potential conflicts of interest. Most BioJava developers contribute as part of their day jobs, and are cautious about handling any revenue personally - collection via the OBF would be open and above board. Possible uses would be to pay for a free T-shirt to the logo designer, but does not seem necessary to track a BioJava earmark which would greatly complicate our accounting.</p> <p>More generally, does the OBF need to look into Trademarks for project names and logos? Note this is separate from the copyright (e.g. unclear copyright of a project logo should not prevent a Trademark application). Dave Clements might know from logo work on Galaxy and GMOD. In USA law at least, copyright is automatic (no registration), but you have to register a Trademark. Would allow us to protect usage of the brand. Minimal costs circa $350 for five years according to Spencer. Hilmar recommends open licensing of the logo (like the source code), but with brand protected by a TradeMark (with precedents including WikiMedia, Apache, Mozilla).</p> <h4 id="other-business">Other business</h4> <ul> <li>Question from Michael Crusoe via UberConf chat: Re: accounting &amp; non-profits: perhaps OBF could join forces with the NPOacct project? <a href="https://sfconservancy.org/npoacct/">https://sfconservancy.org/npoacct/</a></li> <li>Accounting methods for managing several projects under one organizational umbrella</li> <li>Question from Michael Crusoe about getting support for covering prior GSoC expenses (~$500)? Hilmar explains we have not earmarked the GSoC income to the OBF to any specific usage, but a general request would be considered - and might an OBF Travel Fellowship apply?</li> <li>Suggestion from Spencer to actively invite OBF member project developers to join the public OBF board calls (and join the OBF if not already members).</li> </ul> <p>Adjourned at 17:48 UTC</p> <h3 id="todo-after-meeting">TODO (after meeting)</h3> <ul> <li>Can we charge the Amazon hosting to an SPI credit card in future? (Peter to ask)</li> <li>How can we collect money from BioJava T-shirts? Direct to SPI or via Treasurer? (Peter to ask)</li> <li>Spencer to look into Trademarks (ideally not just in USA but also in Europe).</li> <li>Add Heather to board mailing list.</li> <li>Prepare minutes (Peter, with Chris as new secretary)</li> <li>Summarise as blog post (Chris)</li> </ul>https://www.open-bio.org/2016/09/25/bioperl-v1-7-0-released/Sun, 25 Sep 2016 15:10:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/09/25/bioperl-v1-7-0-released/<p>We are happy to announce the long-awaited release of BioPerl v1.7.0.  The release is now <a href="https://metacpan.org/release/BioPerl">available on CPAN</a> and <a href="https://github.com/bioperl/bioperl-live/releases/tag/release-1-7-0">Github</a>.</p> <p>During this release series, we will move some extraneous code to separate repositories and CPAN releases, primarily to reduce the number of dependencies required for BioPerl installation (in many cases for modules that are never used) and also reduce maintenance overhead.</p> <p>This may only impact you if your code incorrectly list the immediate downstream dependencies that you utilize.  For example, we have now moved Bio::Coordinate code to a separate repo and will release it as a separate distribution on CPAN.  If your tools require Bio::Coordinate::Result and list this module as a dependency, you should be fine: a separate Bio::Coordinate release should pull in the latest BioPerl, until then it would pull in the last BioPerl release with that module.  However, if you list Bio::Root::Root or Bio::Perl as a dependency to pull in Bio::Coordinate::Result, your installation will not work correctly (as Bio::Root::Root is not the proper code dependency).  We can work with distributions affected to help with this transition and will be more consistently evaluating reverse dependencies on CPAN for upcoming releases as we split out code.  Please post <a href="https://github.com/bioperl/bioperl-live/issues">issues on Github</a> if you see problems with your code and the latest release.</p> <p>In addition to the above, modules relying on a remote web services that are no longer active or pose a security issue will be deprecated for use and (in some cases) immediately removed.  Normally these don&rsquo;t affect normal tests, but we have noticed some remote services out of our control causing problems with network-requiring or release testing.</p> <p>In addition, the following changes have been made since the last release:</p> <ul> <li>NCBI HTTPS support [Mark Johnson (aka mjohnson) and others]</li> <li>We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!!</li> <li>Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!)</li> <li>Previously deprecated modules have been removed <ul> <li>Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif</li> <li>Bio::DB::SeqHound has been removed due to the service no longer being available</li> <li>Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert</li> <li>Bio::EUtilities, Bio::Biblio are now separate releases on CPAN</li> <li>Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be released independently on CPAN</li> </ul> </li> <li>Docker instances of tagged releases are available! [hlapp]</li> <li>Bio::SearchIO::infernal <ul> <li>Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]</li> <li>Bio::Search::HSP::ModelHSP: Added a &rsquo;noncanonical_string&rsquo; method to retrieve the NC line from CMSEARCH reports [pcantalupo]</li> <li>Bio::Search::Result::INFERNALResult - Added new module to represent features of Infernal reports [pcantalupo]</li> </ul> </li> <li>SQLite support for Bio::DB::Taxonomy - [cjfields]</li> <li>WrapperBase quoted option values [majensen]</li> <li>Various documentation fixes and updates [bosborne]</li> </ul> <p>And many many bug fixes.  Please see the Changes file with the distribution.</p> <p>Thanks, and enjoy!</p> <p>chris</p>https://www.open-bio.org/2016/09/07/bioruby-1-5-1-released/Wed, 07 Sep 2016 15:04:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/09/07/bioruby-1-5-1-released/<p>We are pleased to announce the release of BioRuby 1.5.1.</p> <p>In this new release, NCBI Entrez web client classes, Bio::NCBI::REST and Bio::PubMed, are changed to use HTTPS instead of HTTP, to prepare <a href="https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/">NCBI website transitioning to HTTPS</a>.</p> <p>For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.5.1/RELEASE_NOTES.rdoc" title="RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.5.1/ChangeLog" title="ChangeLog">ChangeLog</a>.</p> <p>The archive is available for download from the following links.</p> <ul> <li>Tar.gz file: <a href="http://bioruby.org/archive/bioruby-1.5.1.tar.gz">http://bioruby.org/archive/bioruby-1.5.1.tar.gz</a></li> <li>Gem file: <a href="https://rubygems.org/gems/bio" title="https://rubygems.org/gems/bio">https://rubygems.org/gems/bio</a> or <a href="http://bioruby.org/archive/gems/bio-1.5.1.gem">http://bioruby.org/archive/gems/bio-1.5.1.gem</a></li> </ul> <p>You can easily install by using RubyGems. First, check the version number by using search command:</p> <p><code>% gem search --remote bio</code></p> <p>and find “bio (1.5.1)” in the list. Then,</p> <p><code>% sudo gem install bio</code></p> <p>Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.</p> <p>Because this release is a minor version up, only few changes picked from the <a href="https://github.com/bioruby/bioruby">git head</a> are included.</p> <p>Acknowledgments: Thanks to Dr. Mark Johnson about information of the NCBI website change.</p>https://www.open-bio.org/2016/08/26/biopython-1-68-released/Fri, 26 Aug 2016 16:23:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/08/26/biopython-1-68-released/<p>Dear Biopythoneers,</p> <p>Source distributions and Windows installers for Biopython 1.68 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the official <a href="http://biopython.org/">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.68">on the Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but <strong>this will be our final release to run on Python 2.6.</strong> It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.</p> <p>Bio.PDB has been extended to parse the RSSB&rsquo;s new binary Macromolecular Transmission Format (MMTF, see <a href="http://mmtf.rcsb.org">http://mmtf.rcsb.org</a>), in addition to the mmCIF and PDB file formats (contributed by Anthony Bradley). This requires an optional external dependency on the <a href="https://github.com/rcsb/mmtf-python">mmtf-python library</a>.</p> <p>Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski). It is now faster, addresses some problems with local alignments, and also now allows gap insertions after deletions, and vice versa, inspired by the <a href="http://dx.doi.org/10.1101/031500">preprint from Flouri et al</a>.</p> <p>The two sample graphical tools SeqGui (Sequence Graphical User Interface) and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide transcription, back-transcription and translation into amino acids using Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython. xbbtools is able to open Fasta formatted files, does simple nucleotide operations and translations in any reading frame using one of the NCBI genetic codes. In addition, it supports standalone Blast installations to do local Blast searches.</p> <p>New <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">NCBI genetic code table</a> 26 (Pachysolen tannophilus Nuclear Code) has been added to Bio.Data (and the translation functionality), and table 11 is now also available under the alias Archaeal.</p> <p>In line with <a href="https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/">NCBI website HTTPS changes</a>, Biopython now uses HTTPS rather than HTTP to connect to the NCBI Entrez and QBLAST API.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 and best practice standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Anthony Bradley (first contribution)</li> <li>Ben Fulton</li> <li>Carlos Pena</li> <li>Connor T. Skennerton</li> <li>Iddo Friedberg</li> <li>Kai Blin</li> <li>Kristian Davidsen (first contribution)</li> <li>Markus Piotrowski</li> <li>Olivier Morelle (first contribution)</li> <li>Peter Cock</li> <li>Tiago Antao</li> <li>Travis Wrightsman</li> <li>Uwe Schmitt (first contribution)</li> <li>Xiaoyu Zhuo (first contribution)</li> </ul> <p>Thank you all.</p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a></p> <p>Checksums:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.68.* </span></span><span style="display:flex;"><span>078e915185485a5327937029b7577ddc biopython-1.68.tar.gz </span></span><span style="display:flex;"><span>362e964543a424a2f7585ea4008ea834 biopython-1.68.win32-py2.6.exe </span></span><span style="display:flex;"><span>772d07d9a6490d674688d00ede2bdfe9 biopython-1.68.win32-py2.7.exe </span></span><span style="display:flex;"><span>fda2d1c8d4a7862f6af85122c86fcd0f biopython-1.68.win32-py2.7.msi </span></span><span style="display:flex;"><span>8de95a90704f15f4c22d5359dbc54b75 biopython-1.68.win32-py3.3.exe </span></span><span style="display:flex;"><span>92f40105761520daeeb9128254a8bc94 biopython-1.68.win32-py3.3.msi </span></span><span style="display:flex;"><span>b1cd3f6b4ad1096347d5019c68128dac biopython-1.68.win32-py3.4.exe </span></span><span style="display:flex;"><span>9403b9b0d01c22b49edb34e2164c31de biopython-1.68.win32-py3.4.msi </span></span><span style="display:flex;"><span>72202792fc387376c07e28997ece181f biopython-1.68.win32-py3.5.exe </span></span><span style="display:flex;"><span>ff0cfc6c835ddf890b69ba872fb46b39 biopython-1.68.win32-py3.5.msi </span></span><span style="display:flex;"><span>adb3e8ce60b02b3b46330bbca68f9732 biopython-1.68.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.68.* </span></span><span style="display:flex;"><span>d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f biopython-1.68.tar.gz </span></span><span style="display:flex;"><span>09449d7204c65e6010545092f2bc1dc662a0b5f6a873e52a08e19392f935fdb7 biopython-1.68.win32-py2.6.exe </span></span><span style="display:flex;"><span>a7c2fe52ce8dcf503a492e4ee006dd8bc62faa77078d04c92abdbf7713bf2166 biopython-1.68.win32-py2.7.exe </span></span><span style="display:flex;"><span>f92dfefc9a4ee61dda838a61d73a38b55552a1771ce411505009a48702aefd41 biopython-1.68.win32-py2.7.msi </span></span><span style="display:flex;"><span>bce6a4cece7b75650d6a478f4ed9d7d1a5351df42a1820866a0cbd74c254565d biopython-1.68.win32-py3.3.exe </span></span><span style="display:flex;"><span>85bd5d499400e594f77d297966f56c139499711513b9cd24b87fece5a0463fbe biopython-1.68.win32-py3.3.msi </span></span><span style="display:flex;"><span>05c1f59933ef35ecb838649f6fabacb823f2a48c2498ed57ac59a6b3629b5369 biopython-1.68.win32-py3.4.exe </span></span><span style="display:flex;"><span>10928347029bc6b0b76567d5f6026a8a002bd3502a7ceeaded7d566938db4bef biopython-1.68.win32-py3.4.msi </span></span><span style="display:flex;"><span>5d08e4de11f920ec5207e10d264fceb837e2000843a56fd684e0ee2dfb948fe5 biopython-1.68.win32-py3.5.exe </span></span><span style="display:flex;"><span>299888c32b36f32542775952e7b863bd9c3d362f61a69b7d8a136a63aeabec36 biopython-1.68.win32-py3.5.msi </span></span><span style="display:flex;"><span>986a0fa6919d2b51959259011dd0674b115383237e109c5a55c37cb18eef999b biopython-1.68.zip </span></span></code></pre></div><p><em>Updated</em> 29 August 2016 to include the Python 3.5 installer checksums.</p>https://www.open-bio.org/2016/07/21/bosc-2016-in-disney-world-with-donald-docker/Thu, 21 Jul 2016 14:18:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/07/21/bosc-2016-in-disney-world-with-donald-docker/<p>First I would like to congratulate OBF that supports diversity in the community with its <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">travel awards initiative</a>. I was very pleased to be one of the <a href="https://news.open-bio.org/2016/05/23/first-obf-travel-fellowships/">three travel fellowship awardees</a>. Thank you OBF! Ιt was great to attend <a href="https://www.open-bio.org/wiki/BOSC_2016">BOSC 2016</a> and meet remarkable people and know their work.It was one of the most welcoming meetings I have attended and Ι liked that is was active on the social media and the conference materials and speaker presentations were available online. It made it fun and useful and we could focus less on our notebooks and more on the speakers. Τhis also attracted a lot of positive comments from the other Special Interest Groups. So “Bravo” to the organizers!On the scientific part, it was nice to see Docker making an impression on the bioinformatics community. Everyone was talking about it. It is an awesome way to package bioinformatics applications and the fact that it received so much attention got me pretty excited. I am planning to use it to package CollOS, an open source web application I presented at the conference, that tracks, annotates and barcodes biological samples to facilitate wet lab scientists to locate and identify biological samples.Last but definitely not least, I would like to congratulate Mónica Muñoz-Torres and the organizers for their reference to the recent tragic shooting incident in Orlando.Hope to see you next year in Prague!Dimitra</p>https://www.open-bio.org/2016/06/14/new-biojava-logo-design-competition-andreas/Tue, 14 Jun 2016 17:47:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/06/14/new-biojava-logo-design-competition-andreas/<p><a href="https://github.com/biojava/logo">BioJava</a> is organizing a <strong>design competition</strong> to come up with a new logo. Anybody can participate:</p> <ul> <li> <p>The logo should look modern and be better than the current one (yellow circle)</p> </li> <li> <p>The logo should be able to be rendered as a favicon, as well as large (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.</p> </li> <li> <p>Logos shall not look similar in any way to the trademarked Java programming language logo. This means no coffee cups in any way.</p> </li> </ul> <p><strong>Deadline:</strong> Deadline for submissions is July 4th.</p> <p><strong>Announcement of Winner:</strong> The winner of the new logo competition will be announced during BOSC 2016.</p> <p><strong>Prize:</strong> We will print t-shirts with the new logo and the designer will get a free t-shirt.</p> <p>If the designer of the winning new logo will be attending ISMB 2016, the attending BioJava developers will take the winner out for dinner.</p> <p>BioJava will carry the new logo on its homepage and GitHub Profile</p> <p><strong>Details:</strong> For full details of the competition and how to make a submission please view here:</p> <p><a href="https://github.com/biojava/logo">https://github.com/biojava/logo</a> <strong>Result Update:</strong></p> <p>As <a href="http://mailman.open-bio.org/pipermail/biojava-l/2016-July/011488.html">announced via the mailing list</a> and at BOSC 2016, the winning logo was by Aleix Latifa:</p> <p><img src="https://raw.githubusercontent.com/biojava/logo/master/submissions/lafita_4/logo.png" alt=""></p>https://www.open-bio.org/2016/06/08/biopython-1-67-released/Wed, 08 Jun 2016 17:39:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/06/08/biopython-1-67-released/<p>This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure.</p> <p>Source distributions and Windows installers for Biopython 1.67 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">official Biopython website</a>, and the release is also on the <a href="https://pypi.python.org/pypi/biopython/1.67">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but support for Python 2.6 is considered to be deprecated. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.</p> <p>Comparison of SeqRecord objects until now has used the default Python object comparison (are they the same instance in memory?). This can be surprising, but comparing all of the attributes would be too complex. As of this release attempting to compare SeqRecord objects should raise an exception instead. If you want the old behaviour, use id(record1) == id(record2) instead.</p> <p>New experimental module Bio.phenotype is for working with Phenotype Microarray plates in JSON and the machine vendor&rsquo;s CSV format (contributed by Marco Galardini).</p> <p>Following the convention used elsewhere in Biopython, there is a new function Bio.KEGG.read(&hellip;) for parsing KEGG files expected to contain a single record only - the existing function Bio.KEGG.parse(&hellip;) is intended to be used to iterate over multi-record files.</p> <p>When a gap character is defined, Bio.Seq will now translate gap codons (e.g. &ldquo;&mdash;&rdquo;) into a single gap (&quot;-&quot;) in the protein sequence. The gap character is inferred from the Seq object&rsquo;s alphabet, but it can also be passed as an argument to the translate method.</p> <p>The new NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria, has been added to Bio.Data (and the translation functionality).</p> <p>The Bio.Entrez interface will automatically use an HTTP POST rather than HTTP GET if the URL would exceed 1000 characters. This is based on NCBI guidelines and the fact that very long queries like complex searches can otherwise trigger an HTTP Error 414 Request URI too long.</p> <p>Foreign keys are now used when creating BioSQL databases with SQLite3 (this was not possible until SQLite version 3.6.19). The BioSQL taxonomy code now updates the taxon table left/right keys when updating the taxonomy.</p> <p>There have been some fixes to the MMCIF structure parser which now uses identifiers which better match results from the PDB structure parse.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the May 2016 release of REBASE.</p> <p>The mmCIF parser in Bio.PDB.MMCIFParser has been joined by a second version which only looks at the ATOM and HETATM lines and can be much faster.</p> <p>The Bio.KEGG.REST will now return unicode text-based handles, except for images which remain as binary bytes-based handles, making it easier to use with the mostly text-based parsers in Biopython.</p> <p>Note that the BioSQL test configuration information is now in a new file Tests/biosql.ini rather than directly in Tests/test_BioSQL_*.py as before. You can make a copy of the provided example file Tests/biosql.ini.sample as Tests/biosql.ini and edit this if you wish to run the BioSQL tests.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 standard coding style, and in converting our docstring documentation to use the reStructuredText markup style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Rosenfeld (first contribution)</li> <li>Anders Pitman (first contribution)</li> <li>Barbara Mühlemann (first contribution)</li> <li>Ben Fulton</li> <li>Ben Woodcroft (first contribution)</li> <li>Brandon Invergo</li> <li>Brian Osborne (first contribution)</li> <li>Carlos Pena</li> <li>Chaitanya Gupta (first contribution)</li> <li>Chris Warth (first contribution)</li> <li>Christiam Camacho (first contribution)</li> <li>Connor T. Skennerton</li> <li>David Koppstein (first contribution)</li> <li>Eric Talevich</li> <li>Jacek Śmietański (first contribution)</li> <li>João D Ferreira (first contribution)</li> <li>João Rodrigues</li> <li>Joe Cora (first contribution)</li> <li>Kai Blin</li> <li>Leighton Pritchard</li> <li>Lenna Peterson</li> <li>Marco Galardini (first contribution)</li> <li>Markus Piotrowski</li> <li>Matt Ruffalo (first contribution)</li> <li>Matteo Sticco (first contribution)</li> <li>Nader Morshed (first contribution)</li> <li>Owen Solberg (first contribution)</li> <li>Peter Cock</li> <li>Steve Bond (first contribution)</li> <li>Terry Jones (first contribution)</li> <li>Vincent Davis</li> <li>Zheng Ruan</li> </ul> <p>Again this list of contributors is longer than usual, which is good, but partly reflects the delay since our last release. My apologies.</p>https://www.open-bio.org/2016/05/27/bosc-2016-panel-growing-and-sustaining-open-source-communities/Fri, 27 May 2016 16:45:21 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/05/27/bosc-2016-panel-growing-and-sustaining-open-source-communities/<p>Every year, <a href="https://www.open-bio.org/wiki/BOSC_2016">BOSC</a> includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. BOSC is all about community, so this year&rsquo;s panel topic&ndash; <a href="https://www.open-bio.org/wiki/BOSC_2016_Panel">Growing and Sustaining Open Source Communities</a>&ndash;is right at the heart of what we do. Since the first BOSC in 2000, we have focused on bringing together open source bioinformatics developers and users to form and expand collaborations and grow the communities that use and improve their tools and resources.</p> <p>Community projects have resulted in some of the most popular bioinformatics resources. However, there are many challenges that may be encountered as a community effort develops and evolves. For example:</p> <ul> <li>How can an open source community integrate a diverse set of participants, including people with different levels of experience, different interests, and different demographic characteristics?</li> <li>How can non-developers (for example, people who primarily write documentation, or who are users of the software) contribute to these projects?</li> <li>What funding approaches have successfully sustained open source communities after any core funding has run out?</li> <li>What technologies have helped open source communities coordinate efficient communication and planning across multiple locations?</li> <li>What organizational models have some of these communities followed?</li> </ul> <p><a href="https://www.open-bio.org/wiki/BOSC_2016_Panel">This panel</a> brings together six people (five panelists plus a moderator) who have worked to sustain open source communities. They will join audience members in an open dialog about challenges encountered during the life cycle of these communities and approaches to addressing them.</p> <p>Panel chair <strong>Mónica Muñoz-Torres</strong> is the biocuration lead for Berkeley Bioinformatics Open-Source Projects (BBOP) at <a href="http://www.lbl.gov">Lawrence Berkeley National Laboratory</a>.</p> <p><strong>Abigail Cabunoc Mayes</strong> is the Lead Developer of the <a href="https://mozillascience.org/">Mozilla Science Lab</a>.</p> <p><strong>Bastian Greshake</strong> co-founded <a href="https://opensnp.org">openSNP</a>, a crowdsourced/citizen science open data project.</p> <p><strong>Jamie Whitacre</strong> is the technical project manager for <a href="http://jupyter.org">Project Jupyter</a>, which grew out of the widely used IPython Notebook.</p> <p><strong>John Chilton</strong> of Penn State is a software developer on the <a href="https://galaxyproject.org/">Galaxy project</a>, and one of the co-founders of the <a href="http://www.commonwl.org/">Common Workflow Language</a>.</p> <p><strong>Natasha Wood</strong> of the University of Cape Town is the co-founder of the <a href="https://thecubhub.wordpress.com/">Cape Unseminars in Bioinformatics</a>.</p> <p>Please see <a href="https://www.open-bio.org/wiki/BOSC_2016_Panel">/wiki/BOSC_2016_Panel</a> for more information about the panelists.</p>https://www.open-bio.org/2016/05/23/first-obf-travel-fellowships/Mon, 23 May 2016 16:05:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/05/23/first-obf-travel-fellowships/<p>The first round of the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> has granted funds to three open source bioinformatics software developers to help them attend the <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC) 2016</a> in Orlando, Florida, this July. The travel fellowship program ( <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">announced 1 May 2016</a>) aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Applications for the first round in 2016 were due on April 15, with two more due dates this year on August 15 and December 15.</p> <p>Out of more than a dozen applicants from four different continents, the OBF Board chose the following three recipients:</p> <ul> <li><a href="https://github.com/dimitras">Dimitra Sarantopoulou</a> of the University of Pennsylvania is an open source bioinformatics developer who focuses on web applications for proteomic analysis.</li> <li>Michael R. Crusoe ( <a href="https://twitter.com/biocrusoe">@biocrusoe</a>) is the Co-founder &amp; Community Engineer for the <a href="http://www.commonwl.org/">Common Workflow Language (CWL)</a>, and previously was the lead developer of <a href="https://github.com/dib-lab/khmer">khmer</a>.</li> <li><a href="http://wurmlab.github.io/team/priyam/">Anurag Priyam</a> is a self-taught bioinformaticst who has created several successful open source tools, including  <a href="https://github.com/wurmlab/sequenceserver">SequenceServer</a> and <a href="https://github.com/wurmlab/oswitch">oswitch</a>, a Docker-based virtual environment switcher.</li> </ul> <p>The OBF Board congratulates the three winners!</p> <p>This first round has also shown several points of improvement, both for the program description and the application form. We are in the process of making small adjustments to both, and expect to reopen the application form for the next round of funding at the latest by the time BOSC 2016 rolls around (July 8). We encourage others for whom travel costs are a barrier to participating in open source bioinformatics events to apply for this next round (due date is August 15, 2016).</p>https://www.open-bio.org/2016/04/25/welcome-gsoc-2016-students/Mon, 25 Apr 2016 08:13:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/04/25/welcome-gsoc-2016-students/<p>The Open Bioinformatics Foundation is participating in the Google Summer of Code 2016 program, and last Friday the selected students were announced. Congratulations to all of you, and welcome. I also want to use this opportunity to thank all students who applied. Resources are limited and your proposals did not make it easy to select our finalists. We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one after all.</p> <p>The Open Bioinformatics Foundation gets to host <a href="https://summerofcode.withgoogle.com/organizations/5693436329984000/#projects">eight student projects this</a> year:</p> <ul> <li><a href="https://github.com/AlishaMechtley/treematcher/wiki/Blog">Alisha Mechtley</a> will work with the ETE toolkit on tree searching using regular-expression-like queries.</li> <li><a href="https://anton-khodak.github.io/argparse2cwl-blog/2016/08/11/gentle-introduction.html">Anton Khodak</a> will work on the Common Workflow Language, creating an automated tool wrapper/converter for CWL.</li> <li><a href="https://chfi.se/posts/2016-08-22-gsoc-final.html">Christian Fischer</a> will work on the GeneNetwork Genome Browser.</li> <li><a href="https://sxibolet.2pitau.org/gsoc.html">Graham Dyer</a> will work on openSNP, extending the quantified-self support.</li> <li><a href="https://github.com/bionode/gsoc16/blob/8a155a14c34d820a3a77d15b3600d4adf225f179/README.md">Julian Mazzitelli</a> will work on a workflow engine for streamed data analysis in Bionode.</li> <li><a href="https://bitbucket.org/mnave/gsoc-blog/">Mariana Nave</a> will improve the prediction for RiPP clusters in antiSMASH.</li> <li><a href="http://mateusjabour.github.io/gsoc-code-submission">Mateus Jabor</a> will work on improving the user experience in openSNP.</li> <li><a href="http://raivivek.in/programming/gsoc-16-wrap-up.html#main">Vivek Rai</a> will work on linking phenotypes to SNPs in openSNP.</li> </ul> <p>Please join me in welcoming all of them in the Open Bioinformatics Foundation community and the respective subprojects. It looks like this will be a great summer.</p> <p>Kai Blin</p> <p>OBF administrator for GSoC 2016</p> <p><em>P.S. We have retrospectively updated this post to add links to the students&rsquo; blog posts.</em></p>https://www.open-bio.org/2016/04/18/phylosoc-supports-obf-travel-fellowships/Mon, 18 Apr 2016 16:01:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/04/18/phylosoc-supports-obf-travel-fellowships/<p>The Open Bioinformatics Foundation is pleased to announce a gift of USD 18,125 from the Phyloinformatics Summer of Code toward the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship program</a>. The program, <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">announced earlier this year on March 1</a>, aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The program includes but is not limited to the annual <a href="https://www.open-bio.org/wiki/BOSC">Bioinformatics Open Source Conference</a> (BOSC), OBF’s flagship event.</p> <p>The funds for this gift are a legacy of the seven years during which the National Evolutionary Synthesis Center ( <a href="https://www.nescent.org/">NESCent</a>) served as a mentoring organization in the <a href="https://developers.google.com/open-source/gsoc/">Google Summer of Code</a> ™. Over the years, NESCent’s program, the <a href="http://informatics.nescent.org/wiki/Main_Page#Phyloinformatics_Summer_of_Code">Phyloinformatics Summer of Code</a>, supported dozens of students for three-month paid internships developing open source software for evolutionary and biodiversity informatics.  Each year, Google made a small award to Duke University, NESCent’s administrative home, to support the program, and when NESCent ceased operations in 2015, the funds for this gift remained.</p> <p>Todd Vision, former Associate Director of Informatics at NESCent, says &ldquo;With this gift, OBF will carry on the legacy of the Phyloinformatics Summer of Code in building a diverse and collaborative open source bioinformatics community.&rdquo;</p> <p>OBF has only been able to underwrite the Travel Fellowship program for an initial 3 years, for at most a handful of awards each year. As Hilmar Lapp, President of OBF’s Board, and former Assistant Director of Informatics at NESCent, explains, “This program is a signature part of our commitment to inclusivity and growing our community, and we are keen to make it a sustained effort. This gift is a key step in that direction, and I hope that we can convince other donors to follow.”</p> <p>The gift is specifically earmarked for awards to increase diversity at bioinformatics community events. “By targeting travel costs, we hope to remove one barrier to participation. Meeting face to face can be a critical step to becoming part of an existing community.”, says Karen Cranston, OBF Board Member, who ran the Phyloinformatics Summer of Code program for several years while at NESCent.</p> <p>There have been long-standing ties between the Phyloinformatics Summer of Code and OBF. They have shared project ideas and mentors, and some graduates from the summer program have subsequently taken on prominent roles in OBF’s projects and community. A student from the 2011 summer program, Sarah Hird, even <a href="https://news.open-bio.org/2015/01/04/bosc-welcomes-sarah-hird/">served as the Outreach Coordinator for BOSC 2015</a>, the theme of which was Increasing Diversity.</p> <p><strong><em>About OBF:</em></strong> The <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a> (OBF) is a nonprofit volunteer run organization founded in 2001 with a mission to promote the practice and philosophy of open-source software development and open science within the biological research community. OBF is incorporated as an affiliate project of <a href="http://www.spi-inc.org/">Software in the Public Interest</a>, Inc., a 501(c)(3) fiscal sponsorship organization.</p> <p><strong><em>About NESCent:</em></strong> The <a href="https://www.nescent.org/">National Evolutionary Synthesis Center</a> (NESCent) was a science center dedicated to cross-disciplinary research in evolution, jointly operated by Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University from 2004-2015, with support largely from the National Science Foundation. In 2015, it transitioned to the <a href="http://tricem.org">Triangle Center for Evolutionary Medicine</a> (TriCEM).</p>https://www.open-bio.org/2016/03/28/bosc-codefest-2016/Mon, 28 Mar 2016 13:56:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/28/bosc-codefest-2016/<p>The <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC)</a> is a two day meeting focused on open source bioinformatics. We aim to encourage and support a friendly, open and productive community that helps us work together to answer hard biological questions. We&rsquo;ll get together this summer, July 8-9, in Orlando, Florida.</p> <p>Abstracts for BOSC 2016 talks and posters are due this Friday, April 1st. We want to hear about your research and encourage everyone to <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">submit an abstract</a>. We love talks from newcomers to BOSC as well as established projects: no idea is too big or small. We also offer <a href="https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/">Travel Fellowships for speakers</a> if money would be a barrier to attending.</p> <p>Prior to BOSC, we organize a free two day collaborative working session called <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest</a>. We&rsquo;ll establish friendships and collaborations while helping new members find fun work and extending existing projects. It&rsquo;s a time to learn, teach, develop and grow. This year we&rsquo;re kindly hosted by the <a href="https://familab.org/">FamiLAB workspace</a> in Orlando. So in addition to getting to work with fellow OpenBio members, you&rsquo;ll have the chance to learn about the Orlando maker community.</p> <p>We hope you&rsquo;ll join us in Orlando this summer for Codefest and BOSC. Please send in your abstracts before Friday and sign up on the Codefest page.</p>https://www.open-bio.org/2016/03/22/bosc-2016-keynote-speakers/Tue, 22 Mar 2016 12:10:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/22/bosc-2016-keynote-speakers/<p>We&rsquo;re delighted to announce the keynote speakers for the <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference, BOSC 2016</a>:</p> <h1 id="jennifer-gardy">Jennifer Gardy</h1> <p><a href="https://www.open-bio.org/wiki/File:JenniferGardy.jpg" title="Jennifer Gardy"><img src="https://www.open-bio.org/w/images/thumb/0/04/JenniferGardy.jpg/240px-JenniferGardy.jpg" alt="Jennifer Gardy"></a></p> <p>Dr. Jennifer Gardy is both a scientist and science communicator. She holds a PhD in Bioinformatics, and is an Assistant Professor of Population and Public Health at the University of British Columbia and a Senior Scientist at the British Columbia Centre for Disease Control (BCCDC). At the BCCDC, she pioneered a new way of investigating outbreaks of infectious diseases – &ldquo;genomic epidemiology&rdquo;, which uses a pathogen&rsquo;s genome sequence as a tool for understanding how an infectious disease spreads. Her group was the first to use genome sequencing to reconstruct a large outbreak of tuberculosis, and she is continuing to apply this novel technique to other outbreak scenarios. She is also involved in other genomics-related research, including replacing traditional laboratory microbiology protocols with single genomic analyses. In 2014, she was appointed the Canada Research Chair in Public Health Genomics, and is Senior Editor at the new open data, open access journal Microbial Genomics.</p> <p>In addition to her career as a research scientist, Dr. Gardy is known for her work in science communication and education, both in print and on TV. She has made regular appearances on CBC&rsquo;s documentary series The Nature of Things, has hosted CBC&rsquo;s eight-part science series Project X, and is a regular guest host on Discovery Channel’s Daily Planet science show. She has written and blogged for the Globe and Mail, has written a children’s book – It’s Catching! The Infectious World of Germs and Microbes – and runs a series of workshops on how to communicate science effectively.</p> <p>Dr. Gardy&rsquo;s keynote topic is “The open-source outbreak: can data prevent the next pandemic?”</p> <p><em>Every century, something comes along that shakes up public health – vaccines, sanitation, antibiotics – and data promises to be the great disrupter of 21st century infectious disease epidemiology. In the last 5-6 years, genomics has dramatically changed how public health agencies diagnose and investigate diseases from food poisoning to tuberculosis, giving us a new tool to understand and control infections. The change is also apparent at a cultural level – genomics and bioinformatics researchers have largely come from an open data, collaborative space and have brought new ways of thinking to public health laboratories, previously secret, closed organizations. In this talk, we’ll explore some of the dramatic changes in public health microbiology that genomics and bioinformatics has facilitated, and look at how future data sharing efforts in areas such as digital disease detection might be the key to preventing future pandemics.</em></p> <p>Homepage: <a href="http://www.jennifergardy.com">Jennifer Gardy</a>, Twitter: <a href="https://twitter.com/jennifergardy">@JenniferGardy</a></p> <hr> <h1 id="steven-salzberg">Steven Salzberg</h1> <p><a href="https://www.open-bio.org/wiki/File:StevenSalzberg.jpg" title="Steven Salzberg"><img src="https://www.open-bio.org/w/images/thumb/3/3b/StevenSalzberg.jpg/210px-StevenSalzberg.jpg" alt="Steven Salzberg"></a></p> <p>Dr. Steven Salzberg is the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics and the Director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. From 2005-2011, he was the Director of the Center for Bioinformatics and Computational Biology and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world&rsquo;s leading DNA sequencing centers at the time.</p> <p>Salzberg&rsquo;s lab currently focuses on next-generation sequence alignment, genome assembly, and microbiome analysis.They have produced several popular systems for alignment of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems. All of the group&rsquo;s software is free and open source, and their systems have been downloaded hundreds of thousands of times.</p> <p>Dr. Salzberg is a Fellow of the American Association for the Advancement of Science (AAAS) and a Fellow of the International Society for Computational Biology (ISCB). He was the 2013 winner of the Benjamin Franklin Award for Open Access in the Life Sciences, in recognition of his many contributions to open access bioinformatics software and his strong advocacy for open access to data, software and publications.</p> <p>Dr. Salzberg will speak about &ldquo;Open source, open access, and open data: why science moves faster in an open world&rdquo;.</p> <p><em>The Human Genome Project established a practice of sharing data rapidly, prior to publication, that has since become a model for many projects in genomics. Data sharing has been slow to penetrate other fields because of many factors, some of which I will discuss in this talk. Nevertheless, sharing of methods, data, and results helps science move ahead faster, and openness is essential for the continual process of checking and self-correction that good science requires. I will discuss some of the successes as well as some noteworthy mistakes that have been discovered thanks to open science.</em></p> <p>Homepage: <a href="https://salzberg-lab.org/">Steven Salzberg</a>, Twitter: <a href="https://twitter.com/StevenSalzberg1">@StevenSalzberg1</a></p> <hr> <p>The <a href="https://www.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/">BOSC 2016 call for abstracts is currently open</a>, and <a href="https://www.iscb.org/ismb2016-registration">BOSC/ISMB 2016 registration</a> will open next week. We hope to see you in Florida!</p>https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/Tue, 01 Mar 2016 20:52:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/<p>We are very pleased to announce our new <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation (OBF) Travel Fellowship program</a>. The program is designed to enable people, whether long-standing members of our community or newcomers, to participate in eligible events for which costs would otherwise be prohibitive. This includes our annual <a href="https://www.open-bio.org/wiki/BOSC">Bioinformatics Open Source Conference (BOSC)</a>.</p> <p>Although not limited to specific groups of people, the program constitutes another major step for us in our ongoing efforts to increase the diversity in our communities in particular, and in the open source / open science bioinformatics community in general. As explained in the just published <a href="http://dx.doi.org/10.1371/journal.pcbi.1004691">BOSC 2015 report</a>, inclusivity was one of the founding principles of the Bio* open-source project communities that came together under the OBF umbrella, and thus also of BOSC, our flagship event. <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">OBF&rsquo;s bylaws</a> have included a nondiscrimination clause from the outset. OBF&rsquo;s major member projects have not only always welcomed new participants to their communities, but embraced passing on leadership to people who hadn&rsquo;t been part of the &ldquo;inner circle&rdquo; from the beginning.</p> <p>However, being on the &ldquo;inside&rdquo; can hide the barriers to joining a community as a newcomer. In practice, the demographics of our member community, and therefore also of BOSC, have mirrored the <a href="http://floss2013.libresoft.es/results.en.html">low diversity observed</a> for open-source project communities in general.</p> <p>We&rsquo;ve committed ourselves to address this. We simply owe it to our mission, which is predicated on being inclusive. For BOSC 2015 we chose to make increasing diversity the main theme, including the <a href="https://news.obf.io/2015/06/05/bosc-2015-panel-increasing-diversity/">BOSC 2015 panel discussion</a>. When asked for a show of hands of who was there for the first time, nearly half of the attendees&rsquo; hands went up! We believe firmly that with enough dedicated and sustained attention, our community <em>can</em> include everyone who shares our mission. We also believe that eventually more diversity at our community events <em>will</em> trickle down to increasing the diversity of participants in our member projects.</p> <p>To fund the OBF Travel Fellowship program, we have for now committed an annual budget of $5,000 from our existing assets. At this level, we should be able to sustain the program for a minimum of 3 years.  We would like to do more, and to commit to the program for at least 10 years. To help us accomplish that, we are <a href="https://www.open-bio.org/wiki/Donate">calling on donors</a> and BOSC sponsors. You can earmark your contribution to be used specifically for funding this program – simply <a href="mailto:board@open-bio.org">email the Board</a> if the donation form does not leave enough space.</p> <p>Special thanks for bringing this program to life go to Karen Cranston, who joined the OBF Board in spring 2015 and shepherded the effort from inception to launch.</p>https://www.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/Tue, 01 Mar 2016 17:42:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/<p>Call for Abstracts for the 17th Annual Bioinformatics Open Source Conference (BOSC 2016), a Special Interest Group (SIG) of <a href="https://www.iscb.org/ismb2016">ISMB 2016</a>.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2016"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]"></a></p> <ul> <li>Dates: July 8-9, 2016</li> <li>Location: Orlando, FL</li> <li>Web site: <a href="https://www.open-bio.org/wiki/BOSC_2016">/wiki/BOSC_2016</a></li> <li>Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></li> <li>BOSC announcements mailing list: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a></li> <li>Twitter: <a href="https://twitter.com/OBF_BOSC" title="OBF Bioinformatics Open Source Conference (BOSC)">@OBF_BOSC</a> and <a href="https://twitter.com/OBF_news" title="Open Bioinformatics Foundation (OBF) News">@OBF_News</a></li> </ul> <p>Important Dates:</p> <p><a href="http://www.iscb.org/ismb2016"><img src="https://news.obf.io/wp-content/uploads/2016/03/ismb2016.png" alt="[ISMB 2016 logo]"></a></p> <ul> <li>Call for one-page abstracts opens: March 1, 2016</li> <li><a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">Abstract submission</a> deadline: April 1, 2016 - <em>extended to Monday 4 April 2016</em></li> <li>Travel fellowship application deadline: April 15, 2016</li> <li>Authors notified: May 6, 2016</li> <li><a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a>: July 6-7, 2016, Orlando, FL (confirming venue)</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2016">BOSC 2016</a>: July 8-9, 2016, Orlando, FL</li> <li><a href="https://www.iscb.org/ismb2016">ISMB 2016</a>: July 8-12, 2016, Orlando, FL</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. It is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results and software.</p> <p>We welcome one-page abstracts on any topic of relevance to open source bioinformatics and open science. Presentation formats are lightning talks, longer talks, and/or posters. We plan to offer a limited number of travel fellowships to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC – please see the <a href="https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/">OBF Travel Fellowship announcement</a> for more information.</p> <p>Session topics include:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Visualization</li> <li>Translational Bioinformatics</li> <li>Bioinformatics Open Source Libraries and Projects</li> </ul> <p>If your company or organization is interested in helping to sponsor BOSC 2016, please contact us! Sponsors in 2015 included <a href="http://www.google.com/">Google</a>, <a href="http://www.gigasciencejournal.com/">GigaScience</a>, <a href="http://curoverse.com/">Curoverse</a> and <a href="http://bina.com/">Bina</a> – we thank them for their support.</p> <p>BOSC 2016 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko</p>https://www.open-bio.org/2015/12/10/online-membership-form/Thu, 10 Dec 2015 05:35:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/12/10/online-membership-form/<p>The Open Bioinformatics Foundation (OBF) is pleased to announce that we’ve finally entered the 21st century and upgraded our membership form from paper (yep!) to an <a href="https://goo.gl/l6WJ23" title="OBF membership form">online form</a>.</p> <p><a href="https://www.open-bio.org/wiki/Membership">Membership in the OBF</a> is free, and is open to anyone who has attended BOSC or can otherwise demonstrate commitment to <a href="https://www.open-bio.org/wiki/Main_Page#About_Us">OBF&rsquo;s goals</a>. The information you enter on the form, including your email address, will be treated confidentially - we are in the business of promoting open source and open science, not in selling email addresses.</p> <p>If you have any questions about OBF or OBF membership, you can contact us at <a href="mailto:board@open-bio.org">board@open-bio.org</a> and/or tweet to <a href="https://twitter.com/obf_news">@OBF_News</a>.</p>https://www.open-bio.org/2015/10/21/biopython-1-66-released/Wed, 21 Oct 2015 19:55:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/10/21/biopython-1-66-released/<p>Source distributions and Windows installers for Biopython 1.66 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">official Biopython website</a> and from the <a href="https://pypi.python.org/pypi/biopython/1.66">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, although support for Python 2.6 is now deprecated. It has also been tested on PyPy 2.4 to 2.6, PyPy3 version 2.4, and Jython 2.7.</p> <p>Further work on the <code>Bio.KEGG</code> and <code>Bio.Graphics</code> modules now allows drawing KGML pathways with transparency.</p> <p>The <code>Bio.SeqIO &quot;abi&quot;</code> parser now decodes almost all the documented fields used by the ABIF instruments - including the individual color channels.</p> <p><code>Bio.PDB</code> now has a <code>QCPSuperimposer</code> module using the Quaternion Characteristic Polynomial algorithm for superimposing structures. This is a fast alternative to the existing <code>SVDSuperimposer</code> code using singular value decomposition.</p> <p>Bio.Entrez now implements the NCBI Entrez Citation Matching function (ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings. <code>Bio.Entrez.parse(...)</code> now supports NCBI XML files using XSD schemas, which will be downloaded and cached like NCBI DTD files.</p> <p>A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand were parsed into CompoundLocations was fixed: <code>complement(join(...))</code> as used by NCBI worked, but <code>join(complement(...),complement(...),...)</code> as used by EMBL/ENSEMBL gave the CompoundLocation parts in the wrong order. A related bug when taking the reverse complement of a SeqRecord containing features with CompoundLocations was also fixed.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work on conforming to the Python PEP8 standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alan Medlar (first contribution)</li> <li>Anthony Mathelier (first contribution)</li> <li>Antony Lee (first contribution)</li> <li>Anuj Sharma (first contribution)</li> <li>Ben Fulton (first contribution)</li> <li>Bertrand Néron (first contribution)</li> <li>Brandon Invergo</li> <li>Carlos Pena</li> <li>Christian Brueffer</li> <li>Connor T. Skennerton (first contribution)</li> <li>David Arenillas (first contribution)</li> <li>David Nicholson (first contribution)</li> <li>Emmanuel Noutahi (first contribution)</li> <li>Eric Rasche (first contribution)</li> <li>Fabio Madeira (first contribution)</li> <li>Franco Caramia (first contribution)</li> <li>Gert Hulselmans (first contribution)</li> <li>Gleb Kuznetsov (first contribution)</li> <li>João Rodrigues</li> <li>John Bradley (first contribution)</li> <li>Kai Blin</li> <li>Kian Ho (first contribution)</li> <li>Kozo Nishida (first contribution)</li> <li>Kuan-Yi Li (first contribution)</li> <li>Leighton Pritchard</li> <li>Lucas Sinclair</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Saket Choudhary</li> <li>Sunhwan Jo (first contribution)</li> <li>Tarcisio Fedrizzi (first contribution)</li> <li>Tiago Antao</li> <li>Vincent Davis</li> </ul> <p>This is a longer list than usual, which is good, but in part this reflects the fact that this release is long overdue. Sorry, that was my fault.</p>https://www.open-bio.org/2015/07/02/bioruby-1-5-0-released/Thu, 02 Jul 2015 14:03:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/07/02/bioruby-1-5-0-released/<p>We are pleased to announce the release of BioRuby 1.5.0. This new release includes support of recent Ruby versions (Ruby 2.0.0, 2.1 and 2.2),  improvement of codes, and bug fixes.</p> <p>Here is a brief summary of changes.</p> <ul> <li>Ruby 2.0.0, 2.1, 2.2 support.</li> <li>Some features are removed because of remote service discontinuance or difficulty of code maintenance.</li> <li>Refactoring of code.</li> <li>Bio::SPTR is renamed as Bio::UniProtKB.</li> <li>Bug fixes.</li> </ul> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.5.0/RELEASE_NOTES.rdoc" title="RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.5.0/ChangeLog" title="ChangeLog">ChangeLog</a>.</p> <p>The archive is available for download from the following links.</p> <ul> <li>Tar.gz file: <a href="http://bioruby.org/archive/bioruby-1.5.0.tar.gz" title="http://bioruby.org/archive/bioruby-1.5.0.tar.gz">http://bioruby.org/archive/bioruby-1.5.0.tar.gz</a></li> <li>Gem file: <a href="https://rubygems.org/gems/bio" title="https://rubygems.org/gems/bio">https://rubygems.org/gems/bio</a> or <a href="http://bioruby.org/archive/gems/bio-1.5.0.gem" title="http://bioruby.org/archive/gems/bio-1.5.0.gem">http://bioruby.org/archive/gems/bio-1.5.0.gem</a></li> </ul> <p>You can easily install by using RubyGems. First, check the version number by using search command:</p> <p><code>% gem search --remote bio</code></p> <p>and find “bio (1.5.0)” in the list. Then,</p> <p><code>% sudo gem install bio</code></p> <p>Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2015/06/05/bosc-2015-panel-increasing-diversity/Fri, 05 Jun 2015 10:29:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/06/05/bosc-2015-panel-increasing-diversity/<p>Every year, BOSC includes a panel discussion that offers all attendees the chance to engage in conversation with the panelists and each other. Two months ago <a href="http://news.open-bio.org/news/2015/04/bosc-2014-diversity/">we announced the theme</a> of the BOSC 2015 panel would be &quot; <em>Open Source, Open Door: increasing diversity in the bioinformatics open source community&quot;</em>. Our complete list of panellists is:</p> <ul> <li>Panel chair <strong>Mónica Muñoz-Torres</strong> ( <a href="https://twitter.com/monimunozto">@monimunozto</a>) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). She is part of the development teams for Web Apollo (a web-based annotation editor designed to support community-based curation of genomes) and the tools of the Gene Ontology (GO) Consortium. She co-leads the Community Curation group within the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5K Initiative), and is a member of the Executive Committee of the International Society for Biocuration (ISB). As a graduate student, Monica founded the first Southeastern Chapter of the Society for Advancement of Hispanics/Chicanos and Native Americans in Science (SACNAS) at Clemson University; the chapter has since been actively involved in outreach activities to local high schools in an attempt to inspire students to pursue careers in STEM. She is currently working on forming the first professional chapter of SACNAS in the San Francisco Bay area.</li> <li><strong>Holly Bik</strong> ( <a href="https://twitter.com/hollybik">@hollybik</a>) is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes.</li> <li><strong>Michael R. Crusoe</strong> ( <a href="https://twitter.com/biocrusoe">@biocrusoe</a>) is the lead for the k-h-mer project at C. Titus Brown&rsquo;s Lab for Data Intensive Biology at the University of California, Davis in the School of Veterinary Medicine. A community-minded bioinformatics research software engineer and Software Carpentry instructor, he is also a member of the Debian Med software packaging team. Michael&rsquo;s social justice background includes a prior seat on the board for the Phoenix, Arizona chapter of GLSEN, the Gay, Lesbian, and Straight Education Network and he is proud to be a supporter of the Ada Initiative.</li> <li><strong>Aleksandra Pawlik</strong> ( <a href="https://twitter.com/aleksandrana">@aleksandrana</a>) is a Training Lead at the Software Sustainability Institute at Manchester University, UK. She coordinates training activities and helps develop strategies and curricula for teaching computational lab skills to researchers across disciplines at all stages of their research career. She is a member of the Steering Committees for Data Carpentry and Software Carpentry Foundation, and supports the development of both initiatives. Currently, Aleksandra is collaborating on training with the ELIXIR project supporting the bioinformatics community. As a certified Software and Data Carpentry instructor Aleksandra has taught at a number of workshops, including Software Carpentry for Women in Science and Engineering, which she co-organised.</li> <li><strong>Jason Williams</strong> ( <a href="https://twitter.com/JasonWilliamsNY">@JasonWilliamsNY</a>) is the Lead of the iPlant Collaborative’s Education, Outreach, Training (EOT) group, based at Cold Spring Harbor Laboratory, where he has worked for over 10 years. He is also a Lead Instructor of “The Science Institute” at Yeshiva University High School for Girls, and the Treasurer of the Software Carpentry Foundation. His background is in molecular biology and bioinformatics. Diversity is a focus of Jason&rsquo;s work at the DNA Learning Center and with iPlant, where he works to target outreach along the entire spectrum of underrepresented and underserved groups ranging from minorities in urban communities to first-generation college students at rural institutions.</li> </ul> <p>In addition the BOSC 2015 co-chairs <strong>Nomi Harris</strong> and <strong>Peter Cock</strong> will be on hand, along with other Open Bioinformatics Foundation (OBF) Board Members and BOSC organising committee members, to comment on what BOSC and the OBF are trying to do to improve diversity in the open source bioinformatics community, and listen to suggestions.</p> <p>P.S. Today is the deadline for discounted early <a href="https://www.iscb.org/ismbeccb2015-registration#registrationfee" title="ISMB/ECCB 2015 registration, including BOSC">registration</a>, and the deadline to submit a late breaking lightning talk or poster abstract. See <a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a> for more details.</p>https://www.open-bio.org/2015/05/12/minutes2015-may-confcall/Tue, 12 May 2015 05:44:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/05/12/minutes2015-may-confcall/<h3 id="agenda">Agenda</h3> <p><strong>Venue:</strong> to be held by conference call on May 12, 2015, 1pm EDT (17:00 UTC, 18:00 BST, 19:00 CEST, 10am PDT)  Dial-in Information: +1-857-216-2939 PIN: 62534 <a href="http://www.uberconference.com/hlapp">http://www.uberconference.com/hlapp</a></p> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2014_Nov_ConfCall">Nov 2014 BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>Term expirations and Elections for the Board</li> <li>BOSC 2015: update from the 2015 chairs (Nomi, Peter)</li> <li>Update on <a href="http://www.iscb.org/iscb-affiliates-cosis">ISCB &ldquo;Community of Special Interest&rdquo;</a> (COSI) (Peter)</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p>Etherpad for notes: <a href="https://etherpad.mozilla.org/OBF-BoD-Meeting-May2015">https://etherpad.mozilla.org/OBF-BoD-Meeting-May2015</a></p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Present: Chris Fields (via phone), Hilmar, Chris Dag., Nomi Harris, Peter Cock.</li> <li>Guests: Karen Cranston (Board candidate)</li> </ul> <p><strong>Minutes:</strong></p> <p>UTC/GMT 17:05- Hilmar called the meeting to order.</p> <ol> <li><strong>Old business</strong> <ul> <li>Unanimous approval of <a href="https://www.open-bio.org/wiki/Minutes:2014_Nov_ConfCall">minutes from Public Board meeting of Nov 2014</a>.</li> <li>Future public meeting will have to present the financial report 2014 (with amendment to 2013 report for late BOSC reimbursement).</li> </ul> </li> <li><strong>Elections for the board.</strong> <ul> <li>One candidate, Karen Cranston.</li> <li>Statement: Karen is Training Coordinator and Informatics Project Manager at the National Evolutionary Synthesis Center (NESCent). Mentor and administrator for NESCent GSoC. She is an evolutionary biologist interested in phylogenetic methods and is the lead PI of Open Tree of Life, an NSF-funded project to synthesize published evolutionary trees. She’s helped organize many events for open source and data interoperability in biology, including Phyloinformatics Summer of Code, iEvoBio, hackathons, and Data / Software Carpentry workshops. Many parallels with what the OBF is interested in, and particularly interested in our recent diversity discussion.</li> <li>Karen confirms monthly meetings at this time (generally the second Tuesday of the month at 1pm ET) will not be a problem for her schedule.</li> <li>Hilmar moves for the board to cast their ballots (for electing Karen Cranston as a new OBF board member) online via heliosvoting.org; 6 votes for, 0 against, 0 abstentions. <a href="https://vote.heliosvoting.org/helios/elections/04a3511e-f8af-11e4-828f-769695b8596f/view">https://vote.heliosvoting.org/helios/elections/04a3511e-f8af-11e4-828f-769695b8596f/view</a></li> <li>ACTION: Peter to update the blog post for this meeting. [Done]</li> <li>The board unanimously thanks the two departing members for their service to the board and wider community since the founding of the OBF, and before.</li> </ul> </li> <li><strong>BOSC</strong> <ul> <li>Good set of abstract received, acceptances sent out (only one has declined so far).</li> <li>Will be calling for &ldquo;late breaking&rdquo; lightning talks and posters in June (with people who were only offered a poster invited to improve their abstract and be considered for a possible late-breaking lightning talk).</li> <li>We are still polishing the schedule, currently reserving 30 minutes for 6 late breaking lightning talks.</li> <li>It is not unusual to have Lightning talks without questions, so we will likely not have questions after them given the tight schedule.</li> <li>Student authors, panellists, keynote speakers, committee members have been offered fee waivers. Thus far we are only planning to pay for travel for our keynote speakers.</li> <li>Looking to record talks via the ISCB this year (to be made open, speakers able to opt out).</li> <li>ACTION: Plan putting COSI membership to the OBF membership, including commitments and consequences (e.g. what happens if we leave with escrow etc).</li> <li>We will be able to access the ISCB membership roll for those who have ticked the OBF as a COSI they are interested in, and check if they want to formally join the OBF.</li> </ul> </li> <li><strong>Membership</strong> <ul> <li>Agreement that current &ldquo;paper&rdquo; system is no longer suitable. Current by-laws mean we want verified email addresses, and do not disclose them. This excludes a public wiki or document on GitHub (like <a href="https://github.com/pjotrp/bioinformatics">https://github.com/pjotrp/bioinformatics</a> for example), Google Forms (cannot check email address), but perhaps a GitHub team might work (this would require OBF members create a GitHub account, but does not force them to disclose their email address).</li> </ul> </li> <li><strong>System Administration:</strong> <ul> <li>Wiki needs updating for Google OpenID</li> </ul> </li> </ol> <p>UTC/GMT 17:53 Meeting Adjoined.</p>https://www.open-bio.org/2015/05/01/public-obf-board-meeting/Fri, 01 May 2015 21:46:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/05/01/public-obf-board-meeting/<p>The next public Board of Directors Meeting of the OBF will take place on May 12th, 2015, at 17:00 UTC (1pm EDT, 10am PDT, 19:00 CEST, see <a href="http://#" title="OBF Meeting in World Clock">World Clock</a>). The developing <a href="https://www.open-bio.org/wiki/Minutes:2015_May_ConfCall" title="Board Meeting agenda">agenda for the meeting</a> is posted, as are the dial-in details.</p> <p>We will have Board elections at this meeting. The terms of Directors Jason Stajich and Chris Dagdigian expire, and they will both step down from the Board. As most of you will know, both have provided truly extraordinary service to the OBF, from the earliest beginnings of the organization and in fact the very community around it. They provided leadership when few others did, and they were there during the most challenging times of OBF.  If you won&rsquo;t be able to attend the meeting, please still find the time to express your appreciation to them for their service, and the work they continue to volunteer.</p> <p>We also have a candidate, Karen Cranston, running for a seat on the Board. If you have not yet met her, Karen (Github, Twitter) is the Training Coordinator and Informatics Project Manager at the National Evolutionary Synthesis Center (NESCent). She is an evolutionary biologist interested in phylogenetic methods and is the lead PI of Open Tree of Life, an NSF-funded project to synthesize published evolutionary trees. She&rsquo;s helped organize many events for open source and data interoperability in biology, including Phyloinformatics Summer of Code, iEvoBio, hackathons, and Data / Software Carpentry workshops.</p> <p>I look forward to the Board meeting, and to seeing many of you in July at the <a href="https://www.open-bio.org/wiki/BOSC_2015" title="BOSC 2015">2015 BOSC</a> in Dublin.</p> <p><a href="http://termpaperhelponline.com/term-papers-for-sale">term papers for sale</a></p> <p>Hilmar Lapp, President, OBF Board of Directors</p> <p><em><strong>Update:</strong></em> Karen Cranston was elected to the board at the <a href="https://www.open-bio.org/wiki/Minutes:2015_May_ConfCall" title="meeting minutes">12 May Public OBF Board Meeting</a>.</p>https://www.open-bio.org/2015/04/02/bosc-2014-diversity/Thu, 02 Apr 2015 22:09:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/04/02/bosc-2014-diversity/<p>The <a href="https://www.open-bio.org/wiki/BOSC_2015">Bioinformatics Open Source Conference (BOSC)</a> has always been about community. Launched in 2000, BOSC aims to provide a forum for both bioinformatics developers and users to share ideas and code and learn about the latest developments in open source bioinformatics and open science.</p> <p>Our goal this year is to welcome even greater participation, opening the door even wider to participants who have historically been underrepresented in the world of open source bioinformatics and, therefore, at BOSC. This includes (but is by no means limited to) women, people who aren&rsquo;t white, older people, people from outside North America and Europe, and non-programmers.</p> <p>During a Birds of a Feather (BoF) session held at <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a>, we discussed ways to increase the diversity of BOSC attendees, and gathered many useful suggestions from the participants, some of which we have already acted upon.</p> <p>One of the suggestions from the 2014 BoF was to add someone to the organizing committee to focus on outreach and community-building. In January 2015, <a href="http://news.open-bio.org/news/2015/01/bosc-welcomes-sarah-hird/">we welcomed Dr. Sarah Hird as our new Outreach Coordinator</a>. Sarah is currently a UC Davis Chancellor&rsquo;s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity. Sarah is also known for her focus on <a href="https://sites.google.com/site/sarahhird/diversity-in-stem">promoting diversity in STEM</a>.  &quot; <em>I am personally and professionally interested in how we can make “the Academy&quot; a more representative sample of the world around us,</em>&quot; she says.</p> <p>During the 2014 BoF, we were asked whether BOSC planned to adopt a Code of Conduct. We felt that this should be an ISCB-wide effort, not one that is limited to a single SIG. Our advocacy efforts with the ISCB were successful with a <a href="https://www.iscb.org/ismbeccb2015-general-info/ismbeccb2015-coc">code of conduct published on the ISMB/ECCB 2015 website</a>. We are very pleased that ISCB joins us in wanting to foster a collegial and productive environment for everyone who attends the conferences. The code of conduct will also be announced in the ISCB April Newsletter.</p> <p>The high price of travel and registration can make it hard for some people to attend BOSC. We are trying to lower this barrier by offering free or half-price registration to a limited number of accepted speakers - please indicate in the Comments section of your abstract submission if you would like to apply for this. We also award Student Travel Fellowships to the authors of the three best student abstracts each year; these provide $250 to offset travel costs, as well as granting free registration to BOSC.</p> <p>Every year, the agenda at BOSC includes a panel that gives all participants the opportunity to engage each other in discussion. This year, our panel discussion will focus on increasing diversity in our community and at our conferences. The panel will be chaired by <em>Monica Munoz-Torres</em> and will include panellists <em>Holly Bik</em> and <em>Jason Williams</em> (see bios below).</p> <ul> <li> <p>Dr. Monica Munoz-Torres (Twitter: @monimunozto) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). She is part of the development teams for Web Apollo (a web-based annotation editor designed to support community-based curation of genomes) and the tools of the Gene Ontology (GO) Consortium. She co-leads the Community Curation group within the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5K Initiative), and is a member of the Executive Committee of the International Society for Biocuration (ISB).</p> </li> <li> <p>Dr Holly Bik (Twitter: @hollybik) is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes.</p> </li> <li> <p>Jason Williams (Twitter: @JasonWilliamsNY) is the Lead of the iPlant Collaborative&rsquo;s Education, Outreach, Training (EOT) group, based at Cold Spring Harbor Laboratory, where he has worked for over 10 years. He is also a Lead Instructor of &ldquo;The Science Institute&rdquo; at Yeshiva University High School for Girls, and the Treasurer of the Software Carpentry Foundation. His background is in molecular biology and bioinformatics.</p> </li> </ul> <p>We are looking for two more panellists, and have some ideas - but your suggestions are welcome! Please [email the BOSC committee](mailto:bosc@open-bio.org?subject=BOSC 2015 Panelists) or just tweet panellist ideas at @OBF_BOSC.</p> <p><a href="http://termpapersnetwork.com/">term paper writing service</a></p> <p>Finally, please spread the word about BOSC! The deadline for <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">submitting abstracts</a> for regular-length talks is tomorrow (Friday, April 3 <em>- update: extended to Tuesday, April 7 due to Easter/Passover weekend</em>), but there will also be opportunities for last-minute lightning talks and posters.</p>https://www.open-bio.org/2015/04/01/gsoc-project-sambamba-published-in-scientific-journal/Wed, 01 Apr 2015 15:21:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/04/01/gsoc-project-sambamba-published-in-scientific-journal/<p><em>(This is a repost of a BLOG on Google Open Source news about Google&rsquo;s open source student programs and software releases)</em></p> <p>One of our goals with GSoC is to inspire young developers to participate in open source development, hopefully continuing well beyond the summer. Pjotr Prins from the Open Bioinformatics Foundation shared this story with us about a GSoC 2012 student who has continued leading the development of a software tool used in laboratories around the world. That tool, Sambamba, was recently featured in an Oxford University Press scientific journal. The Open Bioinformatics Foundation (OBF) participated in Google Summer of Code (GSoC) in 2012 and again in 2014. One of our projects,Sambamba, enables users to rapidly process large sequence alignment files in the SAM, BAM and CRAM formats using parallel processing. Sambamba, which means “parallel” in Swahili, was recently the subject of a paper published in Bioinformatics Journal by GSoC alumnus Artem Tarasov. Since the tool is now used in DNA sequencing centres around the world, Artem has become well known in the bioinformatics community as Sambamba’s creator.</p> <p>When we participated in GSoC 2012, we accepted five students, one of whom was Artem. His project was to “write the fastest parallelized BAM parser in D” as an alternative to the existing SAMtools software written in single-threaded C. I consider the D language to be particularly well-suited to bioinformatics given its modern hybrid OOP/functional syntax with close-to-the-metal performance optimizations.</p> <p>Even before GSoC started that year, Artem was doing research and cranking out code. In his blog, he wrote about learning the D language, dealing with parallel executing code, and the sometimes-buggy compiler and garbage collector. The file formats he was working with are complicated and contain many assumptions, but he made wise choices which led to a very effective piece of software: people tend to rave about Sambamba when they use it the first time. Artem and I continued working on Sambamba after GSoC and before long, I found that he was the one mentoring me!</p> <p>Since then, Artem has been invited to visit the Cuppen sequencing lab in the Netherlands where he added depth analysis to Sambamba. This is also when we started work on the manuscript for the Bioinformatics Journal. Later, the OBF was able to sponsor a second trip to the European Bioinformatics Institute in Cambridge, UK where he and I took part in a Codefest and met with other bioinformatics researchers and developers, including some OBF contributors.</p> <p>Artem isn’t our only GSoC student who has continued making a difference in open source. Four of our five GSoC 2012 students are still active FOSS committers on GitHub, with three of them continuing in the bioinformatics space. Although GSoC can be competitive and we haven’t been accepted into the program every year, we’re grateful for the opportunities it has given us. Organizations like OBF and SciRuby are proof that GSoC and scientific projects work really well together. Without GSoC, Artem and I would probably not have ever met. He and I both hope to introduce more students to scientific open source projects in the future. By Pjotr Prins, Sambamba GSoC Mentor</p>https://www.open-bio.org/2015/03/26/bosc-2015-keynote-speakers/Thu, 26 Mar 2015 16:05:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/03/26/bosc-2015-keynote-speakers/<p>Announcing the keynote speakers for the <a href="https://www.open-bio.org/wiki/BOSC_2015">Bioinformatics Open Source Conference, BOSC 2015</a>:</p> <h1 id="holly-bik">Holly Bik</h1> <p><a href="https://www.open-bio.org/wiki/File:HollyBik.png" title="Holly Bik"><img src="https://www.open-bio.org/w/images/thumb/3/37/HollyBik.png/180px-HollyBik.png" alt="Holly Bik"></a> Dr Holly Bik is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. She obtained her Ph.D. in molecular phylogenetics at the University of Southampton, UK (working in conjunction with the Natural History Museum, London), followed by subsequent postdoctoral appointments at the Hubbard Center for Genome Studies at the University of New Hampshire and the UC Davis Genome Center.</p> <p>Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes. Holly&rsquo;s keynote talk topic is &ldquo;Bioinformatics: Still a scary world for biologists&rdquo;.</p> <p><em>Many biological disciplines remain staunchly traditional, where high-throughput DNA sequencing and bioinformatics have not yet become widely adopted. In this talk, I&rsquo;ll discuss the ongoing challenges and barriers facing biologists in the age of &lsquo;Omics, based on my experiences in transitioning from nematode taxonomy to computational biology research.</em></p> <p>Homepage: <a href="http://www.hollybik.com/about/">Holly Bik</a>, Twitter: <a href="https://twitter.com/hollybik">@hollybik</a></p> <hr> <h1 id="ewan-birney">Ewan Birney</h1> <p><a href="https://www.open-bio.org/wiki/File:EwanBirney2.jpg" title="Ewan Birney"><img src="https://www.open-bio.org/w/images/thumb/0/08/EwanBirney2.jpg/230px-EwanBirney2.jpg" alt="Ewan Birney"></a> Dr Ewan Birney is Joint Associate Director of EMBL-EBI, as well as Interim Head of the Centre for Therapeutic Target Validation. Together with Dr Rolf Apweiler, he has strategic responsibility and oversight for bioinformatics services at EMBL-EBI.</p> <p>Ewan played a vital role in annotating the genome sequences of the human, mouse, chicken and several other organisms; this work has had a profound impact on our understanding of genomic biology. He led the analysis group for the ENCODE project, which is defining functional elements in the human genome. He was also one of the leaders of the BioPerl project. Ewan’s main areas of research include functional genomics, assembly algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences) and compression of sequence information.</p> <p>He has received a number of prestigious awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics. He was elected a Fellow of the Royal Society in 2014.</p> <p>Ewan was a cofounder of the <a href="https://www.open-bio.org/" title="Main Page">Open Bioinformatics Foundation</a>, the organization that sponsors BOSC, and has been involved in BOSC since the first conference in 2000. He chaired the meeting in 2001, and gave one of the keynote talks in 2002. We are delighted to have him back as a keynote speaker for 2015.</p> <p>Ewan&rsquo;s talk topic will be announced soon.</p> <p>Homepage: <a href="https://www.ebi.ac.uk/%7Ebirney/">Ewan Birney</a>, Twitter: <a href="https://twitter.com/ewanbirney">@ewanbirney</a></p> <hr> <p>The <a href="http://news.open-bio.org/news/2015/03/bosc-2015-call-for-abstracts/">BOSC 2015 call for abstracts is currently open</a>, and <a href="https://www.iscb.org/ismbeccb2015-registration">BOSC/ISMB/ECCB 2015 registration</a> has also just opened. We hope to see you in Dublin!</p>https://www.open-bio.org/2015/03/05/bosc-2015-call-for-abstracts/Thu, 05 Mar 2015 21:00:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/03/05/bosc-2015-call-for-abstracts/<p>Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2015"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]"></a></p> <ul> <li>Dates: 10-11 July, 2015</li> <li>Location: Dublin, Ireland</li> <li>Web site: <a href="https://www.open-bio.org/wiki/BOSC_2015">/wiki/BOSC_2015</a></li> <li>Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></li> <li><a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">BOSC announcements mailing list</a></li> <li>Twitter: <a href="https://twitter.com/OBF_BOSC" title="OBF Bioinformatics Open Source Conference (BOSC)">@OBF_BOSC</a> and <a href="https://twitter.com/OBF_news" title="Open Bioinformatics Foundation (OBF) News">@OBF_News</a></li> </ul> <p>Important Dates:</p> <p><a href="http://www.iscb.org/ismbeccb2015"><img src="https://news.obf.io/wp-content/uploads/2015/03/ismb_eccb_2015_dublin.png" alt="ismb_eccb_2015"></a></p> <ul> <li>March 24, 2015: Registration opens for ISMB and BOSC ( <a href="https://www.iscb.org/ismbeccb2015-registration">https://www.iscb.org/ismbeccb2015-registration</a>)</li> <li>April 3, 2015: Deadline for <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">submitting BOSC abstracts</a></li> <li>May 3, 2015: Notification of accepted talk abstracts emailed to authors</li> <li>July 8-9, 2015: <a href="https://www.open-bio.org/wiki/Codefest_2015">BOSC Codefest 2015</a>, Dublin</li> <li>July 10-11, 2015: <a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a>, Dublin</li> <li>July 10-14, 2015: <a href="http://www.iscb.org/ismbeccb2015">ISMB/ECCB 2015</a>, Dublin</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!</p> <p>Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>We invite you to submit one-page abstracts for talks and posters. As mentioned, any topics relevant to open source bioinformatics and open science are welcome. Here are some potential session topics (but please don&rsquo;t feel limited to these!):</p> <ul> <li>Open Science and Reproducible Research</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Visualization</li> <li>Translational Bioinformatics</li> <li>Bioinformatics Open Source Libraries and Projects</li> </ul> <p>If your company or organization is interested in being a sponsor for BOSC 2015, please contact us! Sponsors of <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a> included <a href="http://www.google.com/">Google</a>, <a href="http://www.eaglegenomics.com/">Eagle Genomics</a>, <a href="http://www.gigasciencejournal.com/">GigaScience</a>, and <a href="http://curoverse.com/">Curoverse</a> - we thank them for their support.</p> <p>BOSC 2015 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres.</p>https://www.open-bio.org/2015/03/03/sadly-obf-not-accepted-for-gsoc-2015/Tue, 03 Mar 2015 13:30:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/03/03/sadly-obf-not-accepted-for-gsoc-2015/<p>Last year&rsquo;s <a href="http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/">Google Summer of Code 2014 was very productive for the OBF</a> with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted.</p> <p>Google&rsquo;s program is enormously popular, and over-subscribed, meaning Google has had to rotate organisation membership. The OBF is grateful to have been accepted in 2010, 2011, 2012 and 2014. This year any participation will be down to individual projects to find a willing umbrella group from the <a href="https://www.google-melange.com/gsoc/org/list/public/google/gsoc2015">organisations accepted for GSoC 2015</a>. For example, a <a href="http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013">Biopython project was included under NESCent for GSoC 2013</a>.</p> <p>Other organizations with bioinformatics as keyword are <a href="https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2015-Ideas">Ruby Science Foundation</a>, <a href="https://docs.google.com/document/d/1zJGT5AwnKqx8mJLmoeRnM_iZkEk-i6Ky_M4b3Z38w6o/edit">Department of Biomedical Informatics, Stony Brook University</a>, <a href="http://bcb.dfci.harvard.edu/~cerami/gsoc.html">OncoBlocks</a>, <a href="http://helikarlab.org/GSoC.html">University of Nebraska - Helikar Lab</a>. Other organizations related to sciences are <a href="http://ascend4.org/Student_projects">ASCEND</a> , <a href="http://brlcad.org/wiki/Google_Summer_of_Code/Project_Ideas">BRL-CAD</a>, <a href="https://wiki.debian.org/SummerOfCode2015/Projects">Debian Project</a>, <a href="https://wiki.hpccsystems.com/display/hpcc/HPCC+Systems+GSoC+2015+Ideas+List">HPCC Systems®</a>,  <a href="https://www.incf.org/gsoc/2015/proposals">International Neuroinformatics Coordinating Facility</a> , <a href="http://wiki.lmona.de/get_involved/gsoc">lmonade:</a> <a href="http://wiki.lmona.de/get_involved/gsoc">scientific software distribution</a>, <a href="http://wiki.osgeo.org/wiki/Google_Summer_of_Code_2015_Ideas">OSGeo - Open Source Geospatial F</a> <a href="http://wiki.osgeo.org/wiki/Google_Summer_of_Code_2015_Ideas">oundation</a>, <a href="http://concord.org/GSoC">The Concord Consortium</a>, <a href="http://www.vtk.org/Wiki/VTK/GSoC_2015">The Visualization Toolkit</a>. Languages: <a href="https://www.google-melange.com/gsoc/org2/google/gsoc2015/python">Python</a>, <a href="https://www.google-melange.com/gsoc/org2/google/gsoc2015/scalateam">Scala</a>, <a href="https://www.google-melange.com/gsoc/org2/google/gsoc2015/apache">Apache Foundation</a>. Last but not least : <a href="https://docs.google.com/document/d/1PHPDTzD4Z6xVoxN0Q1F8yEPclSri-JA1vLvMTrLYUi8/edit">Global Alliance for Genomics &amp; Health</a>.</p> <p>On behalf of the OBF, we would like to thank our volunteer GSoC Administrators, Raoul Bonnal and Francesco Strozzi, for organising our application - and all our potential mentors across the Bio* projects who put forward potential project suggestions.</p>https://www.open-bio.org/2015/02/23/obf-gsoc-2014-wrapup/Mon, 23 Feb 2015 23:24:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/02/23/obf-gsoc-2014-wrapup/<p><a href="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo.jpg"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-300x270.jpg" alt="GoogleSummer_2014logo"></a> In 2014, OBF had six students in the <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code 2014™</a> (GSoC) program mentored under its umbrella of Bio* and related open-source bioinformatics community projects: Loris Cro (Bioruby) with mentors Francesco Strozzi and Raoul Bonnal; Evan Parker (Biopython) with mentors Wibowo Arindrarto and Peter Cock; Sarah Berkemer (BioHaskell) with mentors Christian Höner zu Siederdissen and Ketil Malde; and three students contributed to JSBML: Victor Kofia (mentors: Alex Thomas and Sarah Keating), Ibrahim Vazirabad (mentors: Andreas Dräger and Alex Thomas), and Leandro Watanabe (mentors: Nicolas Rodriguez and Chris Myers).</p> <p>As a change from earlier years in which OBF participated in GSoC as a mentoring organization, in 2014 we purposefully defined our umbrella as much more inclusive of the wider bioinformatics open-source community, bringing it more in line with the annual <a href="https://www.open-bio.org/wiki/BOSC" title="BOSC">Bioinformatics Open-Source Conference</a> (BOSC).  In part this was also motivated by &quot; <a href="http://en.wikipedia.org/wiki/Pay_it_forward" title="Pay It Forward - Wikipedia">paying it forward</a>&quot;, a concept central to growing healthy open-source communities, after the larger domain-agnostic language projects such as <a href="http://sciruby.com/" title="SciRuby project">SciRuby</a> and <a href="https://www.python.org/psf/" title="Python Software Foundation">PSF</a> had extended an open hand to OBF mentors when OBF did not get admitted as a GSoC mentoring organization in 2013. In the end, four out of the six succeeding student applications were for projects outside of the traditional core Bio* projects, a result with which everyone won: We had a terrific crop of students, our community grew larger and stronger, and open-source bioinformatics was advanced in a more diverse way than would have been possible otherwise.</p> <p>In addition to our students, huge kudos also go to our mentors (see above), and to Eric Talevich (Biopython) and Raoul Bonnal (Bioruby), who ran our program participation as administrators. They all invested significant amounts of time on behalf of our community and projects. Thank you!</p> <p>Below follows a short summary of each of the 2014 student projects, starting with the three JSBML students.</p> <h3 id="jsbml-and-gsoc2014">JSBML and GSoC 2014</h3> <p><a href="http://sbml.org/Software/JSBML"><img src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png" alt="JSBML logo"></a> <a href="http://sbml.org/Software/JSBML" title="JSBML website">JSBML</a> is an international community-driven, open-source project to develop a Java API library for reading, writing and manipulating <a href="http://sbml.org" title="SBML website">SBML</a>, a data format for representing and exchanging computational models in systems biology. SBML has been in use for over a decade but continues to evolve and grow, and hence so does JSBML. JSBML holds two annual development-oriented workshops, and the three 2014 JSBML GSoC students had the opportunity to participate in and present their work at the autumn event, <a href="http://co.mbine.org/events" title="COMBINE website">COMBINE</a> (Computational Modeling in Biology Network), which was held in Los Angeles, California, right at the end of GSoC. Furthermore, a scientific publication on a new JSBML release, currently under review at Bioinformatics, highlights some of the work done by the students. Hence, <a href="http://sbml.org/GSoC2014" title="JSBML in 2014 GSoC">JSBML&rsquo;s 2014 participation in GSoC</a> was a great success and experience, both for the students as well as the JSBML project and community.</p> <h3 id="ibrahim-y-vazirabad----improving-the-plugin-interface-for-celldesigner">Ibrahim Y. Vazirabad - &quot; <em>Improving the plugin interface for CellDesigner</em>&quot;</h3> <p><a href="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.52.png"><img src="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.52-300x268.png" alt="CellDesigner UML"></a> CellDesigner is a frequently used program in computational systems biology. It features an easy-to-use GUI, powerful graph editing functions, and a rich simulation functionality, among others. To facilitate rapid prototyping of new algorithms in third-party applications, CellDesigner provides a plug-in interface for Java applications to its robust interface and other features. However, the design and implementation of the plug-in interface made developing software for it very difficult and time consuming. To remedy this, a draft version of a JSBML library had been created to allow developing and testing prospective plug-in modules initially as stand-alone software, which can then be turned into a CellDesigner plug-in with very little effort. The goal of Ibrahim&rsquo;s project was to improve the interface provided by the library, and importantly, to revise it to support access to one of CellDesigner&rsquo;s most interesting features, graphical network layout. As a result of <a href="http://jsbmlcelldesigner2014.blogspot.com/" title="Project blog">Ibrahim&rsquo;s work</a>, new CellDesigner test cases and plugins that use this interface have already been implemented, including one that converts between CellDesigner’s proprietary data format and the official SBML layout extension.</p> <h3 id="leandro-h-watanabe----arrays-package">Leandro H. Watanabe - &quot; <em>Arrays Package</em>&quot;</h3> <p>The arrays and dynamic package extensions to SBML have been proposed to overcome SBML&rsquo;s limitation to static static models, which is in contrast to the inherently dynamic nature of many biological systems. The goal of <a href="http://lhwatanabe.blogspot.com/">Leandro&rsquo;s project</a> was to implement the arrays package in JSBML. Rather than enabling models with new behaviors to be constructed, the purpose of the arrays package is to represent regular constructs more efficiently and more compact than SBML core constructs can. To aid the integration of the arrays package into existing tools, Leandro also implemented the option of flattening an arrayed model to use only SBML core constructs, and a validation procedure for array constructs that checks whether a model violates any of the rules imposed on array constructs. As a consequence, his work helped solidify the Arrays Specification document of the SBML standard.</p> <h3 id="victor-kofia----redesign-the-implementation-of-mathematical-formulas">Victor Kofia - &quot; <em>Redesign the implementation of mathematical formulas</em>&quot;</h3> <p><a href="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.16.png"><img src="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.16-300x255.png" alt="Screenshot 2015-02-23 16.30.16"></a> JSBML uses the concept of abstract syntax trees to work with mathematical expressions. For example, the image to the right shows a syntax tree representing the formula k8 · R1. Originally, JSBML implemented different kinds of formula components all in just one complex class with diverse type attributes, which was prone to introducing errors upon code changes and generally made maintenance of the software difficult. <a href="http://kofiav.blogspot.ca/" title="Victor's project blog">Victor implemented a math package</a> for JSBML, in which different kinds of tree nodes that can occur in formulas (e.g., real numbers or algebraic symbols such as &lsquo;plus&rsquo; or &lsquo;minus&rsquo;) are represented with their own, specialized classes. This has made handling of formulas much more straightforward, and also more efficient. In the future, this new representation could even be used for symbolic or numeric calculations.</p> <h3 id="evan-parker----addition-of-a-lazy-loading-sequence-parser-to-biopython">Evan Parker - &quot; <em>Addition of a lazy loading sequence parser to Biopython&rsquo;s SeqIO package</em>&quot;</h3> <p>Though Biopython is already equipped with sequence parsers for a wide array of formats, these generally parsed entire records into memory. For large sequences such as entire chromosomes this quickly degrades performance.  To allow sequences to be loaded on-demand, Evan  designed a general lazy-loading parser by refactoring the existing object model, and then added format-specific modifications to each individual parser. The approach he devised works by pre-indexing the sequence files and then loading only those sequence regions that the user requests. <a href="http://blog.evanaparker.com/2014/08/pre-pull-request-performance-tests-and.html">Benchmarking</a> and <a href="http://blog.evanaparker.com/2014/08/fasta-performance-comparison.html">performance comparisons</a> showed this approach yields significant performance gains when, as is common for genome-scale files, users are interested only in parts of the full sequence. Evan&rsquo;s code is <a href="https://github.com/biopython/biopython/pull/356">currently under review by Biopython core developers</a>, and once merged will make parsing large sequences in Biopython much more tractable.</p> <h3 id="loris-cro----an-ultra-fast-scalable-restful-api-to-query-large-numbers-of-vcf-datapoints">Loris Cro - &quot; <em>An ultra-fast scalable RESTful API to query large numbers of VCF datapoints</em>&quot;</h3> <p>Variant Call Format (VCF) files are commonly generated by genome sequencing projects for sequence variations among different individuals and can get very large. The goal of Loris&rsquo; work was to develop code for Bioruby to determine the common variations (i.e., intersections) between multiple individuals and groups of individuals in a fast and scalable way. In the first phase of the project, Loris tested different technologies for storing large VCF files, from which MongoDB emerged as having superior performance. In the second phase Loris developed the code for efficiently storing VCF data into MongoDB, and then implemented algorithms for performing the intersection queries (see <a href="https://github.com/kappaloris/vcf-mongo" title="Loris Cro 2014 GSoC code repo">Github repo</a> and <a href="http://kappaloris.github.io/GSoC-2014-OBF/" title="Loris Cro 2014 GSoC project blog ">Loris&rsquo; project blog</a>). The code was developed using JRuby and uses the <a href="https://samtools.github.io/htsjdk/" title="HTS-JDK">HTS-JDK library</a> to parse the VCF data. In the course of the project, Loris also provided valuable feedback to the HTS-JDK team that led to improvements of the VCF parser and data model. The result of Loris&rsquo; GSoC work is now available to the community as a Ruby Gem, which has been tested and used already in large international genome re-sequencing projects, including <a href="http://www.gene2farm.eu/" title="Gene 2 Farm Website">Gene2Farm</a> and <a href="http://www.whealbi.eu/" title="WHEAt and barley Legacy for Breeding Improvement">WHEALBI</a>.</p> <h3 id="sarah-berkemer----open-source-high-performance-biohaskell">Sarah Berkemer - &quot; <em>Open source high-performance BioHaskell</em>&quot;</h3> <p>One of the challenges with sequence alignments for the purposes of sequence similarity searches is that for most known genes (i.e., sequences) relatively little is known about their biology, and the few for which a lot is known therefore tend to be only remotely related to a query sequence. <a href="http://dx.doi.org/10.1371/journal.pone.0054422" title="PLoS ONE article on Transitive Alignments">Transitive alignments</a> try to ameliorate this by aligning the query sequence against a large body of known but not deeply understood sequences, the intermediate set, which in turn are then aligned against the core of well-understood sequences. However, in contrast to aligning two sequences, aligning a sequence via a vast intermediate data set to a smaller core set is slow and memory-consuming. As part of her GSoC project, Sarah dug deep into the structure of the algorithm, and rewrote core parts to make use of fusing data structures and efficient tree-like data structures (see <a href="http://biohaskell.org/GSoC_blog" title="Sarah's GSoC project blog">her project blog</a>). <a href="http://biohaskell.org/GSoC_blog/Weeks_12and13" title="Sarah's blog">Her work brought down the runtime</a> for a benchmark by a factor of 3, from 31 to 11 minutes, and, arguably even more important, reduced memory consumption from 53 to 22 gigabytes. This now allows running the program on consumer-grade high-memory PCs. With Sarah having finished her Masters degree (congrats!!) in the meantime, she and her mentors are now in the process of writing a scientific application note and are planning to make the program available as an online web-service.</p> <p>As a rather small family within the much larger OBF umbrella, the chance to have a student contribute to functional programming for computational biology has been a tremendous opportunity and learning experience for the Biohaskell community as well.</p>https://www.open-bio.org/2015/01/04/bosc-welcomes-sarah-hird/Mon, 05 Jan 2015 03:56:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/01/04/bosc-welcomes-sarah-hird/<p><img src="https://news.obf.io/wp-content/uploads/2015/01/sarah-hird.jpeg" alt="sarah-hird">The <a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a> Organizing Committee is pleased to welcome <a href="https://sites.google.com/site/sarahhird/home" title="Sarah Hird">Sarah Hird</a> as our new Outreach Coordinator. BOSC is eager to increase the participation of individuals and groups that have been historically underrepresented at our conferences, and Sarah will be spearheading this effort.</p> <p>Sarah is currently a UC Davis Chancellor&rsquo;s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity.  She earned her PhD in biology and bioinformatics at LSU. Sarah is also known for her focus on <a href="https://sites.google.com/site/sarahhird/diversity-in-stem">promoting diversity in STEM</a>. &ldquo;I am personally and professionally interested in how we can make &ldquo;the Academy&rdquo; a more representative sample of the world around us,&rdquo; she says.</p> <p>Please join us in welcoming Sarah to the <a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC</a> organizing committee, and stay tuned for more information about BOSC 2015 (which will take place July 10-11, 2015, in Dublin).</p>https://www.open-bio.org/2014/12/17/biopython-1-65-released/Wed, 17 Dec 2014 21:06:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/12/17/biopython-1-65-released/<p>Dear Biopythoneers,</p> <p>Source distributions and Windows installers for Biopython 1.65 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">official Biopython website</a> and from the <a href="https://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.</p> <p>The most visible change is that the Biopython <em><strong>sequence objects now use string comparison</strong></em>, rather than Python&rsquo;s object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).</p> <p>The Bio.KEGG and Bio.Graphics modules have been expanded with support for the online KEGG REST API, and parsing, representing and drawing KGML pathways.</p> <p>The <em>Pterobranchia</em> Mitochondrial genetic code has been added to Bio.Data (and the translation functionality), which is the new <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">NCBI genetic code</a> table 24.</p> <p>The Bio.SeqIO parser for the ABI capillary file format now exposes all the raw data in the SeqRecord&rsquo;s annotation as a dictionary. This allows further in-depth analysis by advanced users.</p> <p>Bio.SearchIO QueryResult objects now allow Hit retrieval using its alternative IDs (any IDs listed after the first one, for example as used with the NCBI BLAST NR database).</p> <p>Bio.SeqUtils.MeltingTemp has been rewritten with new functionality.</p> <p>The new experimental module Bio.CodonAlign has been renamed Bio.codonalign (and similar lower case PEP8 style module names have been used for the sub-modules within this).</p> <p>Bio.SeqIO.index_db(&hellip;) and Bio.SearchIO.index_db(&hellip;) now store any relative filenames relative to the index file, rather than (as before) relative to the current directory at the time the index was built. This makes the indexes less fragile, so that they can be used from other working directories. <em>NOTE:</em> This change is backward compatible (old index files work as before), however relative paths in new indexes will not work on older versions of Biopython!</p> <p>Behind the scenes, we have done a lot of work applying <a href="https://www.python.org/dev/peps/pep-0008/">PEP8 coding styles</a> to Biopython, and improving the formatting of the source code documentation ( <a href="https://www.python.org/dev/peps/pep-0257/">PEP257 docstrings</a>).</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alan Du (first contribution)</li> <li>Carlos Pena (first contribution)</li> <li>Colin Lappala (first contribution)</li> <li>Christian Brueffer</li> <li>David Bulger (first contribution)</li> <li>Eric Talevich</li> <li>Evan Parker (first contribution)</li> <li>Hongbo Zhu</li> <li>Kai Blin</li> <li>Kevin Wu (first contribution)</li> <li>Leighton Pritchard</li> <li>Leszek Pryszcz (first contribution)</li> <li>Markus Piotrowski</li> <li>Matt Shirley (first contribution)</li> <li>Mike Cariaso (first contribution)</li> <li>Peter Cock</li> <li>Seth Sims (first contribution)</li> <li>Tiago Antao</li> <li>Travis Wrightsman (first contribution)</li> <li>Tyghe Vallard (first contribution)</li> <li>Vincent Davis</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Zheng Ruan</li> </ul> <p>This is a longer list of contributors and changes than usual, but it was also a longer gap since our last release.</p>https://www.open-bio.org/2014/11/18/minutes2014-nov-confcall/Tue, 18 Nov 2014 05:42:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/11/18/minutes2014-nov-confcall/<h3 id="agenda">Agenda</h3> <p><strong>Venue:</strong> to be held by conference call on Nov 18, 2014, 12.30pm EST (17:30 UTC)  Dial-in Information: +1-857-216-2939 PIN: 62534 <a href="http://www.uberconference.com/hlapp">http://www.uberconference.com/hlapp</a></p> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2013_Dec_ConfCall">Dec 2013 BoD meeting minutes</a></li> <li><a href="https://github.com/OBF/obf-docs/blob/e05413fdcf9bc1b43e171b67651c81d3d5bdc7da/Financial-Reports/Financial%20report%202013.md">2013 Financial Report</a></li> </ul> </li> <li>New business <ol> <li>Review of 2014 financials</li> <li>BOSC 2015: update from the 2015 chairs (Nomi, Peter)</li> <li>Update on <a href="http://www.iscb.org/iscb-affiliates-cosis">ISCB &ldquo;Community of Special Interest&rdquo;</a> (COSI) (Peter)</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p>Etherpad for notes: <a href="https://etherpad.mozilla.org/OBF-BoD-Meeting-Nov2014">https://etherpad.mozilla.org/OBF-BoD-Meeting-Nov2014</a></p> <p><strong>Attending:</strong></p> <ul> <li>Board Members present: Peter Cock, Chris Dagdigian, Chris Fields, Nomi Harris, Hilmar Lapp, Jason Stajich.</li> <li>Board Member regrets: None.</li> <li>Guests: None.</li> </ul> <p><strong>Minutes:</strong></p> <p>Open Bioinformatics Foundation (OBF) Public Board Meeting, held Tuesday 18 November 2014, from 17:30 UTC/GMT, by teleconference using UberConference via <a href="https://www.uberconference.com/hlapp">https://www.uberconference.com/hlapp</a> or +1-857-216-2939 with PIN 62534.</p> <p>Meeting called to order at 17:37 UTC/GMT</p> <h4 id="approval-of-previous-board-meeting-minutes-dec-2013"><strong>Approval of previous board meeting minutes (Dec 2013)&rsquo;</strong></h4> <p>As posted on <a href="https://www.open-bio.org/wiki/Minutes:2013_Dec_ConfCall">/wiki/Minutes:2013_Dec_ConfCall</a></p> <p>Unanimously approved.</p> <h4 id="financial-report-for-2013"><strong>Financial Report for 2013</strong></h4> <p>Hilmar described this as relatively complex, given move from an OBF bank account, to SPI held funds (who use a cash based accountancy approach).</p> <p>In comparison, the 2012 financial report listed pending expenses for 2013.</p> <p>The report is currently on this branch, <a href="https://github.com/OBF/obf-docs/tree/financial-report-2013">https://github.com/OBF/obf-docs/tree/financial-report-2013</a> - the revision discussed was <a href="https://github.com/OBF/obf-docs/blob/e05413fdcf9bc1b43e171b67651c81d3d5bdc7da/Financial-Reports/Financial%20report%202013.md">https://github.com/OBF/obf-docs/blob/e05413fdcf9bc1b43e171b67651c81d3d5bdc7da/Financial-Reports/Financial%20report%202013.md</a></p> <p>This report deliberately includes the ISCB held BOSC escrow account which forms a sizeable part of the OBF assets. Note that as of 2014 with the launch of the ISCB COSI scheme, we are now more able to spend all year round rather than just directly connected to BOSC each Summer.</p> <p>Our only concern is the Amazon hosting costs (which might be reduced) versus the OBF income (typically BOSC sponsorship related).</p> <p>Report unanimously approved</p> <h4 id="preview-of-the-financial-report-for-2014"><strong>Preview of the Financial Report for 2014</strong></h4> <p>BOSC 2014 preliminary summary is that with sponsorship it came out about even. Server costs are our main cost outside BOSC (at about $190/month), and we talked about that a lot&hellip;</p> <p>Chris D reports that with some restructuring we might lower our costs (e.g. are we using the right machine size for buildbot, or should be pre-buy server space a year at a time) and/or get a grant from Amazon. On the other hand, hosting of physical machines is also viable - or a hybrid approach. The current OBF bandwidth needs are trivial. RackSpace is a potential AWS alternative, who might be willing to support Open Source projects (at least they have links to the Python Software Foundation).</p> <p>ChrisD confirms the main website/wiki is running on a medium server, plus we have five micro instances covering MailMan, RedMine, Events, BuildBot, etc. RedMine might need a medium instance (although we plan to phase this out).</p> <p>Note can&rsquo;t pre-pay the micro instances, but should pre-pay a year at a time if possible, and think about moving the wiki etc to ReadTheDocs or GitHub pages/wiki.</p> <p>We may need a final BOSC 2013 account from ISCB, since we have a discrepancy likely due to a late keynote speaker reimbursement.</p> <p>Hilmar would like to complete the FY2014 report much sooner than it took for the FY2013 report.</p> <p><strong>Meeting Adjourned at 18:34 UTC</strong></p>https://www.open-bio.org/2014/09/18/bosc-2015-will-be-in-dublin/Thu, 18 Sep 2014 09:42:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/09/18/bosc-2015-will-be-in-dublin/<p>We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they&rsquo;d like to see, and — most importantly — what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) rather than as an ISMB/ECCB SIG in Dublin (Ireland)..</p> <p>Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. We would have been hosted by <a href="http://www.tgac.ac.uk">The Genome Analysis Centre (TGAC)</a> just after and co-located with the <a href="http://gcc2015.tsl.ac.uk">Galaxy Community Conference 2015</a> (GCC 2015, hosted by <a href="http://www.tsl.ac.uk">The Sainsbury Laboratory</a>). Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority preferred BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin right before ISMB/ECCB 2015.</p> <p>Here is the summary of responses to the questions about the location of BOSC 2015:</p> <p><img src="https://news.obf.io/wp-content/uploads/2014/09/BOSC2015_locations.png" alt="BOSC2015_locations"><img src="https://news.obf.io/wp-content/uploads/2014/09/BOSC2015_GCC.png" alt="BOSC2015_GCC"></p> <p>Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and welcome suggestions of people to invite.) You can reach us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></p> <p>Nomi Harris and Peter Cock Co-Chairs, BOSC 2015</p>https://www.open-bio.org/2014/06/19/bosc-2014-video-recording/Thu, 19 Jun 2014 15:56:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/06/19/bosc-2014-video-recording/<p><img src="https://www.open-bio.org/w/images/thumb/b/b0/Pear.png/100px-Pear.png" alt="">We&rsquo;re pleased to publicly announce that we aim to video record <em>all</em> the talks at <a href="https://www.open-bio.org/wiki/BOSC_2014_Schedule">BOSC 2014</a>, and the panel discussion, to be made freely available online after the conference. This is on an opt-out basis, and thus far none of our speakers have declined to be filmed. <a href="https://www.youtube.com/channel/UCNSng3q18VuQ-13RhhKJ5FA" title="OBF videos on YouTube.com"><img src="https://news.obf.io/wp-content/uploads/2014/06/YouTube2.png" alt="YouTube"></a> Last year we managed to record many of the talks - including both keynotes, which you can watch via the YouTube links on the <a href="https://www.open-bio.org/wiki/BOSC_2013_Schedule">BOSC 2013 Schedule</a>. This year we are hiring a professional from <a href="http://nextdayvideo.com/">Next Day Video</a> ( <a href="https://twitter.com/nextdayvideo">@NextDayVideo</a> on Twitter).</p> <p><a href="https://developers.google.com/open-source/" title="Google's Open Source Programs Office "><img src="https://news.obf.io/wp-content/uploads/2014/06/205px-Google-logo11w.png" alt="Google Logo"></a> This is thanks to very generous support from <a href="https://developers.google.com/open-source/">Google&rsquo;s Open Source Programs Office</a> (who also run the amazing <a href="https://developers.google.com/open-source/soc/">Google Summer of Code program</a> which the OBF and its member projects have regularly <a href="https://www.open-bio.org/news/category/google-summer-of-code/">taken part in</a>), a new sponsor for BOSC this year.</p>https://www.open-bio.org/2014/06/15/obf-mailing-list-outage/Sun, 15 Jun 2014 21:39:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/06/15/obf-mailing-list-outage/<p>This is a belated notice that the OBF mailing lists are down due to a server failure. Posting a tweet is easier than writing a blog post, please follow <a href="https://twitter.com/OBF_news">@OBF_news</a> for updates.</p> <p>We have a complete back up and running as a virtual machine hosted on <a href="http://aws.amazon.com">Amazon Web Services (AWS)</a>, which should become live by Monday pending DNS updates etc.</p> <p>Back in later 2012 we previously <a href="http://news.open-bio.org/news/2012/11/server-transition-to-aws/">migrated the OBF websites AWS</a>, and this has proved very reliable and saves us worrying about looking after physical hardware.</p> <p>Update (Monday 16 June 2014): The replacement mailman server is now live, but our apologies for the inconvenience. Some delayed emails should now be delivered, but unfortunately older emails where you received a failure message will have to be resent.</p>https://www.open-bio.org/2014/05/29/biopython-1-64-released/Thu, 29 May 2014 13:55:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/05/29/biopython-1-64-released/<p>Source distributions and Windows installers for <strong>Biopython 1.64</strong> are now available from the <a href="http://biopython.org/wiki/Download" title="Biopython Downloads">downloads page</a> on the <a href="http://biopython.org/" title="Biopython website">official Biopython website</a> and from the <a href="https://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython 2.7b2.</p> <p>The new experimental module Bio.CodonAlign facilitates building codon alignment and further analysis upon it. This work is from the Google Summer of Code (GSoC) project by Zheng Ruan.</p> <p>Bio.Phylo now has tree construction and consensus modules, from on the GSoC work by Yanbo Ye.</p> <p>Bio.Entrez will now automatically download and cache new NCBI DTD files for XML parsing under the user&rsquo;s home directory (using <em>~/.biopython</em> on Unix like systems, and <em>$APPDATA/biopython</em> on Windows).</p> <p>Bio.Sequencing.Applications now includes a wrapper for the samtools command line tool.</p> <p>Bio.PopGen.SimCoal now also supports fastsimcoal.</p> <p>SearchIO hmmer3-text, hmmer3-tab, and hmmer3-domtab now support output from hmmer3.1b1.</p> <p>BioSQL can now use the mysql-connector package (available for Python 2, 3 and PyPy) as an alternative to MySQLdb (Python 2 only) to connect to a MySQL database.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Chunlei Wu (first contribution)</li> <li>Edward Liaw (first contribution)</li> <li>Eric Talevich</li> <li>Leighton Pritchard</li> <li>Manlio Calvi (first contribution)</li> <li>Markus Piotrowski (first contribution)</li> <li>Melissa Gymrek (first contribution)</li> <li>Michiel de Hoon</li> <li>Nigel Delaney (first contribution)</li> <li>Peter Cock</li> <li>Saket Choudhary</li> <li>Tiago Antao</li> <li>Vincent Davis (first contribution)</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Yanbo Ye (first contribution)</li> <li>Zheng Ruan (first contribution)</li> </ul>https://www.open-bio.org/2014/04/26/obf-gsoc-students-2014/Sat, 26 Apr 2014 18:45:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/04/26/obf-gsoc-students-2014/<p>Hi all, I&rsquo;m pleased to announce the acceptance of OBF&rsquo;s <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code 2014 (GSoC)</a> students: <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2014"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-150x150.jpg" alt="[GSoC 2014 Logo]"></a></p> <ul> <li>Sarah Berkemer - &quot; <em>Open source high-performance BioHaskell</em>&quot; (Mentors: Christian Höner zu Siederdissen, Ketil Malde) ( <a href="http://biohaskell.org/GSoC_blog">blog</a>)</li> <li>Loris Cro - &quot; <em>An ultra-fast scalable RESTful API to query large numbers of VCF datapoints</em>&quot; (Mentors: Francesco Strozzi, Raoul Bonnal &amp; the BioRuby team) ( <a href="http://kappaloris.github.io/GSoC-2014-OBF/">blog</a>)</li> <li>Victor Kofia - &quot; <em>JSBML: Redesign the implementation of mathematical formulas</em>&quot; (Mentors: Alex Thomas, Sarah Keating &amp; the JSBML team) ( <a href="http://kofiav.blogspot.ca/">blog</a>)</li> <li>Evan Parker - &quot; <em>Addition of a lazy loading sequence parser to Biopython&rsquo;s SeqIO package</em>&quot; (Mentors: Wibowo Arindrarto, Peter Cock &amp; the Biopython team) ( <a href="http://evanaparker.com/">blog</a>)</li> <li>Ibrahim Vazirabad - &quot; <em>Improving the Plug-in interface for CellDesigner</em>&quot; (Mentors: Andreas Dräger, Alex Thomas &amp; the JSBML team) ( <a href="http://jsbmlcelldesigner2014.blogspot.com/">blog</a>)</li> <li>Leandro Watanabe - &quot; <em>Dynamic Modeling of Cellular Populations within JSBML</em>&quot; (Mentors: Nicolas Rodriguez, Chris Myers &amp; the JSBML team) ( <a href="http://lhwatanabe.blogspot.co.uk/">blog</a>)</li> </ul> <p>Congratulations to our accepted students!</p> <p>Thanks very much to all the students who applied, we very much appreciate your hard work.</p> <p>We are now in the GSoC Community Bonding Period. Official work starts on May 23rd, and until then, students should prepare for their projects: get on the project mailing lists, solidify your plans, figure out where all the version control repositories are and which branch or fork you&rsquo;ll be working on, and start doing preparatory work.</p> <p>Here&rsquo;s to a great 2014 Summer of Code,</p> <p>Eric &amp; Raoul</p> <p>OBF GSoC 2014 Organization Administrators</p>https://www.open-bio.org/2014/04/02/catering-at-bosc-codefest-2014/Wed, 02 Apr 2014 11:13:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/04/02/catering-at-bosc-codefest-2014/<p>Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!</p> <p>The OBF will be holding the fifth <a href="https://www.open-bio.org/wiki/Codefest">annual BOSC Codefest</a>, an informal two day &ldquo;hackathon&rdquo; or &ldquo;coding festival&rdquo; preceding the <a href="https://www.open-bio.org/wiki/BOSC_2014">Bioinformatics Open Source Conference (BOSC 2014)</a> in Boston (USA).</p> <p>This year, the BOSC Codefest 2014 is being hosted by <a href="http://www.hackreduce.org">hack/reduce</a> (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by <a href="http://curoverse.com">Curoverse</a> (the team behind the open source platform <a href="http://arvados.org">Arvados</a>) and <a href="http://harbinger-partners.com/">Harbinger Partners, Inc.</a><a href="http://www.hackreduce.org/"><img src="https://www.open-bio.org/w/images/4/42/Hack-reduce-logo.png" alt=""></a><a href="http://curoverse.com/"><img src="https://www.open-bio.org/w/images/e/e5/Curoverse.png" alt=""></a><a href="http://harbinger-partners.com/"><img src="https://www.open-bio.org/w/images/a/ac/HP-logo-no-tagline.png" alt=""></a><a href="http://arvados.org/"><img src="https://www.open-bio.org/w/images/4/43/Arvados.png" alt=""></a> Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I&rsquo;m expecting <em>at least</em> coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and <a href="http://en.wikipedia.org/wiki/Jolt_Cola">Jolt Cola</a> doesn&rsquo;t exist in the USA any more&hellip; so I&rsquo;m waiting to see what our local organisers Brad Chapman &amp; Michael Heuer have planned.</p> <p>If you are wondering what happens exactly at a CodeFest, I suggest Brad&rsquo;s <a href="http://bcbio.wordpress.com/2013/07/18/summary-from-bioinformatics-open-science-codefest-2013-tools-infrastructure-standards-and-visualization/">blog post from the BOSC Codefest 2013</a>, or <a href="http://journal.embnet.org/index.php/embnetjournal/article/view/726/998">Möller et al (2013)</a>. Basically these meeting are a chance for developers of open source bioinformatics (not just the OBF&rsquo;s Bio* projects) to get together and work on common interests. Things work best with some pre-meeting planning on the usual project development mailing lists or IRC, but are also a great way to meet other scientists and developers in person with more time to chat than during a conference coffee break.</p> <p>Please note that while there is no registration fee for the <a href="https://www.open-bio.org/wiki/Codefest_2014">BOSC Codefest 2014</a>, please do fill in the registration form to help with the planning/catering.</p> <p>We&rsquo;re hoping all the Codefest participants will stay for the BOSC meeting itself, which requires formal paid registration as one of the big ISCB 2014 conference&rsquo;s SIG satellite meetings. Note that we&rsquo;re offering a <a href="http://news.open-bio.org/news/2014/03/free-student-presenters-bosc-2014/">BOSC fee waiver for student speakers</a>, this year. If you are going to BOSC, please remember to <a href="http://news.open-bio.org/news/2014/03/bosc-2014-call-for-abstracts/">submit your BOSC abstracts</a> this week!</p> <p>Peter</p>https://www.open-bio.org/2014/03/19/free-student-presenters-bosc-2014/Wed, 19 Mar 2014 18:21:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/03/19/free-student-presenters-bosc-2014/<p><a href="https://www.open-bio.org/wiki/BOSC_2014"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt=""></a> To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we&rsquo;re waiving the registration fee for accepted student presenters. When you submit your abstract ( <a href="http://news.open-bio.org/news/2014/03/bosc-2014-call-for-abstracts/">BOSC abstract call open until 4th April</a>), you must tick the student box:</p> <p><em>Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.</em></p> <p>Please note that because BOSC registration is via the ISCB as <a href="https://www.iscb.org/ismb2014-program/ismb2014-sigs-satellite-meetings#bosc">one of the ISCM SIG meetings</a>, eligible students must contact us <strong><em>before</em></strong> filling in their ISCB registration to ensure the BOSC SIG fee is waived. <a href="http://www.eaglegenomics.com/"><img src="https://www.open-bio.org/w/images/thumb/5/5f/Eagle_logo_2013.jpg/120px-Eagle_logo_2013.jpg" alt=""></a></p> <p>Furthermore, as in previous years, BOSC Student Travel Awards sponsored by <a href="http://www.eaglegenomics.com/">Eagle Genomics</a> will be awarded to the top student presentations to help with your travel and accommodation costs.</p> <p><strong>Update (2 May 2014):</strong> We&rsquo;ve just sent out the accepted talk invitations, and are offering a registration fee waiver to four student speakers.</p>https://www.open-bio.org/2014/03/09/obf-gsoc-2014-call-for-student-applications/Mon, 10 Mar 2014 00:54:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/03/09/obf-gsoc-2014-call-for-student-applications/<p><a href="http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2014/about_page"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-300x270.jpg" alt="Google Summer of Code 2014"></a> Are you a university student and interested in spending the summer developing open-source bioinformatics software?</p> <p>(Good! Keep reading.)</p> <p>On Monday, March 10, <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code 2014 (GSoC)</a> will begin accepting student applications to work with mentoring organizations like OBF.</p> <p>Here are the steps for you to prepare an application and apply for GSOC 2014 with OBF:</p> <ol> <li><strong>Check the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas">OBF ideas page</a></strong> for potential projects you&rsquo;d like to work on, and identify one or a few that you&rsquo;re most interested in doing.</li> <li><strong>Read our <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code#Guide_for_prospective_GSoC_students">guide for prospective GSoC students</a></strong> on the OBF wiki. Also see Google&rsquo;s <a href="http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2014/help_page">GSoC FAQ</a> and <a href="http://en.flossmanuals.net/GSoCStudentGuide/">GSoC student guide</a>, if you&rsquo;re with us so far.</li> <li><strong>Introduce yourself</strong> on the <a href="http://lists.open-bio.org/mailman/listinfo/gsoc">OBF GSoC mailing list</a>. Tell us which project(s) you like, any modifications to them you&rsquo;d like to make, or propose your own idea.</li> <li>Once you&rsquo;ve settled on a project or two and contacted your potential mentors, begin preparing a detailed <strong>project timeline</strong> for the summer. This timeline should cover each week of the summer, as far as you can plan it, describing the week&rsquo;s specific goals, coding tasks, anticipated problems and open questions. ( <a href="https://spreadsheets.google.com/pub?key=puFMq1smOMEo20j0h5Dg9fA&amp;single=true&amp;gid=0&amp;output=html">Example 1</a>, <a href="http://informatics.nescent.org/wiki/PhyloSoC:PhyloXML_support_in_BioRuby">Example 2</a>)</li> <li><strong>Submit your application to Google early.</strong> You can keep revising it on the Melange website until the deadline on March 21, but once you&rsquo;ve submitted your basic information we can begin giving you feedback and suggestions to improve your application. In addition to your weekly timeline, you can link to examples of code you&rsquo;ve written (e.g. on GitHub); a small contribution of code (e.g. a bug fix) to the project you&rsquo;re applying to work with would really impress us.</li> </ol> <p>Feel free to contact us on the <a href="http://lists.open-bio.org/mailman/listinfo/gsoc">mailing list</a> or <a href="https://plus.google.com/communities/103096212020630764091">Google Plus</a> if you have any questions.</p>https://www.open-bio.org/2014/03/04/bosc-2014-call-for-abstracts/Tue, 04 Mar 2014 18:18:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/03/04/bosc-2014-call-for-abstracts/<p>Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2014"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]"></a></p> <ul> <li>Dates: July 11-12, 2014</li> <li>Location: Boston, MA, USA</li> <li>Web site: <a href="https://www.open-bio.org/wiki/BOSC_2014">/wiki/BOSC_2014</a></li> <li>Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></li> <li><a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">BOSC announcements mailing list</a></li> <li>Twitter: <a href="https://twitter.com/OBF_BOSC" title="OBF Bioinformatics Open Source Conference (BOSC)">@OBF_BOSC</a> and <a href="https://twitter.com/OBF_news" title="Open Bioinformatics Foundation (OBF) News">@OBF_News</a></li> </ul> <p>Important Dates:</p> <ul> <li>March 24, 2014: <a href="https://www.iscb.org/ismb2014-registration">Registration opens for ISMB and BOSC</a></li> <li>April 4, 2014: Deadline for <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission" title="BOSC abstract submission">submitting BOSC abstracts</a></li> <li>May 1, 204: Notification of accepted talk abstracts emailed to authors</li> <li>July 9-10, 2014: <a href="https://www.open-bio.org/wiki/Codefest_2014" title="BOSC Codefest 2014">BOSC Codefest 2014</a>, Boston</li> <li>July 11-12, 2014: <a href="https://www.open-bio.org/wiki/BOSC_2014" title="BOSC 2014">BOSC 2014</a>, Boston</li> <li>July 11-15, 2014: <a href="https://www.iscb.org/ismb2014" title="ISMB 2014 conference">ISMB 2014</a>, Boston</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.</p> <p>BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>We invite you to submit one-page abstracts for talks and posters. This year&rsquo;s session topics are:</p> <p><a href="http://www.eaglegenomics.com/"><img src="https://www.open-bio.org/w/images/thumb/5/5f/Eagle_logo_2013.jpg/120px-Eagle_logo_2013.jpg" alt="[Eagle Genomics Logo]"></a></p> <ul> <li>Open Science and Reproducible Research</li> <li>Software Interoperability</li> <li>Genome-scale Data and Beyond</li> <li>Visualization</li> <li>Translational Bioinformatics</li> <li>Bioinformatics Open Source Libraries and Projects</li> </ul> <p><a href="http://www.gigasciencejournal.com/"><img src="https://www.open-bio.org/w/images/thumb/b/bb/Gigascience-07.png/200px-Gigascience-07.png" alt="GigaScience Journal Logo"></a></p> <p>Once again we thank <a href="http://www.eaglegenomics.com/">Eagle Genomics</a> for sponsoring the BOSC Student Travel Awards, and welcome the open access journal <a href="http://www.gigasciencejournal.com/">GigaScience</a> as a new sponsor for BOSC 2014.</p> <p>BOSC 2014 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp</p>https://www.open-bio.org/2014/02/28/obf-accepted-as-a-mentoring-organization-for-google-summer-of-code-2014/Fri, 28 Feb 2014 07:51:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/02/28/obf-accepted-as-a-mentoring-organization-for-google-summer-of-code-2014/<p>Open Bio is officially a <a href="http://www.google-melange.com/gsoc/org2/google/gsoc2014/obf">mentoring organization</a> for Google Summer of Code 2014! See <a href="http://google-opensource.blogspot.com/2014/02/mentoring-organizations-for-google.html">Google&rsquo;s official announcement</a> for more details on what this means in general.</p> <p>What&rsquo;s next? <a href="http://www.google-melange.com/gsoc/events/google/gsoc2014">Google&rsquo;s GSoC timeline</a> lays out what we need to do as a mentoring organization during the coming weeks. Students can apply March 10&ndash;21 through the <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014">official GSoC 2014 website</a> to work with OBF. Up to that point, we&rsquo;ll be reaching out to potential students and mentors, and contining to develop <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas">potential project ideas</a>. If you&rsquo;d like to get involved, introduce yourself on our <a href="https://plus.google.com/communities/103096212020630764091">Google Plus community</a> or on the mailing lists.</p>https://www.open-bio.org/2014/02/17/obf-applies-for-google-summer-of-code-2014/Mon, 17 Feb 2014 19:21:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/02/17/obf-applies-for-google-summer-of-code-2014/<p>On Friday, OBF applied to be a mentoring organization for Google Summer of Code 2014. The core of our application to Google is our <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas">list of project ideas</a> and our team of mentors supporting them. (We also have a separate page for <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">general information about GSoC and OBF&rsquo;s involvement</a>.) As another way to interact with potential GSoC students, we&rsquo;ve created a <a href="https://plus.google.com/115564754756543103019/posts">Google Plus page for OBF</a> and a <a href="https://plus.google.com/communities/103096212020630764091">G+ community for</a> <a href="https://plus.google.com/communities/103096212020630764091">OBF&rsquo;s GSoC activities</a>.</p> <p>Highlights of this year&rsquo;s Ideas list:</p> <ul> <li>All of the Bio* projects (except BioSQL and EMBOSS) are represented. BioPerl contributed the greatest number of ideas.</li> <li>The BioJava team focused on a Java implementation of the Structural Biology Markup Language called JSBML. The JSBML developers created a <a href="http://sbml.org/GSoC2014">SBML-specific list of GSoC ideas</a>, which we&rsquo;ve included under the OBF umbrella. There is also a great opportunity here to support SBML in other languages and Bio* projects through the JVM.</li> <li>We also have a category for <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#Cross-project_ideas">cross-language project ideas</a>, i.e. those involving two or more programming languages or Bio* project communities.</li> </ul> <p>But for now we have a lull, until Feb. 24 when Google announces the accepted mentoring organizations. (Fingers crossed!)</p> <p>Thanks to everyone who helped us pull together this application. We&rsquo;re eager to hear your thoughts on how this process went and how we can keep adapting for future GSoCs.</p>https://www.open-bio.org/2014/02/01/call-for-ideas-for-obfs-2014-google-summer-of-code/Sat, 01 Feb 2014 18:08:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/02/01/call-for-ideas-for-obfs-2014-google-summer-of-code/<p><a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code</a> is on again for 2014, and OBF is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors.</p> <p>Since OBF is an umbrella organization covering several member projects, most of these GSoC ideas will likely be associated with a specific Bio* community. For our GSoC application, and for the convenience of students, we aggregate each Bio* project&rsquo;s ideas on the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">GSoC page of the OBF wiki</a>, but the details of each idea are posted on the specific Bio* project&rsquo;s own wiki. So, if you have an idea for a Summer of Code project, please post your idea on your Bio* project mailing list for discussion and start an outline on the corresponding wiki page. Feel free to reuse or adapt ideas from 2013 or previous years that were not taken on by a student already, if you feel the idea is still viable.</p> <p>We also welcome ideas that fit with OBF&rsquo;s mission but are not part of a single Bio* project, or span multiple projects &ndash; these ideas can be posted on the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas">OBF wiki page</a> and discussed on the <a href="http://lists.open-bio.org/mailman/listinfo/open-bio-l">OBF mailing list</a>.</p> <p>Potential students, we&rsquo;re interested in your ideas, too! This is a good occasion to introduce yourself to the OBF community.  If you have an idea for something you&rsquo;d particularly like to work on during GSoC 2014, please ask us on the mailing list and we&rsquo;ll try to find a suitable mentor.</p> <p>Here&rsquo;s to another fun and productive Summer of Code!</p>https://www.open-bio.org/2014/01/14/call-for-org-admins-for-obf-2014-gsoc/Wed, 15 Jan 2014 00:04:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/01/14/call-for-org-admins-for-obf-2014-gsoc/<p><em><strong>Update: The deadline for responding has been extended to January 25.</strong></em> <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-300x270.jpg" alt="GoogleSummer_2014logo"></a> The 2014 Google Summer of Code (GSoC) is coming up soon. The <a href="http://www.google-melange.com/gsoc/events/google/gsoc2014" title="2014 GSoC Timeline">published timeline</a> puts the mentoring organization applications from Feb 3 to 14.</p> <p>OBF participated on behalf of our member projects in <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2010">2010</a>, <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2011">2011</a>, and <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2012">2012</a>. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.</p> <p>To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve.</p> <p>An org admin’s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to “keep it together.” Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org’s mentors. The org admin’s responsibilities include:</p> <ul> <li>Representing our online face to GSoC, in particular to GSoC students</li> <li>Shepherding our mentoring organization application, and submitting it.</li> <li>Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises.</li> <li>Knowing GSoC rules and processes, and making sure ours are consistent with them.</li> <li>Reminding participants of rules, and enforcing them in the event it is necessary.</li> <li>Mediating, and sometimes arbitrating between students and mentors when needed.</li> <li>Ensuring that GSoC timelines are met by everyone.</li> </ul> <p>The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener.</p> <p>If you are interested in helping us out in this role, please email us (by Jan 25, 2014) a statement at <a href="mailto:board@open-bio.org">board@open-bio.org</a> explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project’s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects.</p> <p>We are looking forward to hearing from you!</p>https://www.open-bio.org/2013/12/24/bosc-2014-keynote-speakers/Tue, 24 Dec 2013 05:34:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/24/bosc-2014-keynote-speakers/<p>Thanks to those who participated in the <a href="http://news.open-bio.org/news/2013/12/bosc-2014-keynote-competition/">BOSC 2014 Keynote Competition</a>! Our winner is Manuel Corpas, who correctly surmised <a href="https://twitter.com/pebourne">Philip Bourne</a>:</p> <p><a href="https://twitter.com/manuelcorpas/status/412520369044463616">https://twitter.com/manuelcorpas/status/412520369044463616</a></p> <p>(In fact, we had already confirmed Philip Bourne as our second keynote speaker <em>before</em> his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a>!</p> <p>Dr. Bourne&rsquo;s keynote talk will be entitled &ldquo;Biomedical Research as an Open Digital Enterprise&rdquo;:</p> <blockquote> <p>The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.</p> </blockquote> <p>Our other keynote speaker at BOSC 2014, as already announced, will be <a href="https://twitter.com/ctitusbrown">Titus Brown</a>, whose topic is &ldquo;A History of Bioinformatics (in the Year 2039)&rdquo;.</p>https://www.open-bio.org/2013/12/19/bioperl-release-1-6-923/Thu, 19 Dec 2013 05:24:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/19/bioperl-release-1-6-923/<p>The latest BioPerl release (v1.6.923) is now available on CPAN. This is a point release to address a few bugs, as well as push out the recent code updates that Francisco Ossandón has made to improve Windows support and improve Bio::Location (among other bits and pieces).</p> <p>Contributing to the release:</p> <ul> <li>Francisco Ossandón</li> <li>Brian Osborne</li> <li>Dave Messina</li> <li>Carnë Draug</li> <li>Chris Fields</li> <li>Benjamin Warren</li> </ul> <p>Enjoy!</p> <p>chris</p>https://www.open-bio.org/2013/12/13/bosc-2014-keynote-competition/Fri, 13 Dec 2013 12:24:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/13/bosc-2014-keynote-competition/<p>We&rsquo;re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference ( <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a>) will be C. Titus Brown, as he announced on Twitter recently:</p> <blockquote> <p><a href="https://twitter.com/ctitusbrown/">Titus Brown (@ctitusbrown):</a> <a href="https://twitter.com/ctitusbrown/"><img src="https://pbs.twimg.com/profile_images/2341608206/1v12iz3xg0w80911u76a_normal.png" alt="C. Titus Brown"></a> Excited to be a keynote speaker at BOSC 2014! My title: &ldquo;A History of Bioinformatics (in the year 2039)&rdquo; - plenty of room for mischief ;) <a href="https://twitter.com/ctitusbrown/status/410934403565490176">https://twitter.com/ctitusbrown/status/410934403565490176</a></p> </blockquote> <p>In recognition of the growing use of Twitter and social media within science as a way of connecting across geographical divides, we&rsquo;re announcing a Twitter competition to guess who is scheduled to give the second keynote at BOSC 2014 in Boston.</p> <p>To enter, please tweet using <a href="https://twitter.com/search?q=%23bosc2014" title="#BOSC2014 on Twitter">hashtag #bosc2014</a> and include us via <a href="https://twitter.com/OBF_BOSC" title="@OBF_BOSC on Twitter">@OBF_BOSC</a>, e.g.</p> <blockquote> <p>I think @OBF_BOSC should invite &ldquo;Professor X&rdquo; to be a keynote speaker at #BOSC2014 because &hellip;</p> </blockquote> <p>The first correct entry (within one week) will be awarded one complementary BOSC 2014 registration fee for themselves, or a nominated group member. This does not cover travel or accommodation, and there is no cash substitute if you cannot attend BOSC 2014. Members of the OBF board, BOSC organizing committee, and ISMB SIG committee are not eligible, nor are the keynote speakers themselves.</p> <p>We intend to announce the mystery keynote speaker and any Twitter competition winner in one week&rsquo;s time, but reserve the right to cut short, modify, or cancel the competition.</p> <p>Our ulterior motive is to crowd source ideas for future keynote speakers in BOSC 2015, so some serious suggestions please ;)</p> <p>Further details about BOSC 2014 will be posted here: <a href="https://www.open-bio.org/wiki/BOSC_2014">/wiki/BOSC_2014</a></p> <p>Thank you,</p> <p>Peter Cock &amp; Nomi Harris, BOSC 2014 co-chairs.</p>https://www.open-bio.org/2013/12/12/minutes2013-dec-confcall/Thu, 12 Dec 2013 05:41:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/12/minutes2013-dec-confcall/<h3 id="agenda">Agenda</h3> <p><strong>Venue:</strong> to be held by conference call on Dec 12, 2013, 12pm EDT (17:00 UTC)  Dial-in Number: 1-605-475-5950 (US Midwest)  Participant Access Code: 279610</p> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2013_Apr_ConfCall">Apr 2013 BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>Board elections (by <a href="https://vote.heliosvoting.org/helios/e/obf-board-dec2013">secret electronic ballot</a>): <ul> <li>Hilmar Lapp, running for a 2nd term as President</li> <li>Peter Cock, running for office of Secretary</li> <li>Nomi Harris, running for a 2nd term on the Board, as at-large member</li> </ul> </li> <li>To the extent available, review of 2013 financials (Hilmar)</li> <li>BOSC 2014: update from and vote of confidence for the 2014 chairs (Nomi, Peter)</li> <li>Does OBF and/or BOSC want to be listed as an <a href="http://www.iscb.org/iscb-affiliates-cosis">ISCB &ldquo;Community of Special Interest&rdquo;</a> (COSI) along side other SIGs and communities? See <a href="http://www.iscb.org/iscb-netbio-cosi">NetBio</a> and <a href="http://www.iscb.org/iscb-regsys-cosi">RegSys examples</a>. (Peter)</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p><strong>Attending:</strong></p> <ul> <li>Directors: Hilmar Lapp, Peter Cock, Chris Dagdigian, Chris Fields, Nomi Harris, Jason Stajich</li> <li>Guests: Michael Heuer</li> </ul> <p><strong>Minutes:</strong></p> <p>Draft of the Dec 2013 conference call minutes:</p> <p>Attendees: Board: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Chris Fields, Jason Stajich, Peter Cock Guests: Michael Heuer</p> <p>Meeting called to order at 17:04 UTC. Roll call yields all 6 Board members present. Quorum is therefore established.</p> <ol> <li>Approval of <a href="https://www.open-bio.org/wiki/Minutes:2013_Apr_ConfCall">April 2013 Board meeting minutes</a>. The minutes were approved with unanimous consent.</li> <li>New business. <ul> <li>Board elections. Hilmar remarked that he wants to get aware from implicit continuation of posts, both as a way for the post-holder to explicitly express their interest, and for the board to explicitly re-endorse them. <ul> <li>Hilmar was elected President in Dec 2011. He is standing for re-election despite having previously planned to step down as he enjoyed it more than he expected and realised there is still more that he can do.</li> <li>Peter was elected to the Board as Director at-large in Dec 2011. He is volunteering to serve as Secretary recognising that Hilmar had too many responsibilities serving as both Secretary and President.</li> <li>Nomi was elected Parliamentarian in Dec 2011. She is standing to return as a Director at-large.</li> <li>Election was by <a href="https://vote.heliosvoting.org/helios/e/obf-board-dec2013">electronic ballot</a>. Results confirmed all three posts with six votes (unanimous barring one abstention).</li> </ul> </li> <li>Review of 2013 financials. <ul> <li>Hilmar is waiting for major expenses, specifically the AWS running costs. Major income: $1000 donation from Eagle Genomics for BOSC 2013 (and delayed $1000 from BOSC 2012). Personal donation from Hilmar earmarked for 3 years of renewal for domains he donated. Full 2013 financial report to be reviewed at another public Board meeting in Spring 2014.</li> </ul> </li> <li>BOSC 2014 update. <ul> <li>BOSC 2014 is confirmed by ISCB. Two keynote speakers are also confirmed, and provisional session titles have been planned. The committee has been active active with some new members.</li> <li>Discussed BOSC finances and the fact that due to high SIG registration fees, which are set by ISCB and are outside of our control, we have been running a sizeable surplus. The BOSC committee is considering ideas for how to use the surplus to give back to the community. One idea is to offer all non-commercial speakers (or at least student speakers) a 50% reduction in the registration fees.</li> <li>We agreed to approach other SIG chairs and Scott Markel (ISCB Board of Directors) informally to see if they would also support reducing the SIG fees.</li> <li>The Board made a unanimous vote of confidence in the 2014 BOSC co-chairs (Nomi and Peter), and appreciates their service and time investment.</li> </ul> </li> <li>ISMB COSI <ul> <li>Contingent on there being no expectation of exclusivity with being a COSI (Peter to follow up), the Board unanimously endorses the OBF being an ISCB COSI.</li> </ul> </li> </ul> </li> <li>Ad-hocc business from Directors or the Public. <ul> <li>There was agreement that OBF should try to participate in GSoC 2014, and to confirm with Pjotr Prins that he is willing to lead this. Chris Fields will follow up.</li> <li>Discussed the proposed BOSC twitter competition idea. The Board is positively predisposed to the idea, but leaves discussing the details to the BOSC committee.</li> </ul> </li> </ol> <p>Meeting adjourned with unanimous consent at 17:52 UTC.</p>https://www.open-bio.org/2013/12/09/minutes2013-apr-confcall/Mon, 09 Dec 2013 05:40:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/09/minutes2013-apr-confcall/<h3 id="agenda">Agenda</h3> <p><strong>Venue:</strong> to be held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)  Dial-in Number: 1-605-475-5950 (Midwest)  Participant Access Code: 279610</p> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2012_Nov_ConfCall">Nov 2012 BoD meeting minutes</a></li> <li><a href="https://www.open-bio.org/w/images/1/11/2012-OBF-Treasurers-Report.pdf">Treasurer&rsquo;s 2012 report</a> (Chris Dagdigian)</li> </ul> </li> <li>New business <ol> <li>Administration of O|B|F&rsquo;s 2013 Google Summer of Code participation (Pjotr Prins)</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p><strong>Venue:</strong> held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Chris Fields, Peter Cock; Jason Stajich joined for the last 15 minutes.</li> <li>Guests: none</li> </ul> <p><strong>Minutes:</strong></p> <p>Meeting called to order at 10.37am PDT</p> <h4 id="old-business">Old business:</h4> <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2012_Sep_ConfCall">Minutes from previous Sep 2012 meeting</a> are approved by unanimous consent.</li> <li><a href="https://www.open-bio.org/w/images/1/11/2012-OBF-Treasurers-Report.pdf">Treasurer&rsquo;s 2012 report</a>: <ul> <li>Chris D. summarizes and explains the 2012 expenses and income items, as well those in 2013 up to April 1st, which is when the account was closed in order to transfer our financial assets to SPI.</li> <li>Check was mailed to SPI on April 3, and the SPI Treasurer today has acknowledged receipt of the funds.</li> <li>Closing the account unfortunately means we can no longer obtain online statements for past periods. If we ever need those, Chris D. may have to visit the local branch in person, or we would have to make another formal and authenticated request (which would likely cost a fee).</li> <li>Expenses incurred from hosting VMs on Amazon (AWS) are still being donated by Chris D. Amazon needs a credit (or debit) card for payment. Currently this is Chris&rsquo; card, but we should ask for a credit/debit card from SPI that would charge against our funds with SPI.</li> <li>Peter moves to approve the treasurer&rsquo;s report, motion approved by unanimous consent.</li> </ul> </li> </ul> <h4 id="new-business">New business:</h4> <ul> <li>Pjotr&rsquo;s role in Google Summer of Code: <ul> <li>Pjotr did not attend the Board meeting because just two days prior the O|B|F&rsquo;s mentoring organization application to GSoC was declined.</li> <li>This outcome is unfortunate, but nonetheless there is unanimous support and endorsement for Pjotr continuing to serve in this role next year. The Board thanks him for his work this year, and encourages him to continue this next year.</li> <li>Pjotr is already planning a post-mortem, and has expressed interest in trying again next year.</li> </ul> </li> <li>Updates on BOSC 2013 by Nomi: <ul> <li>Deadline for abstracts is this coming Friday, April 12. A good group of reviewers is lined up.</li> <li>There is some worry with the open-source software sustainability and funding models panel. It lacks in diversity of viewpoints right now, and they need to look further for panelists. If necessary, we registration for panelists could be comp&rsquo;ed. <ul> <li>Several suggestions were brought up, including Eagle Genomics / Richard Holland (doing commercial work on top of ENSEMBL), people or companies doing commercial services on top of Amazon, Scott Markel (Accelrys&rsquo; Pipeline Pilot product uses BioPerl, and has on occasion contributed back), and Alex Pico (Cytoscape ecosystem, which has enabled commercial players to plug commercially sold components into the main open-source platform).</li> </ul> </li> </ul> </li> <li>OBF Interoperability Hackathon at the Broad: <ul> <li>The event has just taken place, organized by Brad Chapman. Unfortunately, Michael Reich and Broad staff had to bow out.</li> <li>According to Brad, it was nonetheless a success. The Board is grateful to Brad for running this.</li> </ul> </li> </ul> <p>Adjourned at 11.15pm PDT by unanimous consent.</p>https://www.open-bio.org/2013/12/06/biopython-1-63-released/Fri, 06 Dec 2013 11:16:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/06/biopython-1-63-released/<p>Source distributions and Windows installers for <strong>Biopython 1.63</strong> are now available from the <a href="http://biopython.org/wiki/Download" title="Biopython Downloads">downloads page</a> on the <a href="http://biopython.org/" title="Biopython website">official Biopython website</a> and ( <em>soon</em>) from the <a href="https://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5).</p> <p>This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.</p> <p>The Biopython Tutorial &amp; Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>from __future__ import print_function </span></span></code></pre></div><p>Similarly we now use the Python 3 style built-in next function in place of the Python 2 style iterators&rsquo; .next() method. This language feature is also available under Python 2.6 and 2.7.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the December 2013 release of REBASE.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Chris Mitchell (first contribution)</li> <li>Christian Brueffer</li> <li>Eric Talevich</li> <li>Gokcen Eraslan (first contribution)</li> <li>Josha Inglis (first contribution)</li> <li>Konstantin Tretyakov (first contribution)</li> <li>Lenna Peterson</li> <li>Martin Mokrejs</li> <li>Nigel Delaney (first contribution)</li> <li>Peter Cock</li> <li>Sergei Lebedev (first contribution)</li> <li>Tiago Antao</li> <li>Wayne Decatur (first contribution)</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul>https://www.open-bio.org/2013/11/27/initial-release-of-bioperl-biocommunity-distribution/Thu, 28 Nov 2013 04:02:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/11/27/initial-release-of-bioperl-biocommunity-distribution/<p><strong>Note</strong>: I&rsquo;m reposting here the <a href="http://lists.open-bio.org/pipermail/bioperl-l/2013-November/071290.html">original announcement</a> from Florent Angly on the BioPerl mail list.</p> <hr> <p>Dear all,</p> <p>Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats.</p> <p>Today, I am happy to announce the release of the first version of these modules, which can be obtained from CPAN:</p> <p><a href="http://search.cpan.org/search?query=Bio-Community&amp;mode=dist">http://search.cpan.org/search?query=Bio-Community&amp;mode=dist</a></p> <p>Obviously, this is just the beginning for these modules and I hope that interested developers will join me to expand them.</p> <p>Best,</p> <p>Florent</p>https://www.open-bio.org/2013/11/12/biopython-1-63-beta-released/Tue, 12 Nov 2013 16:20:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/11/12/biopython-1-63-beta-released/<p>Source distributions and Windows installers for <strong>Biopython 1.63 beta</strong> are now available from the <a href="http://biopython.org/wiki/Download" title="Biopython&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; Downloads">downloads page</a> on the <a href="http://biopython.org/" title="Biopython website">official Biopython website</a>.</p> <p>This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. <strong>This was made possible by dropping Python 2.5 (and Jython 2.5).</strong></p> <p>This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.</p> <p>The Biopython Tutorial &amp; Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> from __future__ import print_function </span></span></code></pre></div><p>Similarly we now use the Python 3 style built-in next function in place of the Python 2 style iterators&rsquo; .next() method. This language feature is also available under Python 2.6 and 2.7.</p> <p><strong>Contributors</strong></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Chris Mitchell (first contribution)</li> <li>Christian Brueffer</li> <li>Eric Talevich</li> <li>Josha Inglis (first contribution)</li> <li>Konstantin Tretyakov (first contribution)</li> <li>Lenna Peterson</li> <li>Martin Mokrejs</li> <li>Nigel Delaney (first contribution)</li> <li>Peter Cock</li> <li>Sergei Lebedev (first contribution)</li> <li>Tiago Antao</li> <li>Wayne Decatur (first contribution)</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul>https://www.open-bio.org/2013/09/07/bioperl-v-1-6-910-released/Sun, 08 Sep 2013 03:48:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/09/07/bioperl-v-1-6-910-released/<p><em><strong>UPDATE:</strong></em></p> <p>As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio <a href="https://metacpan.org/module/Bio::Biblio">to CPAN this past March</a>.</p> <p>Unfortunately that release (v1.7) appears to have version collisions with this one (v.1.6.910); therefore I&rsquo;m packaging a new point release ( <strong>v1.6.920</strong>) that removes Bio::Biblio to prevent this.  That has now been uploaded to CPAN and should be available shortly.</p> <p><strong><em>ORIGINAL POST:</em></strong></p> <p>All,</p> <p>I would like to announce that BioPerl v. 1.6.910 has been released to CPAN and should be showing up imminently.  This is primarily a bug fix release.  Two key items of note:</p> <ol> <li>Beyond minor fixes to address problems on other distributions, this will be the last of the BioPerl 1.6 series.  We will be repackaging code into separate repositories and likewise releasing them as separate distributions on CPAN during the next (1.7.x) releases.</li> <li>Two distributions have already been split out:</li> </ol> <ul> <li>Bio::FeatureIO has been moved into a separate distribution.  The code for Bio::FeatureIO is undergoing revision and will be released at a future point.  If you need access to it, it is available <a href="https://github.com/bioperl/Bio-FeatureIO">on GitHub</a>.</li> <li>Bio::DB::EUtilities and it&rsquo;s related modules have also been into a separate distribution and are now available on CPAN.  I will be updating the release on that code as well.</li> </ul> <p>The first 1.7 release is scheduled for sometime in <strong>late fall-early winter</strong>, with the primary focus (as mentioned above) being repackaging of core code.</p> <p>Thanks all!</p> <p>chris</p>https://www.open-bio.org/2013/08/28/biopython-1-62-released/Wed, 28 Aug 2013 22:14:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/08/28/biopython-1-62-released/<p>Source distributions and Windows installers for <strong>Biopython 1.62</strong> are now available from the <a href="http://biopython.org/wiki/Download" title="Biopython Downloads">downloads page</a> on the <a href="http://biopython.org/" title="Biopython website">official Biopython website</a> and ( <em>soon</em>) from the <a href="https://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p><strong>Python support</strong></p> <p>This is our first release of Biopython which <em>officially supports Python 3</em>. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are <em>not</em> supported.</p> <p>We still fully support Python 2.5, 2.6, and 2.7. Support under <a href="http://www.jython.org/">Jython</a> is available for versions 2.5 and 2.7 and under <a href="http://pypy.org/">PyPy</a> for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.</p> <p>Please note that this release marks our last official for support Python 2.5. Beginning from Biopython 1.63, the minimum supported Python version will be 2.6.</p> <p><strong>Highlights</strong></p> <ul> <li>The translation functions will give a warning on any partial codons (and this will probably become an error in a future release). If you know you are dealing with partial sequences, either pad with &ldquo;N&rdquo; to extend the sequence length to a multiple of three, or explicitly trim the sequence.</li> <li>The handling of joins and related complex features in Genbank/EMBL files has been changed with the introduction of a <code>CompoundLocation</code> object. Previously a <code>SeqFeature</code> for something like a multi-exon CDS would have a child <code>SeqFeature</code> (under the <code>sub_features</code> attribute) for each exon. The <code>sub_features</code> property will still be populated for now, but is deprecated and will in future be removed. Please consult the examples in the help (docstrings) and Tutorial.</li> <li>Thanks to the efforts of Ben Morris, the Phylo module now supports the file formats NeXML and CDAO. The Newick parser is also significantly faster, and can now optionally extract bootstrap values from the Newick comment field (like Molphy and Archaeopteryx do). Nate Sutton added a wrapper for FastTree to <code>Bio.Phylo.Applications</code>.</li> <li>New module <code>Bio.UniProt</code> adds parsers for the GAF, GPA and GPI formats from UniProt-GOA.</li> <li>The <code>BioSQL</code> module is now supported in Jython. MySQL and PostgreSQL databases can be used. The relevant JDBC driver should be available in the <code>CLASSPATH</code>.</li> <li>Feature labels on circular <code>GenomeDiagram</code> figures now support the <code>label_position</code> argument (start, middle or end) in addition to the current default placement, and in a change to prior releases these labels are outside the features which is now consistent with the linear diagrams.</li> <li>The code for parsing 3D structures in mmCIF files was updated to use the Python standard library&rsquo;s <code>shlex</code> module instead of C code using flex.</li> <li>The <code>Bio.Sequencing.Applications</code> module now includes a BWA command line wrapper.</li> <li><code>Bio.motifs</code> supports JASPAR format files with multiple position-frequence matrices.</li> </ul> <p>Additionally there have been other minor bug fixes and more unit tests.</p> <p><strong>Contributors</strong></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alexander Campbell (first contribution)</li> <li>Andrea Rizzi (first contribution)</li> <li>Anthony Mathelier (first contribution)</li> <li>Ben Morris (first contribution)</li> <li>Brad Chapman</li> <li>Christian Brueffer</li> <li>David Arenillas (first contribution)</li> <li>David Martin (first contribution)</li> <li>Eric Talevich</li> <li>Iddo Friedberg</li> <li>Jian-Long Huang (first contribution)</li> <li>Joao Rodrigues</li> <li>Kai Blin</li> <li>Lenna Peterson</li> <li>Michiel de Hoon</li> <li>Matsuyuki Shirota (first contribution)</li> <li>Nate Sutton (first contribution)</li> <li>Peter Cock</li> <li>Petra Kubincová (first contribution)</li> <li>Phillip Garland</li> <li>Saket Choudhary (first contribution)</li> <li>Tiago Antao</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Xabier Bello (first contribution)</li> </ul>https://www.open-bio.org/2013/07/17/bosc-2013/Wed, 17 Jul 2013 14:33:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/07/17/bosc-2013/<p>Hello from Berlin, where the pre-BOSC informal <a href="https://www.open-bio.org/wiki/Codefest_2013">CodeFest 2013</a> meeting is already underway. We&rsquo;re looking forward to seeing even more of you on Friday and Saturday for <a href="https://www.open-bio.org/wiki/BOSC_2013">BOSC 2013</a>.</p> <p>BOSC 2013 will be the 14th annual <em>Bioinformatics Open Source Conference</em>, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the <a href="http://www.iscb.org/ismbeccb2013">ISMB/ECCB 2013 is in Berlin</a>, Germany.</p> <p>You can follow <a href="https://twitter.com/OBF_BOSC">BOSC on Twitter @OBF_BOSC</a>, and we&rsquo;ll be using the <a href="https://twitter.com/search?q=%23BOSC2013">Twitter Hashtag #BOSC2013</a>.</p> <p>We also have a low-volume <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">BOSC announcements mailing list</a>, please sign up if you&rsquo;d consider attending or submitting a talk or poster for next year - BOSC 2014 and the ISMB 2014 will be in Boston, USA in July 2014.</p>https://www.open-bio.org/2013/05/27/bioruby-1-4-3-0001-released/Mon, 27 May 2013 12:44:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/05/27/bioruby-1-4-3-0001-released/<p>We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs.</p> <ul> <li>&ldquo;gem install bio&rdquo; failed with Ruby 2.0 or later versions.</li> <li>lib/bio/db/gff.rb script encoding issue</li> <li>Bio::Blast::Default::Report parse error when subject sequence contains spaces.</li> </ul> <p>For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.4.3.0001/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.4.3.0001/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz">http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz</a> Gem file is also available at: <a href="http://bioruby.org/archive/gems/bio-1.4.3.0001.gem">http://bioruby.org/archive/gems/bio-1.4.3.0001.gem</a></p> <p>We also put RubyGems pacakge at RubyGems.org and RubyForge.</p> <p>You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.3.0001)” in the list. Then, % sudo gem install bio</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.</p>https://www.open-bio.org/2013/02/05/biopython-1-61-released/Tue, 05 Feb 2013 21:14:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/02/05/biopython-1-61-released/<p>Source distributions and Windows installers for Biopython 1.61 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>The updated <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> is online ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p><strong>Platforms/Deployment</strong></p> <p>We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and <a href="http://www.jython.org">Jython</a> 2.5 and <a href="http://pypy.org">PyPy</a> 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ‘beta’ installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows.</p> <p>Please note we are phasing out support for Python 2.5. We will continue support for at least one further release (Biopython 1.62). This could be extended given feedback from our users. Focusing on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier.</p> <p><strong>Features</strong></p> <p>GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows an octagonal shape, like the existing BOX sigil but with the corners cut off. JAGGY shows a box with jagged edges at the start and end, intended for things like NNNNN regions in draft genomes. Finally BIGARROW is like the existing ARROW sigil but is drawn straddling the axis. This is useful for drawing vertically compact figures where you do not have overlapping genes.</p> <p>New module Bio.Graphics.ColorSpiral can generate colors along a spiral path through HSV color space. This can be used to make arbitrary &lsquo;rainbow&rsquo; scales, for example to color features or cross-links on a GenomeDiagram figure.</p> <p>The Bio.SeqIO module now supports reading sequences from PDB files in two different ways. The &ldquo;pdb-atom&rdquo; format determines the sequence as it appears in the structure based on the atom coordinate section of the file (via Bio.PDB, so NumPy is currently required for this). Alternatively, you can use the &ldquo;pdb-seqres&rdquo; format to read the complete protein sequence as it is listed in the PDB header, if available.</p> <p>The Bio.SeqUtils module how has a seq1 function to turn a sequence using three letter amino acid codes into one using the more common one letter codes. This acts as the inverse of the existing seq3 function.</p> <p>The multiple-sequence-alignment object used by Bio.AlignIO etc now supports an annotation dictionary. Additional support for per-column annotation is planned, with addition and splicing to work like that for the SeqRecord per-letter annotation.</p> <p>The Bio.Motif module has been updated and reorganized. To allow for a clean deprecation of the old code, the new motif code is stored in a new module Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif.</p> <p><strong>Experimental Code - SearchIO</strong></p> <p>This release also includes <a href="http://biopython.org/wiki/SearchIO">Bow&rsquo;s Google Summer of Code work</a> writing a unified parsing framework for NCBI BLAST (assorted formats including tabular and XML), HMMER, BLAT, and other sequence searching tools. This is currently available with the new <code>BiopythonExperimentalWarning</code> to indicate that this is still somewhat experimental. We&rsquo;re bundling it with the main release to get more public feedback, but with the big warning that the API is likely to change. In fact, even the current name of Bio.SearchIO may change since unless you are familiar with BioPerl its purpose isn&rsquo;t immediately clear.</p> <p><strong>Contributors</strong></p> <ul> <li>Brandon Invergo</li> <li>Bryan Lunt (first contribution)</li> <li>Christian Brueffer (first contribution)</li> <li>David Cain</li> <li>Eric Talevich</li> <li>Grace Yeo (first contribution)</li> <li>Jeffrey Chang</li> <li>Jingping Li (first contribution)</li> <li>Kai Blin (first contribution)</li> <li>Leighton Pritchard</li> <li>Lenna Peterson</li> <li>Lucas Sinclair (first contribution)</li> <li>Michiel de Hoon</li> <li>Nick Semenkovich (first contribution)</li> <li>Peter Cock</li> <li>Robert Ernst (first contribution)</li> <li>Tiago Antao</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul>https://www.open-bio.org/2012/11/13/minutes2012-nov-confcall/Tue, 13 Nov 2012 05:39:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/11/13/minutes2012-nov-confcall/<h3 id="agenda">Agenda</h3> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2012_Sep_ConfCall">Sep 2012 BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>Election of new Board members. Nominated candidate is Chris Fields.</li> <li>Review and possibly revamping of the procedure for joining and maintaining the OBF membership</li> <li>Asset transfer to SPI</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p><strong>Venue:</strong> held by conference call Nov 13, 2012, 11.30am EST (16:30 UTC)</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Jason Stajich, Nomi Harris, Peter Cock, Hilmar Lapp</li> <li>Guests: Scott Markel, Chris Fields</li> </ul> <p><strong>Minutes:</strong></p> <p>Hilmar called meeting to order at 11:34am EST.</p> <h4 id="old-business">Old business:</h4> <ul> <li>Hilmar moved to approve <a href="https://www.open-bio.org/wiki/Minutes:2012_Sep_ConfCall">Sep 2012 BoD meeting minutes</a>. Motion approved with unanimous consent.</li> </ul> <h4 id="new-business">New business:</h4> <p><strong>i. Election of new Board members.</strong></p> <ul> <li>Richard Holland was interested in running for the Board, but had to withdraw his candidacy for now due to pending corporate changes in Eagle Genomics, his employer.</li> <li>Chris Fields is running for Board member at-large. Chris has been an active programmer for about 13 years. He joined BioPerl&rsquo;s core developers group in 2007. While he became involved early on with fixing bugs etc., he also soon thereafter took on further responsibilities, including pushing releases out. His professional affiliation is now with the Bioinformatics Core of the U. Illinois at Urbana-Champaign&rsquo;s Center for Integrative Genomics. In this role, he is involved in completely revamping the Bioinformatics resources on the UIUC campus. Chris has meanwhile moved into other languages and toolkits, based on the realization that there is no perfect language or tool. Chris is Interested in finding tools and toolkits that could be used across the board at OBF.</li> <li>Proceeded to vote after there were no further questions and comments. <a href="https://vote.heliosvoting.org/helios/e/obf-bod-nov2012">Voting was by electronic ballot</a>. <ul> <li>Results: 4 votes for electing Chris Fields to the Board, 0 against, 0 abstain.</li> <li>We congratulate Chris and welcome him to the O|B|F Board. His Board membership will become effective immediately after this meeting ends.</li> </ul> </li> </ul> <p><strong>ii. Review and possible revamping of the procedure for joining and maintaining the OBF membership</strong></p> <ul> <li>Our current membership enrollment and maintenance procedures are onerous, poorly automated, and involve a lot of manual steps and intervention. <ul> <li>To enroll, interested people have to fill out a form on PDF or paper, scan it, and email the scan. (Once a year at BOSC, they can also return the paper form to a BOSC organizer.) If accepted, the Board officer who handles the membership (currently Hilmar) then transfers email and name by hand to a spreadsheet (that constitutes the &ldquo;official&rdquo; membership roll), and subscribes the new member to the members mailing list.</li> <li>Maintenance is ad-hoc and completely manual. If membership email addresses are flagged as bouncing by mailman, the membership officer (currently Hilmar) tries to hunt down the new email address for the member, and if this and all other contact attempts fail, the member is considered to have resigned his or her membership. While bouncing email incidents have increased in frequency in the last two years, we have only a handful of members who we can no longer reach.</li> </ul> </li> <li>Originally, O|B|F&rsquo;s incorporation status required (or was understood to require) us to have verifiable evidence in hand of someone&rsquo;s identity, as well as agreement with our stated mission. As we are now SPI-associated project, this is no longer a requirement; in essence we can set ourselves what our requirements for a desirable process should be.</li> <li>There is strong agreement among the Board that the current procedure is undesirable in multiiple ways, and creates unnecessary barrierrs, and that it should be replaced with a different one, now that we aren&rsquo;t under legal requirements anymore.</li> <li>Which procedure to replace the current one with is less clear. <ul> <li>One suggestion is to simply allow (user-initiated) subscription to the members mailing list to count as joining the membership. This would pose minmal burden on joining, which is desirable, but also bears the risk that eventually a sizable fraction of the membership does not represent active members actually endorsing and interested in contributing to the OBF&rsquo;s objectives. This may then also inflate the quorum (10% of members) that has to be met for elections put before the membership.</li> <li>An alternative model is an electronic web-based form that asks people interested in joining to provide a short statement of purpose that explains how they meet the membership criteria (currently, agreeing with and endorsing OBF&rsquo;s objectives).</li> <li>The SPI has two tiers of membership: non-contributing members, for which one has to agree with the SPI&rsquo;s principles, and contributing members, for which one has to be an active participant in the free software community. For becoming a contributing member, one has to provide a statement explaining how one meets the criteria. Forms for signing up are all electronic. Only contributing members are eligible to vote in SPI matters.</li> <li>SPI&rsquo;s two-tier membership model is not so dissimilar from what we have, although our process is not as formalized. The participants (users, developers, lurkers) in the Bio* projects could be considered as the equivalent to SPI&rsquo;s &ldquo;non-contributing&rdquo; members, whereas those on the O|B|F membership roll are equivalent to SPI&rsquo;s &ldquo;contributing&rdquo; members. (As for SPI, these overlap quite a bit.)</li> <li>Google Groups is another option, because unlike mailman a Google Group can be set up so that people interested in joining must request an invite by filling out a form, including a free text field that could be used to require a statement of purpose.</li> </ul> </li> <li>Of the candidates on the table, none seems like the obvious way to move forward right now. We want a mechanism that is online, automatically verifies email address for new signups, yet still allows requiring some statement of purpose and endorsement of O|B|F&rsquo;s objectives for becoming a member.</li> <li>Hilmar offers to look into the mechanism that SPI is using, and whether we can take advantage of that in some way. <ul> <li>Peter moves to proceed in this way, first investigating the SPI mechanism and what it would take for us to deploy that. Motion approved with unanimous consent.</li> </ul> </li> </ul> <p><strong>iii. Asset transfer to SPI.</strong></p> <ul> <li>Hilmar recaps the need for us to transfer all of our assets to SPI, now that there is no OBF incorporation anymore that could hold those assets in ownership. Instead, SPI will be holding them in trust for us.</li> <li>With Chris D. absent, we can&rsquo;t discuss enumerating all assets that we have, or how to transfer each of them. Assets that we are aware of right now include our financial reserves in the bank account, and our member projects&rsquo; domain names.</li> <li>For this year (2012), it will still be us who is invoicing Google for the mentoring organizartion payment and the mentor summit expenses, because at the time our SPI association became effective, Chris D had already requested, and received, a PO from Google. Chris D has submitted the invoice last week.</li> <li>We are holding off on the asset transfer until we receive payment from Google so we don&rsquo;t have to do this piecemeal.</li> <li>With Chris D absent, it&rsquo;s unclear who is paying right now for the AWS machines we fired up recently. Assuming that for now this is coming out of Chris D&rsquo;s credit card, O|B|F will need to reimburse him, either before (from O|B|F) or after asset transfer to SPI (from SPI).</li> </ul> <p><strong>iv. BOSC 2013</strong></p> <ul> <li>Nomi has sent SIG application for BOSC to the ISMB&rsquo;s SIG Committee. Approval is pending, but since we have a stroing track record of turn-out and correspondingly generating surplus, we don&rsquo;t expect any negative surprises.</li> <li>Got a few new people on the committee, including Jeremy Goecks (Galaxy), and have one keynote speaker already confirmed.</li> <li>In 2012, BOSC barely broke even, due at least in part by lower attendance and registration, and we also disbursed a small fraction of the registration revenue as travel awards. <ul> <li>Nomi will not be able to continue serving as BOSC chair in 2014, and we thus will need to recruit a new person who is willing to serve in this role.</li> </ul> </li> </ul> <p><strong>v. Improve and sustain system administration help</strong></p> <ul> <li>System administration for O|B|F&rsquo;s systems rests, and for years has rested, on a very small group of people (essentially Chris D, Jason, Mauricio) who are also very busy. <ul> <li>This is a real bottleneck, and has made it very challenging to keep our systems and software properly upgraded.</li> <li>Because this small group of volunteers has remained essentially the same for many years, our institutional knowledge related to installing, configuring, and deploying our systems is concentrated among this group, and mostly undocumented, making it difficult for others willing to pitch in to quickly identify what needs to be done and how.</li> <li>Attempts to recruit additional help have largely failed over the years, so there has been little incentive to more thoroughly document our SysAdmin procedures and conventions.</li> </ul> </li> <li>We are hosting services for which it is questionable whether us doing so provides real benefits over having them hosted externally by 3rd party providers. <ul> <li>Examples include our Wordpress blog, which could be hosted at Wordpress.com for a nominal annual fee; our wikis, which could be migrated to github.com wikis; and our mailing lists, which could be migrated to Google Groups.</li> </ul> </li> <li>The need for better documentation and for broadening the pool of volunteers is acknowledged by everyone. A recent recruitment drive in the wake of the system corruption and the following move of services to AWS has actually turned up some volunteers who we had not previously been aware of. <ul> <li>The Basecamp site started by Chris D lists the tasks that need doing along with commentary and progress. This could also be used for creating and centralizing sysadmin-related documentation.</li> <li>New volunteers could create and expand documentation based on the questions they find themselves needing to ask in order to do necessary tasks, and the answers they receive.</li> <li>However, the Basecamp site also has a key that allows logging in as root with all permissions, which is not a good starting point for newly recruited volunteer helpers.</li> </ul> </li> <li>The hold-up at this point seems to be to set up individual user accounts on the AWS machine so that new sysadmin volunteers can start with a custom and small set of privileges. <ul> <li>Peter agrees to spearhead this effort, and to keep our recent prospective volunteers in the loop as to what is happening, and when they can expect to take on a task.</li> </ul> </li> <li>It is also not out of the question that O|B|F pays hourly university students who work with or for one of our Board or other members. Chris F and Peter will look into the opportunities for that at their respective home institutions.</li> </ul> <p><strong>Action items from above:</strong></p> <ol> <li>Hilmar to look into the mechanism that SPI is using for maintaining membership roll, and whether we can take advantage of that in some way.</li> <li>Peter to spearhead effort to set up individual user accounts on the AWS machine so that new sysadmin volunteers can start with a custom and small set of privileges.</li> <li>Peter to keep our recent prospective volunteers in the loop as to what is happening, and when they can expect to take on a task.</li> <li>Chris F and Peter to look into the opportunities at their respective home institutions to pay hourly university students who work with or for one of our Board or other members.</li> </ol> <p>Hilmar moves to adjourn the meeting. Meeting adjourned by unanimous consent at 12.46pm EST.</p>https://www.open-bio.org/2012/11/06/obf-board-meeting-13-nov/Tue, 06 Nov 2012 15:58:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/11/06/obf-board-meeting-13-nov/<p>The Open Bioinformatics Foundation (OBF) will be holding a public <a href="https://www.open-bio.org/wiki/Board">Board of Directors</a> meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT).</p> <p>The meeting will be held online or over conference call. We will post details about how to dial in or connect closer to the date ( <a href="https://www.open-bio.org/wiki/Minutes:2012_Nov_ConfCall">here</a>).</p> <p>On the agenda Richard Holland and Chris Fields are running for election to the Board, and some other items primarily up for discussion, including how to keep our membership roll up-to-date and increasing with the least barriers. We will post a more detailed agenda in advance of the meeting ( <a href="https://www.open-bio.org/wiki/Minutes:2012_Nov_ConfCall">here</a>).</p> <p>OBF members should have already received notice of this meeting via the <a href="http://lists.open-bio.org/mailman/listinfo/members">OBF member’s mailing list</a>.</p>https://www.open-bio.org/2012/11/04/server-transition-to-aws/Mon, 05 Nov 2012 01:10:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/11/04/server-transition-to-aws/<p>Our aging server which has run for 5+ years the OBF sites has finally reached end of its lifespan. We are currently migrating sites to AWS volumes and sites for a temporary period while we decide about how to continue to support these services in the future.  There will be some downtime while the all-volunteer OBF admin team makes time to fix this.</p> <p>Nearly all projects use public source code repositories such as github or sourceforge so no problems with access to the code should be limiting. Mailing lists are still using the old server but will be moved to the AWS site in the next few days and we are working to have little downtime for the lists.  Mediawiki sites are moving in stages and so far Bioperl, Biopython, and the OBF wikis have been migrated.  This news site has also been migrated to AWS and this is the 1st post from it (will it work!?)</p>https://www.open-bio.org/2012/10/12/obf-now-spi-associated/Fri, 12 Oct 2012 19:01:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/10/12/obf-now-spi-associated/<p>I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a <a href="http://www.spi-inc.org">Software in the Public Interest (SPI)</a> associated project, rather than its own not-for-profit incorporation.</p> <p>An electronic vote of O|B|F members on whether or not to provisionally approve the invitation from SPI closed yesterday at 19:00 UTC. We had a participation of 39 out of 105 eligible, or 37%, which is far above the quorum of 10%. The tally is 38 for provisionally accepting and 1 against. The tally can be seen (and audited) here: <a href="https://vote.heliosvoting.org/helios/e/OBFjoiningSPI">https://vote.heliosvoting.org/helios/e/OBFjoiningSPI</a></p> <p>The SPI Board vote on resolution <a href="http://www.spi-inc.org/meetings/agendas/2012/2012-10-11/">2012-09-28.jb.1</a> (&ldquo;Open Bioinformatics Foundation as associated project&rdquo;) resulted in 8 yes, 0 no, 0 abstain. Given the result of our election, I accepted the invitation right away.</p> <p>Thanks to everyone who voted. On behalf of the Board, I am thrilled about the turnout!</p> <p>This terminates O|B|F&rsquo;s status as its own corporation, which over the years has been more trouble than gain. As an SPI-associated project, we can now accept donations that are 501(c)3 tax-exempt in the US, aside from other <a href="http://www.spi-inc.org/projects/services/">benefits</a>. In the coming weeks and months we will be articulating what kind of objectives, platforms, and activities we can or should pursue, given our new status. I&rsquo;ll communicate separately about that once it gets off the ground.</p> <p>Finally, please join me in thanking Josh Berkus (SPI &amp; PostgreSQL) for shepherding our joining SPI all the way through. And please also join me in saying hi to the SPI community - as I have done earlier I&rsquo;d like to encourage everyone to consider joining the SPI as well. It&rsquo;s a friendly community, and I like to think we can enrich it.</p> <p>This is a historic day for our organization. Have a drink tonight :-)</p> <p>Cheers,</p> <p>-hilmar</p> <p>Note: This post is based on an email sent yesterday to the <a href="http://lists.open-bio.org/mailman/listinfo/members">OBF member&rsquo;s mailing list</a>.</p>https://www.open-bio.org/2012/09/11/minutes2012-sep-confcall/Tue, 11 Sep 2012 05:37:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/09/11/minutes2012-sep-confcall/<h3 id="agenda">Agenda</h3> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2011_Dec_ConfCall">2011 December BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>Approval of <a href="https://github.com/OBF/obf-docs/pull/8">changes to O|B|F Bylaws</a></li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p><strong>Venue:</strong> held by WebEx conference with audio bridge through phone (donated by BioTeam), scheduled for Sep 11, 2012, 11.30am EDT (15:30 UTC)</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Jason Stajich, Peter Cock</li> <li>Guests: Scott Markel</li> </ul> <p><strong>Minutes:</strong></p> <p>Hilmar called meeting to order at 11:38am EDT.</p> <h4 id="old-business">Old business:</h4> <ul> <li>Hilmar moves to approve <a href="https://www.open-bio.org/wiki/Minutes:2011_Dec_ConfCall">Dec 11 meeting minutes</a>. Motion approved with unanimous consent.</li> </ul> <h4 id="new-business">New business:</h4> <p>i. Approval of <a href="https://github.com/OBF/obf-docs/pull/8">changes to O|B|F Bylaws</a>.</p> <ul> <li>This is the first change of the O|B|F Bylaws since their initial enactment in 2004.</li> <li>Aside from from cosmetic corrections and removal of stipulations that have since expired, they address important changes necessary to reflect the termination of our own incorporation status with our impending associated project status with the <a href="http://www.spi-inc.org/">SPI</a>.</li> <li>Hilmar asks whether there are any further questions or concerns that should be discussed prior to proceeding to vote on approving the changes. <ul> <li>Unfortunately, Github was experiencing major technical problems at the time of the Board meeting, and so the changes could not be inspected at this moment. However, they have been produced with active participation of and agreement of most Board members.</li> <li>Chris D., Nomi, and Peter endorse the changes, and have participated in creating them.</li> </ul> </li> <li>Hilmar moves to proceed to vote on approving the changes. Motion accepted with unanimous consent. <ul> <li>The vote was conducted as electronic ballot.</li> <li>Result: 5 out of 5 votes &ldquo;For&rdquo; approving the changes.</li> <li>The changes to the bylaws are therefore unanimously approved, and become effective immediately.</li> </ul> </li> <li>Hilmar informs the Board that the SPI will discuss the OBF application for SPI-associated project status at the next SPI Board meeting, scheduled for Sep 13 at 20:00 UTC. The meeting is held on IRC and public, and Hilmar encourages everyone on the Board to join the meeting.</li> <li>Hilmar also relates to the Board one concern expressed by Jimmy Kaplowitz of the SPI Board about the member liability shield in O|B|F Bylaws Article I, Item 6. Kaplowitz suggests that SPI&rsquo;s liability shield may not offer this protection for liabilities that the OBF incurs when acting as OBF rather than as an SPI agent. <ul> <li>This may need further consideration and discussion by legal counsel, one of the services that SPI has access to.</li> <li>It is not considered a hold-up, neither on the SPI side nor on the OBF side.</li> </ul> </li> </ul> <p>Hilmar moves to adjourn the meeting. Motion accepted with unanimous consent. Meeting adjourns at 11:54am EDT.</p>https://www.open-bio.org/2012/08/21/bioruby-1-4-3-released/Tue, 21 Aug 2012 16:47:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/08/21/bioruby-1-4-3-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/">BioRuby</a> 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius.</p> <p>Here is a brief summary of changes.</p> <ul> <li>Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element.</li> <li>Many failures and errors running on JRuby and Rubinius are resolved.</li> <li>Strange behavior related with “circular require” is fixed.</li> <li>Fixed: Genomenet remote BLAST does not work.</li> <li>Fixed: Bio::NucleicAcid.to_re(“s”) typo.</li> <li>Fixed: Bio::EMBL#os raises RuntimeError.</li> <li>Fixed: bin/bioruby: Failed to save object with error message &ldquo;can’t convert Symbol into String&rdquo; on Ruby 1.9.</li> </ul> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.4.3/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.4.3/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.3.tar.gz">http://bioruby.org/archive/bioruby-1.4.3.tar.gz</a></p> <p>Gem file is also available at: <a href="http://bioruby.org/archive/gems/bio-1.4.3.gem">http://bioruby.org/archive/gems/bio-1.4.3.gem</a></p> <p>We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:</p> <p>% gem search &ndash;remote bio</p> <p>and find “bio (1.4.3)” in the list. Then,</p> <p>% sudo gem install bio</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2012/07/30/travis-ci-for-testing/Mon, 30 Jul 2012 13:24:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/07/30/travis-ci-for-testing/<p>Earlier this year <a href="http://bioruby.org">BioRuby</a> and then <a href="http://biopython.org">Biopython</a> and <a href="http://bioperl.org">BioPerl</a> started using <a href="http://travis-ci.org">Travis-CI.org</a>, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their <a href="http://github.com">GitHub</a> repositories are updated:</p> <ul> <li><a href="http://travis-ci.org/bioruby/bioruby/"><img src="https://secure.travis-ci.org/bioruby/bioruby.png?branch=master" alt="BioRuby on Travis-CI.org"></a><a href="http://travis-ci.org/bioruby/bioruby/">BioRuby</a></li> <li><a href="http://travis-ci.org/biopython/biopython/"><img src="https://secure.travis-ci.org/biopython/biopython.png?branch=master" alt="Biopython on Travis-CI.org"></a><a href="http://travis-ci.org/biopython/biopython/">Biopython</a></li> <li><a href="http://travis-ci.org/bioperl/bioperl-live/"><img src="https://secure.travis-ci.org/bioperl/bioperl-live.png?branch=master" alt="BioPerl on Travis-CI.org"></a><a href="http://travis-ci.org/bioperl/bioperl-live/">BioPerl</a></li> </ul> <p>The BioRuby team are also using Travis-CI for automated testing of their new &lsquo;plugin&rsquo; ecosystem, BioRuby Gems, or <a href="http://www.biogems.info/">BioGems</a>.</p> <p>Travis-CI gives us continuous testing, but for the moment only covers <a href="http://about.travis-ci.org/docs/user/ci-environment/">one operating system</a> (currently 32 bit Ubuntu Linux using Virtual Machines). This automated testing is therefore complementary to our existing <a href="http://testing.open-bio.org/">OBF BuildBot server</a> which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.</p> <p>However, Travis-CI are working on a new feature - <a href="http://about.travis-ci.org/blog/announcing-pull-request-support/">automatic testing of pull requests</a>, currently only available on a donation basis - which the OBF was happy to support.</p> <p>What this means is that when a contributor has some code ready for integration, they can issue a <a href="https://help.github.com/articles/using-pull-requests/">GitHub pull request</a>, and then Travis-CI will automatically run the unit tests with those proposed changes. This is something that currently the core-developers would normally do manually as part of evaluating proposed changes, so having this happen automatically should be a big help.</p> <p>We&rsquo;re excited about making more use of Travis-CI for other <a href="https://www.open-bio.org/wiki/Projects">OBF projects</a>. Thus far we&rsquo;ve been really impressed with Travis-CI.</p>https://www.open-bio.org/2012/06/25/biopython-1-60-released/Mon, 25 Jun 2012 18:17:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/06/25/biopython-1-60-released/<p>Source distributions and Windows installers for <strong>Biopython 1.60</strong> are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <h3 id="platformsdeployment">Platforms/Deployment</h3> <p>We currently support Python 2.5, 2.6 and 2.7 and also test under <a href="http://www.jython.org/">Jython</a> 2.5 and <a href="http://pypy.org/">PyPy</a> 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported.</p> <p>Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy). We are now encouraging early adopters to help beta testing on these platforms, and have included a &lsquo;beta&rsquo; installer for Python 3.2 under 32-bit Windows.</p> <h3 id="features">Features</h3> <p>New module <code>Bio.bgzf</code> supports reading and writing BGZF files (Blocked GNU Zip Format), a variant of GZIP with efficient random access, most commonly used as part of the <a href="http://samtools.sourceforge.net/">BAM file format</a> and in <a href="http://samtools.sourceforge.net/tabix.shtml">tabix</a>. This uses Python&rsquo;s <code>zlib</code> library internally, and provides a simple interface like Python&rsquo;s gzip library. Using this the <code>Bio.SeqIO</code> indexing functions now support BGZF compressed sequence files. See this blog post for <a href="http://custom-essay-service-help.co.uk/">more</a> background on <a href="http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html">BGZF and SeqIO</a>.</p> <p>The GenBank/EMBL parser will now give a warning on unrecognized feature locations and continue parsing (leaving the feature&rsquo;s location as None). Previously it would abort with an exception, which was often unhelpful.</p> <p>The <code>Bio.PDB.MMCIFParser</code> is now compiled by default (but is still not available under Jython, PyPy or Python 3).</p> <p>The SFF parser in <code>Bio.SeqIO</code> now decodes Roche 454 &lsquo;universal accession number&rsquo; 14 character read names, which encode the timestamp of the run, the region the read came from, and the location of the well.</p> <p>In the Phylo module, the &ldquo;draw&rdquo; function for plotting tree objects has become much more flexible, with improved support for <a href="http://matplotlib.sourceforge.net/">matplotlib</a> conventions and new parameters for specifying branch and taxon labels. Writing in the <a href="http://www.phyloxml.org/">PhyloXML</a> format has been updated to more closely match the output of other programs. A wrapper for the program <a href="http://sco.h-its.org/exelixis/software.html">RAxML</a> has been added under <code>Bio.Phylo.Applications</code>, alongside the existing wrapper for PhyML.</p> <p>Additionally there have been other minor bug fixes and more unit tests.</p> <h3 id="contributors">Contributors</h3> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Brandon Invergo</li> <li>Eric Talevich</li> <li>Jeff Hussmann (first contribution)</li> <li>John Comeau (first contribution)</li> <li>Kamil Slowikowski (first contribution)</li> <li>Kevin Jacobs</li> <li>Lenna Peterson (first contribution)</li> <li>Matt Fenwick (first contribution)</li> <li>Peter Cock</li> <li>Paul T. Bathen</li> <li>Wibowo Arindrarto</li> </ul>https://www.open-bio.org/2012/05/23/biojava-3-0-4-released/Wed, 23 May 2012 16:18:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/05/23/biojava-3-0-4-released/<p>BioJava 3.0.4 has been released and is available from <a href="http://www.biojava.org/wiki/BioJava:Download">http://www.biojava.org/wiki/BioJava:Download</a> as well as from the</p> <p>BioJava maven repository at <a href="http://www.biojava.org/download/maven/">http://www.biojava.org/download/maven/</a> .</p> <p>- This is mainly a bug fix release addressing issues with the protein</p> <p>structure and disorder modules</p> <p>- One new feature: SCOP data can now be accessed from either the <a href="http://scop.mrc-lmb.cam.ac.uk/">original SCOP</a> site in the UK (v. 1.75) or <a href="http://scop.berkeley.edu/">from Berkeley</a> (v. 1.75A) .</p>https://www.open-bio.org/2012/04/24/students-selected-for-gsoc/Tue, 24 Apr 2012 09:08:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/04/24/students-selected-for-gsoc/<p>Hello all,</p> <p>I&rsquo;m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 5 very capable students to work on OBF projects this summer as part of the <a href="http://code.google.com/soc/">Google Summer of Code (GSoC) program</a>.</p> <p>The accepted students, their projects, and their mentors (in alphabetical order):</p> <ul> <li><strong><a href="http://bow.web.id/blog/tag/gsoc/">Wibowo Arindrarto</a></strong>: <em>SearchIO Implementation in Biopython</em> mentored by Peter Cock</li> <li><strong><a href="http://arklenna.tumblr.com/tagged/gsoc2012">Lenna Peterson</a></strong>: <em>Diff My DNA: Development of a Genomic Variant Toolkit for Biopython</em> mentored by Brad Chapman, Reece Hart, James Casbon</li> <li><strong><a href="http://blog.mpthecoder.com/tagged/gsoc">Marjan Povolni</a></strong>: <em>The worlds fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby</em> mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal</li> <li><strong><a href="http://lomereiter.wordpress.com/tag/gsoc/">Artem Tarasov</a></strong>: <em>Fast parallelized GFF3/GTF parser in C++, with Ruby FFI bindings</em> mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal</li> <li><strong><a href="http://csw.github.com/bioruby-maf/">Clayton Wheeler</a></strong>: <em>Multiple Alignment Format parser for BioRuby</em> mentored by Francesco Strozzi and Raoul Bonnal</li> </ul> <p>As in every year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF&rsquo;s open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.</p> <p>For the accepted students: congratulations! You have risen to the top of a very competitive application process. Now it&rsquo;s time to &ldquo;put your money where your mouth is&rdquo;, as the saying goes. Let&rsquo;s get out there and write some great code this summer!</p> <p>Best regards,</p> <p>Robert Buels OBF GSoC 2012 Organization Administrator</p>https://www.open-bio.org/2012/03/25/obf-summer-of-code-2012/Sun, 25 Mar 2012 21:27:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/25/obf-summer-of-code-2012/<p>Applications due 19:00 UTC, April 6, 2012. <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">/wiki/Google_Summer_of_Code</a></p> <p>The Open Bioinformatics Foundation (OBF) Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the <a href="http://code.google.com/soc/">Google Summer of Code (GSoC)</a>.</p> <p>Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.</p> <p>The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">initial project ideas are listed on the website</a>. These range from sequence search I/O in <a href="http://biopython.org/wiki/Google_Summer_of_Code">Biopython</a> to lightweight sequence objects and lazy parsing in <a href="http://bioperl.org/wiki/Google_Summer_of_Code">BioPerl</a>, a next-generation <a href="http://www.bioruby.org/wiki/Google_Summer_of_Code">BioRuby</a> interface to Ensembl to developing cloud-optimized versions of <a href="http://biojava.org/wiki/Google_Summer_of_Code">BioJava</a> modules. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also particularly welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves.</p> <p><strong>TO APPLY:</strong> Apply online at the Google Summer of Code website (<a href="http://socghop.appspot.com/)">http://socghop.appspot.com/)</a>, where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 26 through Friday, April 6th, 2012.</p> <p><strong>INQUIRIES:</strong></p> <p>We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details.</p> <p>2012 OBF Summer of Code: <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">/wiki/Google_Summer_of_Code</a></p> <p>Google Summer of Code FAQ: <a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs">http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs</a></p> <p>Rob Buels OBF GSoC 2012 Admin</p>https://www.open-bio.org/2012/03/16/obf-accepted-for-gsoc-2012/Fri, 16 Mar 2012 21:53:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/16/obf-accepted-for-gsoc-2012/<p>Google announced today that the <a href="http://open-bio.org/">Open Bioinformatics Foundation (OBF)</a> has been accepted as a mentoring organization for <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2012">Google Summer of Code 2012</a>!</p> <p><a href="http://code.google.com/soc/"><img src="http://code.google.com/images/GSoC2012_300x200.png" alt="GSoC 2012 Logo"></a><a href="http://code.google.com/soc/">Google Summer of Code (GSoC)</a> is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the <a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs">GSoC 2012 FAQ</a>.</p> <p>Student applications are due April 6, 2012 at 19:00 UTC. Students who are interested in participating should look at the <a href="http://open-bio.org/wiki/Google_Summer_of_Code">OBF&rsquo;s GSoC page</a>, which lists project ideas, and whom to contact about applying.</p> <p>For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project&rsquo;s GSoC wiki page.</p> <p>Thanks to all who helped make OBF&rsquo;s application to GSoC a success, and let&rsquo;s have a great, productive summer of code!</p> <p>Rob Buels OBF GSoC 2012 Administrator</p>https://www.open-bio.org/2012/03/05/call-for-abstracts-for-bosc-2012/Mon, 05 Mar 2012 19:54:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/05/call-for-abstracts-for-bosc-2012/<p>Call for Abstracts for the 13th Annual <a href="https://www.open-bio.org/wiki/BOSC_2012">Bioinformatics Open Source Conference (BOSC 2012)</a>, a Special Interest Group (SIG) of <a href="http://www.iscb.org/ismb2012">ISMB 2012</a>.</p> <p>Dates: July 13-14, 2012 Location: Long Beach, California Web site: <a href="https://www.open-bio.org/wiki/BOSC_2012">/wiki/BOSC_2012</a> Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> BOSC announcements mailing list: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a></p> <p>Important Dates:</p> <ul> <li>April 13, 2012: Deadline for submitting abstracts</li> <li>May 7, 2012: Notification of accepted talk abstracts emailed to authors</li> <li>July 11-12, 2012: Codefest 2012 programming session</li> <li>July 13-14, 2012: <a href="https://www.open-bio.org/wiki/BOSC_2012">BOSC 2012</a></li> <li>July 15-17, 2012: <a href="http://www.iscb.org/ismb2012">ISMB 2012</a></li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>We invite you to submit one-page abstracts for talks and posters. This year&rsquo;s session topics are:</p> <ul> <li>Cloud and Parallel Computing</li> <li>Linked Data</li> <li>Genome-scale Data Management</li> <li>Data Visualization and Imaging</li> <li>Translational Bioinformatics</li> <li>Software Interoperability (possibly a joint session with <a href="http://www.broadinstitute.org/software/bsi-sig/">BSI-SIG, the Bioinformatics Software Interoperability SIG</a>)</li> <li>Bioinformatics Open Source Project Updates</li> <li>Interfacing with Industry (panel)</li> </ul> <p>Thanks to generous sponsorship from <a href="http://eaglegenomics.com/">Eagle Genomics</a> and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards. Each winner will be awarded $250 to defray the costs of travel to BOSC 2012.</p> <p>For instructions on submitting your abstract, please visit <a href="https://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts">/wiki/BOSC_2012#Submitting_Abstracts</a></p> <p>BOSC 2012 Organizing Committee: Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice</p>https://www.open-bio.org/2012/03/02/cross-links-in-genomediagram/Fri, 02 Mar 2012 16:56:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/02/cross-links-in-genomediagram/<p>I&rsquo;ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in <a href="http://news.open-bio.org/news/2012/02/biopython-1-59-released/">Biopython 1.59</a>. You can now control the start and end points of individual tracks, and you can add cross-links between regions of different tracks, as shown here:</p> <p><a href="https://www.open-bio.org/wp-content/uploads/2012/03/three_track_cl2.png"><img src="https://news.obf.io/wp-content/uploads/2012/03/three_track_cl2-1024x724.png" alt="GenomeDiagram with cross-links between tracks"></a></p> <p>This example attempts a simplified reproduction of Figure 6 in <a href="http://dx.doi.org/10.1128/%E2%80%8BJB.184.21.6026-6036.2002">Proux et al. (2002)</a>, and shows three related phage genomes one above the other. Different classes of genes have been given different colors, while the strength of the red shaded cross-links indicates the percentage identity of the linked genes. Note there are some minor differences in the GenBank annotation we&rsquo;ve used and the genes shown in the original figure.</p> <p>Note while this example is in the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Tutorial HTML</a> and <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a> online, it was not in the zip/tarball for Biopython 1.59, and nor was the <a href="https://github.com/biopython/biopython/blob/master/Doc/examples/Proux_et_al_2002_Figure_6.py">Proux_et_al_2002_Figure_6.py</a> script. It will be in future releases.</p> <p>Another motivating use case for this functionality was to produce vector images of whole genome alignments in the style of the <a href="http://www.sanger.ac.uk/resources/software/act/">Artemis Comparison Tool (ACT)</a> or <a href="http://asap.ahabs.wisc.edu/mauve/">Mauve</a>. We&rsquo;ve got a poster printer in the building just crying out to be used for showing whole genome comparison of a dozen bacteria strains!</p>https://www.open-bio.org/2012/02/24/biopython-1-59-released/Fri, 24 Feb 2012 15:09:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/02/24/biopython-1-59-released/<p>Source distributions and Windows installers for <strong>Biopython 1.59</strong> are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <h3 id="platformsdeployment">Platforms/Deployment</h3> <p>We currently support <a href="http://python.org">Python</a> 2.5, 2.6 and 2.7 and also test under <a href="http://jython.org">Jython</a> 2.5 (which does not cover NumPy). Please note that this release will not work on Python 2.4</p> <p>Most functionality is also working under Python 3.1 and 3.2 (including modules using <a href="http://numpy.scipy.org/">NumPy</a>), and under <a href="http://pypy.org/">PyPy</a> (excluding our NumPy dependencies). We are now encouraging early adopters to help beta testing on these platforms.</p> <p>The installation setup.py now supports &lsquo;install_requires&rsquo; when setuptools is installed. This avoids the manual dialog when installing Biopython via easy_install or pip and numpy is not installed. It also allows user libraries that require Biopython to include it in their install_requires and get automatic installation of dependencies.</p> <h3 id="features">Features</h3> <p>New module <code>Bio.TogoWS</code> offers a wrapper for the <a href="http://togows.dbcls.jp/site/en/rest.html">TogoWS REST API</a>, a web service based in Japan offering access to KEGG, DDBJ, PDBj, CBRC plus access to some NCBI and EBI resources including PubMed, GenBank and UniProt. This is much easier to use than the NCBI Entrez API, but should be especially useful for Biopython users based in Asia.</p> <p>The <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html">NCBI Entrez Fetch</a> function <code>Bio.Entrez.efetch</code> has been updated to handle the NCBI&rsquo;s stricter handling of multiple ID arguments in EFetch 2.0 (released February 2012, see this <a href="http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000086.html">announcement</a>), however the NCBI have also changed the <code>retmode</code> default argument so <em>you</em> may need to make this explicit. e.g. add <code>retmode=&quot;text&quot;</code> to your EFetch calls (see this <a href="http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000085.html">announcement</a>).</p> <p>The position objects used in <code>Bio.SeqFeature</code> now act almost like integers, making dealing with fuzzy locations in EMBL/GenBank files much easier. Also the <code>SeqFeature</code>&rsquo;s strand and any database reference are now properties of the <code>FeatureLocation</code> object (a more logical placement), with proxy methods for backwards compatibility.</p> <p><code>Bio.Graphics.BasicChromosome</code> has been extended to allow simple sub-features to be drawn on chromosome segments, suitable to show the position of genes, SNPs or other loci.</p> <p><code>Bio.Graphics.GenomeDiagram</code> has been extended to allow <a href="http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/">cross-links between tracks</a>, and track specific start/end positions for showing regions. This can be used to imitate the output from the <a href="http://www.sanger.ac.uk/resources/software/act/">Artemis Comparison Tool (ACT)</a>. Also, a new attribute circle_core makes it easier to have an empty space in the middle of a circular diagram (see tutorial).</p> <p>Note <code>Bio.Graphics</code> requires the <a href="http://www.reportlab.com/software/opensource/">ReportLab library</a>.</p> <p><code>Bio.Align.Applications</code> now includes a wrapper for command line tool <a href="http://www.clustal.org/omega/">Clustal Omega</a> for protein multiple sequence alignment.</p> <p><code>Bio.AlignIO</code> now supports sequential <a href="http://evolution.genetics.washington.edu/phylip.html">PHYLIP</a> files (as well as interlaced PHYLIP files) as a separate format variant.</p> <p>Additionally there have been other minor bug fixes and more unit tests, and updates to the documentation including the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <h3 id="contributors">Contributors</h3> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Andreas Wilm (first contribution)</li> <li>Alessio Papini (first contribution)</li> <li>Brad Chapman</li> <li>Brandon Invergo</li> <li>Connor McCoy</li> <li>Eric Talevich</li> <li>João Rodrigues</li> <li>Konrad Förstner (first contribution)</li> <li>Michiel de Hoon</li> <li>Matej Repič (first contribution)</li> <li>Leighton Pritchard</li> <li>Peter Cock</li> </ul>https://www.open-bio.org/2011/12/13/minutes2011-dec-confcall/Tue, 13 Dec 2011 05:36:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/12/13/minutes2011-dec-confcall/<p>The meeting was held conference call.</p> <h3 id="agenda">Agenda</h3> <ol> <li> <p>Old business</p> <ul> <li> <p><a href="https://www.open-bio.org/wiki/Minutes:2010_Financial_report">2010 Financial Report</a></p> </li> <li> <p><a href="https://www.open-bio.org/wiki/Minutes:2011_ConfCall">2011 BoD meeting minutes</a></p> </li> </ul> </li> <li> <p>New business</p> <ol> <li>Treasurer&rsquo;s 2011 report: <a href="https://www.open-bio.org/wiki/File:2011-OBF-Treasurers-Report_v1.pdf">File:2011-OBF-Treasurers-Report v1.pdf</a> (Chris Dagdigian)</li> <li>Elections: <ul> <li>Hilmar Lapp, running for office of President</li> <li>Nomi Harris, running for office of Parliamentarian</li> <li>Peter Cock, running for BoD member-at-large</li> </ul> </li> <li>Alternative procedure(s) for elections (Jason Stajich)</li> </ol> </li> </ol> <h3 id="minutes">Minutes</h3> <p><strong>Venue:</strong> held by conference call, scheduled for Dec 13, 11am EST (16:00 UTC) (originally scheduled for 12pm EST, by mistake started 1 hour earlier)</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Hilmar Lapp, Jason Stajich, Chris Dagdigian (ChrisD), Nomi Harris</li> <li>Guests: Scott Markel (on behalf of the nominating committee), Peter Cock (running for election onto the Board), Peter Rice</li> </ul> <p><strong>Minutes:</strong></p> <p>Hilmar calls meeting to order at 11.10am.</p> <h4 id="approval-of-old-business">Approval of old business:</h4> <ul> <li>The status of one travel award is still missing, and therefore Still can&rsquo;t vote on 2010 report due to missing status on travel awards.</li> <li>2011 BoD meeting minutes from November: ChrisD moves to approve, Jason, Hilmar, and Nomi second. Minutes of the 2011 BoD meeting in Nov approved by animous consent.</li> </ul> <h4 id="new-business">New Business:</h4> <p><strong>i. 2011 Financial Report.</strong></p> <ul> <li>There are items pending or scheduled to clear (such as the Google Summer of Code mentoring and mentor summit travel reimbursement invoice) before the end of the year.</li> <li>However, this may be the case in any calendar year if we hold the BoD meeting before the end of the year. Hence, for the purposes of approval for being current and accurate we set a date of Nov 30, 2011. Hilmar moves to approve the 2011 Financial Report, Jason, Nomi, and ChrisD second. 2011 Financial Report approved by unanimous consent.</li> <li>ChrisD paid the 2011 BOSC Travel Awards out of his own PayPal account (to accommodate the recipients requests), and asks for approval to reimburse himself from the O|B|F bank account at the sum of $775.15. Hilmar moves to approve the request, Jason and Nomi second. Approved by unanimous consent. ChrisD will issue a paper check to himself using the Bank of America Billpay feature.</li> <li>ChrisD reports that we are not in good standing anymore with the state of Delaware where we are incorporated as an organization. To remain in good standing, we would need an annual filing (with a small filing fee). This normally requires a business agent, which are, however, easy to find in Delaware, even online. <ul> <li>This prompts the question whether going forward the best solution is to retain our Delaware incorporation and repair our standing, or instead to start incorporating fresh in another state. There are various considerations in terms of our organizational goals and mission that should be discussed and thought through further before an informed decision can be made, and therefore this topic is postponed for 2012.</li> </ul> </li> </ul> <p><strong>ii. Elections to the Board:</strong> Peter Cock (running for Director at-large), Hilmar Lapp (running for President), Nomi Harris (running for Parliamentarian).</p> <ul> <li>On behalf of the nominating committee, Scott Markel conveys feedback from two O|B|F members expressing their unanimous support for all three candidates.</li> <li>Hilmar nominates Peter Cock for election to the Board of Directors. Aside from having been a core-developer of the Biopython project for several years, he has also been very active on other O|B|F member projects, as well as taken initiative and leadership on various questions and issues that cut across projects. <ul> <li>Election held by secret electronic ballot. Results: 4 of 4 votes for, 0 of 4 votes agains, 0 of 4 votes abstain. Peter Cock is elected to the O|B|F Board of Directors. (For the following elections, Peter cast a ballot as BoD member, too.)</li> </ul> </li> <li>Jason Stajich has expressed his desire to step down from President since the 2010 BoD meeting. Hilmar Lapp is running to replace him, with the goal to get the organization and its procedures into a shape that others would be attracted to step up to this leadership role in 1 or 2 years. Jason will continue to serve as Director At-Large for now. <ul> <li>Election held by secret electronic ballot. Results: 4 of 5 votes for, 0 of 5 votes against, and 1 of 5 votes abstain. Hilmar Lapp is elected President of the Board of Directors of the O|B|F. Jason Stajich is now Director at-large.</li> </ul> </li> <li>Nomi Harris runs for the now-vacant Parliamentarian office on the Board. Her goal for this office is in particular to recruit new members to O|B|F as well as to the Board, and to increase community and membership engagement. <ul> <li>Election held by secret electronic ballot. Results: 5 of 5 votes for, 0 of 5 votes agains, 0 of 5 votes abstain. Nomi Harris is elected Parliamentarian of the Board of Directors of the O|B|F.</li> </ul> </li> </ul> <p><strong>iii. Alternative procedure for elections.</strong></p> <ul> <li>Jason has suggested that certain matters could be amenable to and benefit from voting or deciding outside of public BoD conference call meetings. <ul> <li>This would allow us to handle matters of a mostly procedural nature, and matters that have already been discussed but for which voting had to be delayed due to procedural or administrative reasons, in a much more expedient and efficient way.</li> <li>Jason cited experience from other societies in which he serves where this is used successfully. Hilmar could not find any evidence in the O|B|F Bylaws that suggests or requires that all decisions and votes be in the context of a BoD meeting.</li> <li>Nonetheless, we should not (ab)use this to have even fewer BoD conference calls, as these happen rather infrequently already anyway.</li> <li>The BoD is unanimously in favor of pursuing this further. As a next step, Hilmar will draft a procedure.</li> </ul> </li> </ul> <p><strong>iv. Other items.</strong></p> <ul> <li>Nomi reports that both keynote speakers for BOSC are now committed (Suzi Lewis and Jonathan Eisen). The BOSC committee decided not to have a third keynote.</li> </ul> <p>Hilmar moves to adjourn. Jason, Nomi, ChrisD, and Peter second. Meeting adjourned at 12.04pm with unanimous consent.</p> <p><strong>Action Items:</strong></p> <ul> <li>ChrisD to determine missing or pending status of 2010 BOSC travel awards so that the 2010 financial report can be approved.</li> <li>Hilmar to draft a procedure for handling suitable matters for voting or decision outside of BoD meetings.</li> </ul>https://www.open-bio.org/2011/11/08/minutes2011-confcall/Tue, 08 Nov 2011 05:33:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/11/08/minutes2011-confcall/<h3 id="agenda">Agenda</h3> <ol> <li> <p>Old business</p> <ul> <li> <p><a href="https://www.open-bio.org/wiki/Minutes:2010_ConfCall">2010 BoD meeting minutes</a></p> </li> <li> <p><a href="https://www.open-bio.org/wiki/Minutes:2010_Financial_report">2010 Financial Report</a></p> </li> </ul> </li> <li> <p>Action items from the 2010 meeting</p> </li> <li> <p>New business</p> <ol> <li>BOSC <ul> <li>BOSC 2011 (Nomi) - held with <a href="http://www.iscb.org/ismbeccb2011">ISMB2011</a> in Vienna, Austria <ul> <li>Money spent/made, attendee number, any other feedback</li> </ul> </li> <li>BOSC 2012 - with <a href="http://www.iscb.org/ismb2012">ISMB 2012</a> in Long Beach, CA <ul> <li>2012 Organizing Committee chair</li> <li>Plans for the conference</li> </ul> </li> </ul> </li> <li>Google Summer of Code <ul> <li>Org admin&rsquo;s summary report (Rob Buels)</li> </ul> </li> <li>Treasurer&rsquo;s 2011 report: <a href="https://www.open-bio.org/wiki/File:2011-OBF-Treasurers-Report_v1.pdf">File:2011-OBF-Treasurers-Report v1.pdf</a> (Chris Dagdigian)</li> <li>BoD membership and succession. <ul> <li>Nominations: Peter Cock</li> <li>Plan to elect new BoD members and rotate officers.</li> </ul> </li> <li>Additional topics proposed by community <ul> <li>How to become an affiliate project? (Alan R Williams)</li> <li>BioSmalltalk as an OBF member project? (Hernán Morales)</li> <li>CloudBiolinux as an OBF member project? (Pjotr Prins, Brad Chapman)</li> <li>OBF Europe and Asia (Steffen Möller), branch organisations for tax free donations from the public or industry. Possibly in conjunction with <a href="http://www.spi-inc.org/">Debian&rsquo;s Software in the Public Interest</a> setup.</li> <li>OBF holding copyright as a community organization using the Apache model for licensing (Jean Peccoud)</li> </ul> </li> </ol> </li> </ol> <h3 id="minutes-from-the-meeting">Minutes from the meeting</h3> <p><strong>Venue:</strong> held by conference call, scheduled for Nov 8, 2011, 11am EST (16:00 UTC).</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Jason Stajich, Chris Dagdigian (until 12pm), Hilmar Lapp, Nomi Harris</li> <li>Guests: Neil Bahroos, Pjotr Prins, Brad Chapman, Alan Williams, Peter Rice, Neil Bahroos, Steffen Möller, Peter Cock (call report shows about 12 people who called in for significant amounts of time).</li> </ul> <p><strong>Minutes:</strong></p> <p>Hilmar calls meeting to order at 11.08am EST.</p> <h4 id="approval-of-old-business">Approval of old business:</h4> <ul> <li>Approval of 2010 BoD meeting minutes. Hilmar moves to approve, Nomi, Jason, and Chris second. 2010 BoD minutes approved by unanimous consent.</li> <li>2010 Financial Report still not ready for approval, because the missing 2010 BOSC travel award still has not been added. Postponed for a second 2011, or the 2012 BoD meeting.</li> </ul> <h4 id="2010-action-items">2010 action items</h4> <ul> <li>Status of 2010 BOSC keynote speaker reimbursements unclear. Hilmar to follow up with Kam.</li> <li>BOSC proceedings: Didn&rsquo;t do a survey but talked to several people. Resolution was that the effort wasn&rsquo;t worth making, and consequently proceedings weren&rsquo;t planned for 2011. Can be revisited for 2012, though.</li> <li>Codefest: Did a brief verbal announcement about what happened at the 2011 BOSC. Should expand this a bit in 2012.</li> <li>Documentation for and status of 2010 BOSC travel fellowships: ChrisD will investigate and follow up with Kam to make sure all 3 awards have been paid and are accounted for in the financial report.</li> <li>Board membership recruitment hasn&rsquo;t been but should be pursued among member projects.</li> <li>Biopython.org domain ownership transfer: in the process of being completed, control being transfered to ChrisD, which is the same as for the other Bio* domain names. Complete for admin and technical contacts, not yet for billing contacts.</li> <li>Hosting services plan: happened in a mostly organic manner on root-l. But our server hardware is very old and can fail any time. We imminently need a plan forward so we can determine whether we migrate to all-cloud or continue to host some services on our own hardware. This is particularly urgent as our web presence is at risk.</li> <li>BOSC 2010 mailing list: turned out not to be necessary.</li> <li>GMOD getting more involved with BOSC: there has been contact with Scott Cain and encouragement to submit an abstract. There needs to be more reaching out to member and affiliated projects to participate in the conference.</li> </ul> <h4 id="bosc-2011">BOSC 2011</h4> <ul> <li>Very well attended: 115 attendees, which marks the best attended BOSC since 2004; also received a record number of abstracts (78), most of which were of pretty high quality. We were able to award talk slots only to 35 submissions.</li> <li>Had a poster session, to which abstracts were admitted that did not get a talk slot. Oral presenters were also given the option to present a poster in addition to their talk, and more than half of them accepted.</li> <li>Preliminary balance from the conference is a surplus is about $6,000. Final balance sheet still due from Stephen Leard. The surplus will be added to our ISMB escrow account, which currently (before the BOSC 2011 balance) stands at about $15,000.</li> <li>The 2011 keynote speakers had a significant fractions of their expenses paid by other sources, which helped with the surplus.</li> <li>Feedback overall very positive, except for some things that we have little control over (such as catering running out of coffee). These were relayed back to ISMB. Feedback on the poster session was quite positive, and we plan to repeat it in 2012. The poster session does not incur any additional expenses, as it is already included in ISMB&rsquo;s SIG package.</li> <li>Program received very good feedback. Some questions arose about people presenting almost the same talk at BOSC and subsequently at ISMB. However, the topics were highly relevant and appropriate for BOSC, so excluding them if they also present at ISMB does not seem a good option. In the future encourage them to choose different emphases for both talks so that they are complementary rather than redundant. Some of the Bio* projects felt ignored. This will be addressed for 2012 by having a track devoted to member project updates, and we will personally approach project representatives and encourage them to present updates at BOSC 2012.</li> <li>Can OBF subsidize representatives from OBF member projects to attend BOSC if they couldn&rsquo;t otherwise afford to come? <ul> <li>This could provide an opportunity to leverage the funds sitting in the otherwise locked up ISCB escrow account for the good of the community.</li> <li>Nonetheless, would need to make sure that the process is well-defined, fair, and makes the best use of the escrow account. Things to consider include: <ul> <li>For subsidizing people, it would be simpler to absorb their registration fee rather than reimburse them for travel expenses.</li> <li>There are other categories of people deserving of or benefitting from support than OBF member project affiliates, including students (we already offer a few student travel fellowships, but there are other students who would like to attend BOSC), BOSC organizing committee members, and &ldquo;invited speakers&rdquo; (in addition to keynote speakers).</li> </ul> </li> </ul> </li> <li>Hilmar moves for the Board to express a vote of gratitude and appreciation for Nomi&rsquo;s service. Jason and ChrisD second, approved by unanimous consent.</li> </ul> <h4 id="bosc-2012">BOSC 2012</h4> <ul> <li>Nomi volunteered to serve again and is the sole chair. (Peter Rice will be changing jobs, but will maintain a supporting role.)</li> <li>Organizing committee will have two new members, Jan Aerts and Chris Fields. Also, 2 (Darin London and Ron Taylor) of the 2011 committee are rotating off due to other obligations, but remain committed to help out with reviewing abstracts.</li> <li>ISMB SIGs have to re-apply every 3 years, which for us was this year. Our application (put together by Nomi) has just been accepted. <ul> <li>One of the recommendations was to interface (or even merge) with the (also accepted) new Software Interoperability SIG (led by Galaxy and GenePattern PIs). If we do this, it needs to happen in a way that doesn&rsquo;t take much talk time away, so we don&rsquo;t further constrain the already very limited time available for awarding slots to submissions.</li> <li>Another point raised in the review comments is that unlike 12 years ago when BOSC started, the value of open source projects is widely recognized today, and this should be considered when thinking about where BOSC should concentrate in the future.</li> </ul> </li> <li>Ongoing questions for the program include whether or not to schedule a 3rd keynote, in an effort to stem attendee attrition in the afternoon of the second day. One keynote speaker (Suzi Lewis) is already confirmed, conversation with a second one to nail down a suitable talk topic are ongoing.</li> <li>We are keeping some of the popular session topics from last year (e.g., Cloud Computing), retiring some, and introducing some new ones, such as Translational Bioinformatics. We will make an effort to solicit talks for these new sessions by contacting researchers in those areas and encouraging them to submit abstracts.</li> <li>Other plans for BOSC 2012 include a session dedicated to affiliated project updates (Bio*, etc.); a panel discussion, tentatively on &ldquo;Interfacing with Industry&rdquo;; an &ldquo;audience favorite&rdquo; talk award; and an explicit time slot for the CodeFest organizers to present a summary.</li> <li>Nomi is asking everyone who has ideas and suggestions to come forward and contact either her or the committee through the BOSC mailing list.</li> <li>Hilmar moves for the Board to give a vote of confidence and appreciation for her service to Nomi. Jason and ChrisD second. Motion approved by unanimous consent.</li> </ul> <h4 id="google-summer-of-code">Google Summer of Code</h4> <ul> <li>Rob Buels, our organization admin for 2011, was not on the call to report.</li> <li>Hilmar (who served as backup admin) reports as a heads-up that we had 6 students, all of whom seem to have been successful in their projects and passed. We also sent two mentors (Andreas Prlic - Biojava, Rob Buels - BioPerl, GMOD) to the Google Summer of Code Mentor Summit, which took place at Google&rsquo;s headquarters in Mountain View, CA, in October.</li> <li>Participation in the program, aside from the main benefits for the students, the participating affiliate projects, and the mentors, yielded a $3,000 payment ($500 per student mentored) from Google to the mentoring organization, i.e., O|B|F. This has been invoiced, and receiving the funds is expected before year end.</li> <li>The mentoring organization payment for our 2010 participation (also $3,000) has been forfeited because we failed to invoice in a timely manner. This is true also for reimbursement for the flight costs of our 2010 Mentor Summit delegates (who were also Andreas and Rob), and hence OBF had to absorb those costs (see financial report).</li> <li>See attached written report from Rob Buels for further details.</li> </ul> <h4 id="additional-community-proposed-topics">Additional community-proposed topics:</h4> <ul> <li>How to become an affiliate project? What is the process one has to go through, and what are the criteria applied? (Alan R Williams) <ul> <li>There hasn&rsquo;t been an official process. Will also depend on what resources are being needed.</li> <li>Historically, (most of) our member projects came first, and then the need for the OBF umbrella organization arose to better run and fund the IT infrastructure for collaborative software development. However, meanwhile most or all of the IT infrastructure can be found at 3rd party service providers, often for free, and at sophisticated and robust levels of quality and service.</li> <li>Our aim isn&rsquo;t to compete with organizations such as Bioinformatics.org where open-source projects can enlist for infrastructure. So what are the specific advantages that being an OBF member or affiliate project would provide that can&rsquo;t be easily had from these other organizations?</li> <li>Most notable advantage would be being part of a community of bioinformatics projects. It&rsquo;s not the listing, but a community in which projects work together, for example in activities such as the Codefest.</li> <li>OBF affiliation could supply the community and a stamp of expectation that the project will stick around. In this sense, some projects don&rsquo;t have critical mass yet to join the OBF.</li> <li>Does it need to be the Board that decides this? Couldn&rsquo;t it be the community instead? Perhaps have a committee established that makes the process reasonably efficient, and among other things votes on applications of projects to join. <ul> <li>Should still have some form of oversight, monitoring, or perhaps final approval by the BoD, though, so that decisions made and their consequences don&rsquo;t overwhelm the means of the OBF.</li> <li>Brad, Peter, Pjotr, and Neil will draft, with community and membership input, a proposal on what this process could look like. Hilmar will for now serve as the Board liaison in this group, and weigh in accordingly.</li> </ul> </li> </ul> </li> <li>CloudBioLinux as an OBF member project? (Pjotr) <ul> <li>Deployment is a difficult part of software lifecycle. Idea is that CloudBioLinux simplifies and standardizes this for all Bio* (or OBF) member projects, and thus works with all of them. OBF can help with preventing duplication and maintaining the community and project ties.</li> <li>Future status as an OBF member project will be subject to the to-be-drafted process (see above).</li> </ul> </li> <li>OBF Europe and Asia (Steffen Möller) <ul> <li>Idea is to create separate, local branches for the OBF organization.</li> <li>One immediate opportunity that this could provide is better ability to raise funds in local currency. Also, acquiring and maintaining tax-exempt status is much cheaper in Germany, and therefore depending on local laws there may be very little reason for why donations can&rsquo;t be tax-deductible.</li> <li>Could also serve as a vehicle to organize local meetings when ISMB (and therefore BOSC) are in the US.</li> <li>Acquiring and maintaining tax-exempt 501(c)3 status in the US is expensive, though. However, as has been discussed at a previous Board meeting, we can accomplish tax-deductible donations to fund most of our expenses through a fiscal sponsorship organization, such as the Software Freedom Conservancy, or Software in the Public Interest. <ul> <li>Such organizations exist, for example, in Europe (Germany, Italy, UK), too, and we could affiliate with different ones to cover different currencies and jurisdictions. Doing so need not require creating local branches.</li> <li>Steffen will gather further information about relevant organizations and contacts in European jurisdictions.</li> </ul> </li> </ul> </li> </ul> <p>Adjourned at 1.03pm. Board elections could not be held as planned due to loss of quorum with ChrisD leaving the call at shortly after 12pm.</p> <h3 id="google-summer-of-code-2011-report-for-obf">Google Summer of Code 2011 Report for OBF</h3> <p>Prepared by Rob Buels, who served as organization administrator for the OBF.</p> <blockquote> <p>We had 6 students this year, the same number as last year. I had hoped we might grow the program somewhat over last year&rsquo;s numbers, but the number and quality of applications turned out approximately the same. However, the solicitations for student applications went out quite a bit later this year than last year. I think us having a similar applicant pool despite the late solicitations may point to there being a latent potential to grow the program next year, if I make sure to be more on top of the schedule, which I intend to do. As for this year&rsquo;s 6 students, they were quite a good group. Pasted from the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">OBF GSoC page</a>, the 6 student projects were:</p> <p>BioPython</p> </blockquote> <blockquote> <p>Justinas Vygintas Daugmaudis, Michele dos Santos da Silva (2 students), mentored by Thomas Hamelryck and Eric Talevich Mocapy++Biopython: from data to probabilistic models of biomolecules BioPython Integration and Mocapy++ Plugin System</p> <p>BioJava Chuan Hock Koh, mentored by Peter Troshin, Andreas Prlic, and Jay Vyas: Amino Acid Physico-Chemical Properties Calculation</p> <p>BioRuby Michał Koziarski, mentored by Raoul J.P. Bonnal and Francesco Strozzi: Represent bio-objects and related information with images</p> <p>BioPerl Sheena Scroggins, mentored by Robert Buels and Chris Fields: Major BioPerl reorganization</p> <p>BioPython Mikael Eric Trellet, mentored by João Rodrigues and Eric Talevich: Interface analysis module for BioPython</p> <p>Happily, all of the students accomplished their project objectives and were eligible for full stipend payments from Google. This is a bit better than last year, when we had one student who failed to complete the program.</p> <p>I myself only have direct experience with the BioPerl project, which I also mentored, but all of the projects turned their evaluations in on time, and all of them also satisfactorily maintained frequently-updated progress report pages (which are <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">linked from the OBF wiki</a>).</p> <p>Based on conversations I had with other organization administrators at the Google Summer of Code Mentor Summit (a GSoC unconference held a couple of weeks ago at the Google headquarters in California), the OBF is very fortunate in having a very GSoC-ready pool of project members on which to draw. That is, since most participants in OBF projects come from academia, they are already quite familiar with the process of mentoring students to complete projects, and generally need relatively little prompting to keep their students on track.This contrasts with the stories I heard from other organization administrators at the mentor summit: apparently, many other organizations have considerably more difficulties with mentors and students failing to complete projects, turning evaluations in late or failing to turn them in at all, and so forth. This makes me feel quite optimistic for the continued success of the GSoC students mentored by OBF organizations.</p> </blockquote>https://www.open-bio.org/2011/10/28/obf-annual-meeting-2011/Fri, 28 Oct 2011 20:54:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/10/28/obf-annual-meeting-2011/<p>The annual Board of Directors Meeting of the Open Bioinformatics Foundation will take place on November 8, 2011. As in previous years, it will be held by conference call, estimated to be about 2 hrs long.</p> <p>The meeting will on Tuesday 8 November 2011, at 11am EST, 8am PST, 16:00 UTC/GMT, 17:00 CET, or Wednesday 9 November 1am JST. Note for translating into other time zones that by then both Europe and the US have gone off DST.</p> <p>Note that this meeting, like all O|B|F Board meetings, is public; every member may call in at their leisure. Please see the <a href="https://www.open-bio.org/wiki/Minutes:2011_ConfCall">agenda of the meeting</a> (including dial-in information), see also the <a href="https://www.open-bio.org/wiki/Board">current board</a>.</p>https://www.open-bio.org/2011/10/28/chromosome-diagrams-in-biopython/Fri, 28 Oct 2011 15:44:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/10/28/chromosome-diagrams-in-biopython/<p>One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen <a href="http://twitter.com/#!/pjacock/status/121676973054496768">via Twitter</a>. I&rsquo;ve just been updating the Biopython Tutorial (current version <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">here</a>, <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>) to include an example drawing this:</p> <p><img src="https://github.com/biopython/biopython/raw/1574d8112914ea147f4e62c6b980543db1abdc7d/Doc/images/tRNA_chrom.png" alt="tRNA genes in Arabidopsis thaliana"></p> <p>Here&rsquo;s a <a href="https://github.com/biopython/biopython/raw/1574d8112914ea147f4e62c6b980543db1abdc7d/Doc/images/tRNA_chrom.pdf">PDF version</a> too. This example just parses the <em>Arabidopsis thaliana</em> GenBank files to get the chromosome lengths and the tRNA gene placements. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. Here the figure just uses a different color for each chromosome, but you can color each feature individually.</p> <p>This kind of diagram is often used for showing the placement of SNPs or other loci of interest (e.g. disease or breeding markers).</p> <p>P.S. Biopython produces these and other graphics using <a href="http://www.reportlab.com/software/opensource/">ReportLab</a>, an open source Python library capable of outputting PDF, SVG, PNG, etc. Very handy.</p>https://www.open-bio.org/2011/08/26/bioruby-1-4-2-released/Fri, 26 Aug 2011 09:49:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/08/26/bioruby-1-4-2-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/" title="BioRuby">BioRuby</a> 1.4.2. This new release fixes bugs existed in 1.4.1 and adds new features and improvement of performance.</p> <p>Here is a brief summary of changes.</p> <p><strong>Speed-up of Bio::RestrictionEnzyme::Analysis.cut:</strong> The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written by Tomoaki NISHIYAMA and Naohisa Goto.</p> <p><strong>New classes Bio::DDBJ::REST, REST interface for DDBJ Web API for Biology (WABI) web service</strong> in additon to SOAP. Currently, only selected APIs are implemented.</p> <p><strong>Bio::Blast with remote DDBJ server uses REST instead of SOAP</strong> because Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9. We can now use remote DDBJ BLAST server with Ruby 1.9.</p> <p><strong>The Tutorial.rd is updated</strong> by Pjotr Prins and Michael O&rsquo;Keefe.</p> <p><strong>Many unit tests are added</strong> for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB and so on. Most of them are developed by Kazuhiro Hayashi during the Google Summer of Code 2010. <strong>New methods:</strong> Bio::Fastq#to_s, Bio::NCBI::REST::EFetch.nucleotide, Bio::NCBI::REST::EFetch.protein.</p> <p><strong>Bug fixes:</strong></p> <ul> <li>Bio::Blast: Failure of remote BLAST execution is fixed, due to the changes in GenomeNet and DDBJ.</li> <li>Bio::Blast: When executing remote BLAST with &ldquo;genomenet&rdquo; server, options &ldquo;-b&rdquo; and &ldquo;-v&rdquo; are now correctly used to limit the number of hits to be reported.</li> <li>Bio::SPTR (Bio::UniProt): Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines were not correctly parsed.</li> <li>Bio::Reference#pubmed_url: Updated to follow recent NCBI changes.</li> <li>Bio::Newick#reparse failure.</li> <li>Bio::MEDLINE#reference: doi field should be filled.</li> <li>Bio::Reference#endnote fails when url is not set.</li> <li>Bio::FastaFormat#query passes nil to the given factory object.</li> <li>BioRuby Shell: efetch(), getent(), and demo() fail.</li> </ul> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.4.2/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.4.2/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.2.tar.gz">http://bioruby.org/archive/bioruby-1.4.2.tar.gz</a></p> <p>Gem file is also available at:  <a href="http://bioruby.org/archive/gems/bio-1.4.2.gem">http://bioruby.org/archive/gems/bio-1.4.2.gem</a></p> <p>We also put RubyGems pacakge at RubyForge and RubyGems.org. You can easily install by using RubyGems. First, check the version number by using search command: % gem search &ndash;remote bio and find “bio (1.4.2)” in the list. Then, % sudo gem install bio</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches. In addition, thanks to <a href="http://biosciencedbc.jp/?lng=en">NDBC</a> / <a href="http://dbcls.rois.ac.jp/en/">DBCLS</a> <a href="http://2011.biohackathon.org/">BioHackathon2011</a> participants and organizers who try BioRuby during the BioHackathon2011.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2011/08/18/biopython-1-58-released/Thu, 18 Aug 2011 17:06:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/08/18/biopython-1-58-released/<p>Source distributions and Windows installers for <strong>Biopython 1.58</strong> are available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>A new interface and parsers for the <a href="http://abacus.gene.ucl.ac.uk/software/paml.html">PAML (Phylogenetic Analysis by Maximum Likelihood)</a> package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the <code>Bio.Phylo.PAML</code> module.</p> <p>Bio.SeqIO now includes read and write support for the <a href="http://seqxml.org">SeqXML</a>, a simple XML format offering basic annotation support. See <a href="http://dx.doi.org/10.1093/bib/bbr025">Schmitt et al (2011) in Briefings in Bioinformatics</a>.</p> <p>Bio.SeqIO now includes read support for ABI files (&ldquo;Sanger&rdquo; capillary sequencing trace files, containing called sequence with PHRED qualities).</p> <p>The Bio.AlignIO &ldquo;fasta-m10&rdquo; parser was updated to cope with the marker lines as used in <a href="http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml">Bill Pearson&rsquo;s FASTA</a> version 3.36, without this fix the parser would only return alignments for the first query sequence.</p> <p>The Bio.AlignIO &ldquo;phylip&rdquo; parser and writer now treat a dot/period in the sequence as an error, in line with the official PHYLIP specification. Older verions of our code didn&rsquo;t do anything special with this character. Also, support for &ldquo;phylip-relaxed&rdquo; has been added which allows longer record names as used in <a href="http://wwwkramer.in.tum.de/exelixis/software.html">RAxML</a> and <a href="http://www.atgc-montpellier.fr/phyml/">PHYML</a>.</p> <p>Of potential interest to anyone subclassing Biopython objects, any remaining &ldquo;old syle&rdquo; Python classes have been switched to &ldquo;new style&rdquo; classes. This allows things like defining properties.</p> <p>Bio.HMM&rsquo;s Viterbi algorithm now expects the initial probabilities explicitly.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Gallagher (first contribution)</li> <li>Bartek Wilczynski</li> <li>Bogdan T. (first contribution)</li> <li>Brandon Invergo (first contribution)</li> <li>Connor McCoy (first contribution)</li> <li>David Cain (first contribution)</li> <li>Eric Talevich</li> <li>Fábio Madeira (first contribution)</li> <li>Hongbo Zhu</li> <li>Joao Rodrigues</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Thomas Schmitt (first contribution)</li> <li>Tiago Antao</li> <li>Walter Gillett</li> <li>Wibowo Arindrarto (first contribution)</li> </ul>https://www.open-bio.org/2011/04/26/announcing-obf-google-summer-of-code-accepted-students/Tue, 26 Apr 2011 19:29:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/26/announcing-obf-google-summer-of-code-accepted-students/<p>I&rsquo;m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program.</p> <p>The accepted students, their projects, and their mentors (in alphabetical order):</p> <p>Justinas Vygintas Daugmaudis Michele dos Santos da Silva (2 students!) Mocapy++Biopython: from data to probabilistic models of biomolecules mentored by Thomas Hamelryck and Eric Talevich</p> <p>Chuan Hock Koh BioJava - Amino acids physico-chemical properties calculation mentored by Peter Troshin, Andreas Prlic, and Jay Vyas</p> <p>Michał Koziarski Representing bio-objects and related information with images (BioRuby) mentored by Raoul J.P. Bonnal and Francesco Strozzi</p> <p>Sheena Scroggins Major BioPerl Reorganization mentored by Robert Buels and Chris Fields</p> <p>Mikael Eric Trellet Interface analysis module for BioPython mentored by João Rodrigues and Eric Talevich</p> <p>Once again this year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked.  Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF&rsquo;s open source projects, even without Google funding.  I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.</p> <p>For the accepted students: congratulations!  You have risen to the top of a very competitive application process.  Now it&rsquo;s time to &ldquo;put your money where your mouth is&rdquo;, as the saying goes.  Let&rsquo;s get out there and write some great code this summer!</p>https://www.open-bio.org/2011/04/21/bioperl-db-bioperl-run-bioperl-network-1-6-9-release/Thu, 21 Apr 2011 20:12:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/21/bioperl-db-bioperl-run-bioperl-network-1-6-9-release/<p>The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN:</p> <ul> <li><a href="http://search.cpan.org/dist/BioPerl-Run/">BioPerl-Run</a></li> <li><a href="http://search.cpan.org/dist/BioPerl-DB/">BioPerl-DB</a></li> <li><a href="http://search.cpan.org/dist/BioPerl-Network/">BioPerl-Network</a></li> </ul> <p>Please report any bugs to our <a href="https://redmine.open-bio.org/">Redmine server</a>.</p> <p>Enjoy!</p> <p>chris</p>https://www.open-bio.org/2011/04/14/bioperl-1-6-9-released/Thu, 14 Apr 2011 20:03:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/14/bioperl-1-6-9-released/<p><a href="http://search.cpan.org/~cjfields/BioPerl-1.6.900/">BioPerl 1.6.9</a> is now available in CPAN.  In this release:</p> <ul> <li>Refactored Bio::Species/Bio::Tree</li> <li>New SeqIO modules (gbxml, msout, mbsout)</li> <li>Updates for perl 5.12</li> <li>Bio::Assembly support for SAM/BAM, Newbler, ace output</li> <li>Bio::DB::SeqFeature updates</li> <li>PAML updated to work with v. 4.4d</li> <li>lots of various bug fixes, around 50</li> </ul> <p>Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way.  This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make.  In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet).    Please post if there are any problems.</p> <p>Enjoy!</p>https://www.open-bio.org/2011/04/02/biopython-1-57-released/Sat, 02 Apr 2011 12:17:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/02/biopython-1-57-released/<p>The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index.</a></p> <p>Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary.</p> <p>Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the ability to run the BLAST tools and save the output as ASN.1 format, and then convert this to any other supported BLAST ouput format (plain text, tabular, XML, or HTML) with the blast_formatter tool. The wrappers were also updated to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.</p> <p>The SeqRecord object now has a reverse_complement method (similar to that of the Seq object). This is most useful to reversing per-letter-annotation (such as quality scores from FASTQ) or features (such as annotation from GenBank).</p> <p>Bio.SeqIO.write&rsquo;s QUAL output has been sped up, and Bio.SeqIO.convert now uses an optimised routine for FASTQ to QUAL making this much faster.</p> <p>Biopython can now be installed with pip. Thanks to David Koppstein and James Casbon for reporting the problem.</p> <p>Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and IMGT output.</p> <p>The Bio.PDB module received several fixes and improvements, including starting to merge João&rsquo;s work from GSoC 2010; consequently Atom objects now know their element type and IUPAC mass. (The new features that use these attributes won&rsquo;t be included in Biopython until the next release, though, so stay tuned.)</p> <p>The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary (previously it was a list of key,value tuples) to better match the standard.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Brad Chapman</li> <li>Eric Talevich</li> <li>Erick Matsen (first contribution)</li> <li>Hongbo Zhu</li> <li>Jeffrey Finkelstein (first contribution)</li> <li>Joanna &amp; Dominik Kasprzak (first contribution)</li> <li>Joao Rodrigues</li> <li>Kristian Rother</li> <li>Leighton Pritchard</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Peter Thorpe (first contribution)</li> <li>Phillip Garland</li> <li>Walter Gillett (first contribution)</li> </ul> <p>Feedback is most welcome on the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a>, or <a href="http://redmine.open-bio.org/projects/biopython">redmine</a>.</p>https://www.open-bio.org/2011/03/18/obf-gsoc-2011/Fri, 18 Mar 2011 21:44:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/18/obf-gsoc-2011/<p>Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer&rsquo;s Google Summer of Code!</p> <p>GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see <a href="http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs">GSoC 2011 FAQ</a>.</p> <p>Student applications are due April 8, 2011 at 19:00 UTC. Students who are interested in participating should look at the <a href="http://open-bio.org/wiki/Google_Summer_of_Code">OBF&rsquo;s GSoC page</a>, which lists project ideas, and whom to contact about applying.</p> <p>For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on the <a href="http://open-bio.org/wiki/Google_Summer_of_Code">OBF wiki page</a>, and on the relevant project&rsquo;s GSoC wiki page.</p> <p>Thanks to all who helped make OBF&rsquo;s application to GSoC a success, and let&rsquo;s have a great, productive summer of code!</p> <p>Rob Buels OBF GSoC 2011 Administrator</p>https://www.open-bio.org/2011/03/17/introduction-of-openid-logins-for-obf-wikis/Thu, 17 Mar 2011 17:29:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/17/introduction-of-openid-logins-for-obf-wikis/<p>Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding <a href="http://openid.net/">OpenID</a> logins for the OBF wikis (BioPerl <a href="http://www.bioperl.org/w/index.php?title=Special:OpenIDLogin&amp;returnto=Main_Page">example</a>). User account creation via the old login system will be disabled and OpenID will be the default path for new accounts so users to make wiki changes.  This currently appears to have cut the incidence of spam significantly.  We will be adding information to the login pages to redirect new users to the new login page.</p> <p>We also have one wiki ( <a href="http://biolib.open-bio.org">BioLib</a>) that is testing out manual account approval via a wiki bureaucrat in case we have to take more extreme measures, though we would like to leave the barrier to community involvement with projects at the lowest possible level.</p>https://www.open-bio.org/2011/03/17/obf-redmine-server-now-available/Thu, 17 Mar 2011 17:07:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/17/obf-redmine-server-now-available/<p>The OBF now has a sparkly new <a href="http://redmine.open-bio.org">Redmine instance</a> running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly).  Bugs and user names (along with email contacts) from our old <a href="http://bugzilla.open-bio.org">Bugzilla</a> v2 server have been migrated over, though some links need to be <a href="http://redmine.open-bio.org/issues/3183">fixed</a>.</p> <p><a href="http://www.redmine.org">Redmine</a> is a project management web application that has <a href="http://www.redmine.org/projects/redmine/wiki/Features">several nice features</a> over other systems, including issue tracking, multiple project management, wikis, forums, and calendaring.</p> <p>Previous Bugzilla users will need to either <a href="http://redmine.open-bio.org/account/lost_password">reset their password</a> using their original Bugzilla login (an email address) or contact the OBF Helpdesk to get their password.</p>https://www.open-bio.org/2011/03/04/bosc-2011-abstract-call/Fri, 04 Mar 2011 15:42:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/04/bosc-2011-abstract-call/<p><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]">Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( <a href="https://www.open-bio.org/wiki/BOSC_2011">BOSC 2011</a>), an <a href="http://www.iscb.org/ismbeccb2011-program/satellite-meetings">ISMB 2011 Special Interest Group (SIG)</a>.</p> <p>Dates: July 15-16, 2011 Location: Vienna, Austria Web site: <a href="https://www.open-bio.org/wiki/BOSC_2011">/wiki/BOSC_2011</a> Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> BOSC announcements mailing list: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a></p> <p>Important Dates:</p> <ul> <li>April 18, 2011: Deadline for submitting abstracts to BOSC 2011</li> <li>May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors</li> <li>July 13-14, 2011: <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> programming session</li> <li>July 15-16, 2011: BOSC 2011</li> <li>July 17-19, 2011: ISMB 2011</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation (O|B|F)</a>, a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>We invite you to submit abstracts for <em>talks and posters</em>. Sessions include:</p> <ul> <li>Approaches to parallel processing</li> <li>Cloud-based approaches to improving software and data accessibility</li> <li>The Semantic Web in open source bioinformatics</li> <li>Data visualization</li> <li>Tools for next-generation sequencing</li> <li>Other Open Source software</li> </ul> <p>In addition to the above sessions, there will be a panel discussion about <em>&ldquo;Meeting the challenges of inter-institutional collaboration&rdquo;</em>. We are also working to arrange a joint session with one of the other ISMB SIGs.</p> <p>Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three <em>Student Travel Awards</em> for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011.</p> <p>For instructions on submitting your abstract, please visit <a href="https://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information">/wiki/BOSC_2011#Abstract_Submission_Information</a></p> <p>BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor</p>https://www.open-bio.org/2010/12/21/bosc-2010-proceedings-published-today-in-bmc-bioinformatics/Tue, 21 Dec 2010 19:29:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/12/21/bosc-2010-proceedings-published-today-in-bmc-bioinformatics/<p>On behalf of the BOSC 2010 Organizing Committee, I am pleased to announce that the <a href="http://www.biomedcentral.com/1471-2105/11?issue=S12">BOSC 2010 Proceedings</a> has been published today in BMC Bioinformatics.  Special thanks go to the abstract and proceedings reviewers who helped make this possible.</p>https://www.open-bio.org/2010/11/26/biopython-1-56-released/Fri, 26 Nov 2010 16:05:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/11/26/biopython-1-56-released/<p>The Biopython team is pleased to release Biopython 1.56, almost exactly three months after our last stable release ( <a href="http://news.open-bio.org/news/2010/08/biopython-1-55-released/">Biopython 1.55</a>).</p> <p>The <code>Bio.SeqIO</code> module has been updated to support protein EMBL files (used for the patents database), IMGT files (a variant of the EMBL file format, with help from Uri Laserson), and UniProt XML files (thanks to Andrea Pierleoni). Also the <code>SeqFeature</code> object gained some new methods, and the <code>Bio.Seq</code> translation function can now be used with an arbitrary genetic code.</p> <p><code>Bio.Entrez</code> will now try to download any missing NCBI DTD files and cache them in the user&rsquo;s home directory, and includes the latest current DTD files.</p> <p>The provisional <a href="http://biosql.org">BioSQL</a> SQLite Schema we&rsquo;ve been using since <a href="http://news.open-bio.org/news/2009/12/biopython-release-153/">Biopython 1.53</a> is now official, and has been updated slightly.</p> <p>For population genetics, <code>Bio.PopGen.FDist</code> now supports the DFDist command line tool as well as FDist2.</p> <p>Note that <a href="http://news.open-bio.org/news/2010/11/dropping-python24-support/">as previously announced</a>, this is expected to be <strong>our last release to support Python 2.4</strong>. We also support Python 2.5, 2.6 and 2.7, while work is on going for Python 3.</p> <p>(At least) 13 people have contributed to this release, including 6 new people - thank you all:</p> <ul> <li>Andrea Pierleoni (first contribution)</li> <li>Bart de Koning (first contribution)</li> <li>Bartek Wilczynski</li> <li>Bartosz Telenczuk (first contribution)</li> <li>Cymon Cox</li> <li>Eric Talevich</li> <li>Frank Kauff</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Phillip Garland (first contribution)</li> <li>Siong Kong (first contribution)</li> <li>Tiago Antao</li> <li>Uri Laserson (first contribution)</li> </ul> <p>Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website (biopython.org)</a>.</p> <p>As usual, feedback is most welcome on the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/11/18/dropping-python24-support/Thu, 18 Nov 2010 15:09:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/11/18/dropping-python24-support/<p>This is a reminder that the forthcoming Biopython 1.56 release is <em>planned</em> to be our last release to support Python 2.4.</p> <p>Looking back, we supported Python 2.3 for about six years - it was released July 2003, and <a href="http://news.open-bio.org/news/2009/04/biopython-release-150/">Biopython 1.50</a> released in April 2009 was the last to support it. Similarly, Python 2.4 was released six years ago (November 2004).</p> <p>Dropping Python 2.4 support will allow use to assume standard library modules like the <a href="http://docs.python.org/library/xml.etree.elementtree.html">ElementTree XML parser</a> and <a href="http://docs.python.org/library/sqlite3.html">SQLite 3 support</a> will be available. There are also several <a href="http://docs.python.org/whatsnew/2.5.html">new language features in Python 2.5+</a> which will be useful, and it should make supporting Python 3 a little easier as well.</p> <p>Most operating systems which come with Python now ship with Python 2.5 or later, with the notable exception of <a href="http://centos.org">CentOS</a> where Python 2.4 is still used. Also, those of you running a Linux server may still be running an old but still supported OS - for example the <a href="http://www.ubuntu.com/">Ubuntu</a> 6.06 LTS (Dapper Drake) server edition is maintained until June 2011, and comes with Python 2.4.</p> <p>If you would be negatively affected by Biopython dropping support for Python 2.4, please let us know as soon as possible, ideally via the <a href="http://biopython.org/wiki/Mailing_lists">mailing list</a>.</p> <p>Thank you.</p>https://www.open-bio.org/2010/10/22/bioruby-1-4-1-released/Fri, 22 Oct 2010 06:36:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/10/22/bioruby-1-4-1-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/" title="BioRuby">BioRuby</a> 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added.</p> <p>Here is a brief summary of changes.</p> <p><strong>PAML Codeml support is significantly improved:</strong> PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins.</p> <p><strong>KEGG PATHWAY and KEGG MODULE parsers are added:</strong> The code is developed by Kozo Nishida and Toshiaki Katayama.</p> <p><strong>Bio::KEGG::GENES and Bio::KEGG::GENOME and bug fixes and new methods:</strong> Some of them are due to the file format changes.</p> <p><strong>Test codes are added and improved:</strong> Test codes are added and improved. Tney are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince, and Naohisa Goto.</p> <p><strong>Bug fixes in Bio::Tree:</strong> somemethods did not work correctly.</p> <p><strong>Platform-dependent bug when calling external programs:</strong> Detection of platform is improved not to call fork(2) on platforms that do not support it (e.g. JRuby).</p> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="http://github.com/bioruby/bioruby/blob/1.4.1/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="http://github.com/bioruby/bioruby/blob/1.4.1/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.1.tar.gz">http://bioruby.org/archive/bioruby-1.4.1.tar.gz</a></p> <p>Gem file is also available at:  <a href="http://bioruby.org/archive/gems/bio-1.4.1.gem">http://bioruby.org/archive/gems/bio-1.4.1.gem</a></p> <p>We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.1)” in the list. Then, % sudo gem install bio</p> <p>Finally, we are sorry that many new features are waiting to be merged to BioRuby, including  HMMER3 support. These will be included in the next major release version.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2010/10/05/minutes2010-confcall/Tue, 05 Oct 2010 05:21:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/10/05/minutes2010-confcall/<h3 id="agenda">Agenda</h3> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2009_ConfCall">2009 BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>BOSC <ul> <li>BOSC 2010 (Kam) - held with <a href="http://www.iscb.org/ismb2010">ISMB2010</a> in Boston, MA, USA <ul> <li>Money spent/made attendee number, any other feedback</li> </ul> </li> <li>BOSC 2011 - with <a href="http://www.iscb.org/about-ismb#ismb2011">ISMB 2011 Vienna, Austria</a> <ul> <li>2011 Organizing Committee chairs</li> <li>Plans for the conference</li> </ul> </li> </ul> </li> <li>Treasurer&rsquo;s 2010 report (ChrisD) <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2010_Financial_report">2010 Financial report</a></li> </ul> </li> <li>BoD membership and succession. <ul> <li>Kam Dahlquist is resigning from the BoD. Jason Stajich wants to resign in the near future, too.</li> <li>Nominations</li> <li>Plan to elect new BoD members and rotate officers.</li> </ul> </li> <li>OBF Hardware &amp; Sysadmin report (JasonS and ChrisD) <ul> <li>Domain name registrar and registration payment</li> </ul> </li> <li>Additional topics proposed by community</li> </ol> </li> </ol> <h3 id="minutes-from-the-meeting">Minutes from the meeting</h3> <p><strong>Venue:</strong> held by conference call, scheduled for 5pm EDT (21:00 UTC).</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Kam Dahlquist, Jason Stajich, Chris Dagdigian, Hilmar Lapp, Nomi Harris</li> <li>Guests: Ron Taylor, Peter Cock, Mauricio Herrera Cuadra</li> </ul> <p><strong>Minutes:</strong></p> <h4 id="hilmar-calls-meeting-to-order-at-505pm-edt">Hilmar calls meeting to order at 5.05pm EDT.</h4> <ul> <li>Approval of previous meeting minutes. <ul> <li>Jason moves to approve, Nomi, and Chris second. 2009 minutes approved by unanimous consent.</li> </ul> </li> </ul> <h4 id="bosc-2010">BOSC 2010</h4> <ul> <li>93 paid delegates, 5 complementary, total of 98. This is almost the same number as last year.</li> <li>Kam has accounting spreadsheet from Stephen Leard.</li> <li>We currently have $16,127.96 in escrow. However there are outstanding expenses: reimbursement of the two keynote speakers, who haven&rsquo;t fully turned in their receipts and paperwork yet. This may amount to $2,000-3,000.</li> <li>Had large number of speakers, very well attended.</li> <li>We are going forward with the proceedings. There are 13 submitted papers (about half of the number of eligible to submit), all have been reviewed, and today was the deadline for turning in revisions (3 still outstanding). 2-3 required major substantive revisions, none were rejected. Most required only minor revisions. Entire package will be sent to BMC (probably within the next 2-3 weeks) which will do the formatting and invoice the authors for publication charges. We don&rsquo;t know how much time it will take BMC from there. <ul> <li>Many of the submissions were in the cloud computing area. Given the ratio of submitted to elgible, there clearly is a demand. However, for Bio* projects this may not be a very suitable venue for publication (and none of the submissions were from Bio* project updates). People decided for themselves whether they wanted to submit, there was no active recruiting.</li> <li>Caveat for whoever shepherds this next year is that BMC doesn&rsquo;t offer a lot of support. Call for papers, lining up reviewers, following up, etc all need to be done by us.</li> <li>Question is what the return for the cost of investment is. How many speakers wouldn&rsquo;t have come if they wouldn&rsquo;t have had the opportunity to submit to a proceedings. Also might ask those who ddn&rsquo;t submit to the proceedings whether the option to do so was a factor in decision making. BOSC 2011 committee might want to conduct a survey (ask Stephen Leard for participant list).</li> </ul> </li> </ul> <h4 id="codefest-2010">CodeFest 2010</h4> <ul> <li>Seems to have gone pretty well, resulted in useful connections, work got done, and a lot of enthusiasm got generated to do it again in 2011.</li> <li>Someone should present a summary about the 2011 event right afterwards at BOSC 2011. The BOSC 2011 will follow up with that, as well on posting a report about the 2010 codefest on the wiki.</li> </ul> <h4 id="bosc-2011">BOSC 2011</h4> <ul> <li>Nomi Harris and Peter Rice will co-chair the 2011 conference. <ul> <li>Nomi reports that they would like to better exploit synergy with the other SIGs, both in terms of speakers and attendees. There&rsquo;s been a lot of floating observed. Possibly share keynote speakers, which might allow sharing the expenses. Nomi will talk with Hershel Safer (ISMB SIG coordinator)</li> <li>This would be Nomi&rsquo;s first time to chair the event. She has participated in the organization since 1999, though, and has co-organized the GMOD meeting in 2003 (in Berkeley). She would like to reach out to the GMOD crowd to increase participation at BOSC.</li> <li>Hilmar moves to give a vote of confidence to Nomi and Peter as the BOSC 2011 chairs and to give them authority to run the conference. Kam, Jason, and Chris second. Approved by unanimous consent.</li> </ul> </li> <li>Nomi asks for volunteers from the OBF Board to join the committee.</li> </ul> <h4 id="2010-treasurers-report">2010 Treasurer&rsquo;s report</h4> <ul> <li>Have cash assets of around $31,000, sitting in two checking accounts. This does not include the funds held in escrow by ISCB, to which we don&rsquo;t get direct accesss.</li> <li>There are issues with sending money to international recipients.</li> <li>We had 3 travel fellowship recipients at BOSC 2010. The 3rd one is missing from the treasurer&rsquo;s report.</li> <li>Can we somehow better tap into the funds held in escrow by ISCB? <ul> <li>Kam advises that the 6 complementary BOSC registrations could easily be used for organizing committee members.</li> <li>Can the escrow funds somehow be used to help defray publication costs for Bio* proceedings submissions?</li> <li>We could use the escrow funds towards catering (social dinner?) or poster session. Maybe include a question about the value of a poster session in a survey.</li> </ul> </li> <li>ACTION: ChrisD will send records to Kam that those fellowship awards were all paid out. ChrisD to amend the financial report with the missing $250 award payment.</li> <li>Approval of the 2010 financial report was postponed until after it is corrected.</li> </ul> <h4 id="board-of-directors-membership-and-succession">Board of Directors membership and succession</h4> <ul> <li>Kam is stepping down from the Board effective today. She enjoyed working with us, and may consider rejoining at a later time when she can make the time available. The Board expresses their collective gratitude to Kam for volunteering her time and her service, which was very much appreciated. Ron seconds that on behalf of the public.</li> <li>Jason has served for a long time and would like to step down. He has not submitted a resignation letter yet, because he would like to assist in the transition process. There is no candidate yet who could step up.</li> <li>We need to reach out to tap into the energy among the community.</li> <li>There hasn&rsquo;t been much time and attention invested in increased outreach, which would need to go hand-in-hand with any fundraising efforts (and vice versa). Alternatively, we could restrict ourselves to the currentl role (support of Bio* projects).</li> <li>It is worth noting that we formed at a time when code hosting and remote collaboration services were sparse and unreliable. This has drastically changed in the meantime.</li> <li>Do we to issue a Call to Arms? Or go back to just support of coding?</li> <li>Is standardization initiatives another possible purview in terms of mission? There are already a number of organizations that do this.</li> <li>We need to reach out and nominate at least 5 new members for the BoD. Would it be worthwhile to reach out to CIOs of the big genome sequencing / genomics centers? Another possibility could be the US federal government institutions?</li> <li>ACTION: Hilmar (with Nominating Committee) to Identify candidates by the end of the year. Also, the Bio* projects should solicit BoD candidates from within their ranks.</li> </ul> <h4 id="obf-hardware-and-non-cash-assets">OBF Hardware and Non-cash Assets</h4> <ul> <li>There is a question about the Biopython.org domain. It is not owned by OBF, but by Jeff Chang. Peter will get in contact with Jeff Chang to establish consent to ownership transfer.</li> <li>We will move our domain registrar from Network Solutions to a cheaper alternative in 2 years at the latest, which is when registrations will come up for renewal again.</li> <li>Our hardware continues to age and is at the point where it could die. The question is how to deal with that: Should we upgrade our hardware, or should we start a process of migrating our services to hosted solutions. These days, there are many providers, and costs are low or even zero.</li> <li>ACTION: Jason and ChrisD draft a plan for what looks like the best way forward, then circulate this on the root-l mailing list for input and feedback.</li> </ul> <p>Next Board of Directors meeting is targeted for December 2010, as there is a lot of remaining stuff to be discussed and decided, especially hardware, hosting of services, nominations, financial report amendment, etc.</p> <p>Meeting is adjourned at 6.36pm EDT.</p>https://www.open-bio.org/2010/08/31/biopython-1-55-released/Tue, 31 Aug 2010 22:49:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/08/31/biopython-1-55-released/<p>The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable release ( <a href="http://news.open-bio.org/news/2010/05/biopython-release-154/">Biopython 1.54</a>) and the <a href="http://news.open-bio.org//news/2010/08/biopython-1-55-beta-released/">beta release</a> earlier in August.</p> <p>A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn&rsquo;t notice any changes ;)</p> <p>In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated <a href="http://www.biopython.org/wiki/Documentation">documentation</a>.</p> <p>Additionally GenBank and EMBL parsing has been sped up, the <a href="http://www.biopython.org/wiki/BioSQL">BioSQL</a> classes act more like Python dictionaries, and Bio.PDB should handle model numbers and a missing element column better.</p> <p>Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution).</p> <p>(At least) 12 people have contributed to this release, including 6 new people - thank you all:</p> <ul> <li>Andres Colubri (first contribution)</li> <li>Carlos Rios Vera (first contribution)</li> <li>Claude Paroz (first contribution)</li> <li>Cymon Cox</li> <li>Eric Talevich</li> <li>Frank Kauff</li> <li>Joao Rodrigues (first contribution)</li> <li>Konstantin Okonechnikov (first contribution)</li> <li>Michiel de Hoon</li> <li>Nathan Edwards (first contribution)</li> <li>Peter Cock</li> <li>Tiago Antao</li> </ul> <p>Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website (biopython.org)</a>.</p> <p>As usual, feedback is most welcome on the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/08/26/bioruby-paper-published/Fri, 27 Aug 2010 00:13:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/08/26/bioruby-paper-published/<p>After 10 years of development, the BioRuby paper is finally published in the <a href="http://bioinformatics.oxfordjournals.org/"><em>Bioinformatics</em></a> journal.  The article is open access, so please take a look.</p> <p>BioRuby: Bioinformatics software for the Ruby programming language Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama <em>Bioinformatics</em> 2010; <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq475">doi: 10.1093/bioinformatics/btq475</a></p>https://www.open-bio.org/2010/08/18/biopython-1-55-beta-released/Wed, 18 Aug 2010 20:52:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/08/18/biopython-1-55-beta-released/<p>We&rsquo;ve just released a <em>beta</em> of Biopython 1.55 for user testing.</p> <p>Since <a href="http://news.open-bio.org/news/2010/05/biopython-release-154/">Biopython 1.54</a> was released three months ago, we&rsquo;ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we&rsquo;ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we&rsquo;ve accidentally broken things - which is why we&rsquo;re doing this beta release.</p> <p>In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated <a href="http://www.biopython.org/wiki/Documentation">documentation</a>.</p> <p>Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution).</p> <p>(At least) 10 people have contributed to this release (so far), including 5 new people:</p> <ul> <li>Andres Colubri (first contribution)</li> <li>Carlos Rios Vera (first contribution)</li> <li>Claude Paroz (first contribution)</li> <li>Eric Talevich</li> <li>Frank Kauff</li> <li>Joao Rodrigues (first contribution)</li> <li>Konstantin Okonechnikov (first contribution)</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Tiago Antao</li> </ul> <p>Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website (biopython.org)</a>.</p> <p>So, please let us know what works and what doesn’t through the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/05/20/biopython-release-154/Thu, 20 May 2010 19:04:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/05/20/biopython-release-154/<p>The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes.</p> <p>This is the first stable release to feature the new <a href="http://www.biopython.org/wiki/Phylo" title="Bio.Phylo documentation on the wiki">Bio.Phylo</a> module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and <a href="http://www.phyloxml.org/" title="PhyloXML decription">PhyloXML</a> formats. The module is the result of Eric Talevich&rsquo;s Google Summer of Code project which was supported by <a href="http://www.nescent.org/index.php">The National Evolutionary Synthesis Center (NESCent)</a>.</p> <p>Biopython now supports the reading, writing and indexing of Standard Flowgram Format (SFF) files produced in 454 sequencing. Jose Blanca (the brains behind the widely used <a href="http://bioinf.comav.upv.es/sff_extract/" title="sff_extract homepage">sff_extract</a> tool) provided code to handle SFF files and Peter Cock has integrated that code with <code>Bio.SeqIO</code>. Adding SFF support to <code>SeqIO</code> makes it possible to convert these files to the FASTQ, FASTA and QUAL formats (as trimmed or untrimmed reads).</p> <p>As well as adding features the new release tweaks and extends some of the core modules:</p> <ul> <li>Both <code>Bio.SeqIO</code> and <code>Bio.AlignIO</code> will accept filenames as well as handles, <a href="http://news.open-bio.org/news/2010/04/biopython-seqio-and-alignio-easier/">as detailed here</a>.</li> <li>The multiple sequence alignment object that underlies Bio.AlignIO has been improved.</li> <li><code>Bio.SeqIO</code> can read and write EMBL nucleotide files.</li> <li>The dictionary-like objects returned by <code>Bio.SeqIO.index()</code> have a new method &quot; <code>get_raw</code>&quot; that gets unparsed data from a file as a string, <a href="http://news.open-bio.org/news/2010/04/partial-seq-files-biopython/">as detailed here</a>.</li> <li><code>Bio.Entrez</code> includes some more DTD files, in particular <code>eLink_090910.dtd</code>, used by our NCBI Entrez Utilities XML parser.</li> </ul> <p>Binaries and source files for Biopython 1.54 are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a>. The <a href="http://www.biopython.org/wiki/Documentation" title="Biopython Documentation">documentation</a> has been updated to include the changes made since our last release.</p> <p>A big thanks to every one who tested our beta release or submitted bugs since <a href="http://news.open-bio.org/news/2009/12/biopython-release-153/">Biopython 1.53</a>. And an especially big thanks to everyone who contributed to this release, including five first time contributors:</p> <ul> <li>Anne Pajon (first contribution)</li> <li>Brad Chapman</li> <li>Christian Zmasek</li> <li>Diana Jaunzeikare (first contribution)</li> <li>Eric Talevich</li> <li>Jose Blanca (first contribution)</li> <li>Kevin Jacobs (first contribution)</li> <li>Leighton Pritchard</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Thomas Holder (first contribution)</li> </ul>https://www.open-bio.org/2010/05/14/bioperl-has-moved-to-github/Fri, 14 May 2010 04:18:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/05/14/bioperl-has-moved-to-github/<p>BioPerl has migrated to <a href="http://git-scm.com/">git</a> and <a href="http://github.com/bioperl">GitHub</a>!  We have also set up a mirror set of several key repositories at the great public git hosting site <a href="http://repo.or.cz/w">repo.or.cz</a>.</p> <p>If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID.  Also, add the extra email <a href="https://www.open-bio.org/wp-content/uploads/2010/05/generic.jpg"><img src="https://www.open-bio.org/wp-content/uploads/2010/05/generic.jpg" alt=""></a> (where &lsquo;DEVNAME&rsquo; is your <strong>original Subversion account ID</strong>).  This should map any previous commits from the older Subversion and CVS repository to your new GitHub account.</p> <p>The following are ways everyone can download the latest code.</p> <h2 id="using-git">Using git</h2> <p>Note you can replace &lsquo;bioperl-live.git&rsquo; with any of the repository names (bioperl-db, bioperl-run, etc).  For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone git@github.com:bioperl/bioperl-live.git </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone https://bioperl@github.com/bioperl/bioperl-live.git </span></span></code></pre></div><p>The open read-only link (for everyone):</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone git://github.com/bioperl/bioperl-live.git </span></span></code></pre></div><p>or using the mirror site:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone git://repo.or.cz/bioperl-live.git </span></span></code></pre></div><h2 id="using-svn-read-only">Using SVN (read-only)</h2> <p>We will also support read-only access to GitHub with Subversion.  We may allow write support at some later point.  To use svn:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> svn checkout http://svn.github.com/bioperl/bioperl-live.git </span></span></code></pre></div><h2 id="direct-downloads">Direct downloads</h2> <p>Tagged releases can be found here:</p> <p><a href="http://github.com/bioperl/bioperl-live/downloads">http://github.com/bioperl/bioperl-live/downloads</a></p> <p>The latest source code here:</p> <p><a href="http://github.com/bioperl/bioperl-live/archives/master">http://github.com/bioperl/bioperl-live/archives/master</a></p> <h2 id="forking-bioperl-and-pull-requests"><strong>Forking BioPerl and Pull Requests</strong></h2> <p>We intend on using git and GitHub to their fullest.  With that in mind, we encourage users to <a href="http://help.github.com/forking/">fork</a> BioPerl code, make changes, commit them to your forked repository, and submit <a href="http://github.com/guides/pull-requests">pull requests</a>.</p> <h2 id="documentation">Documentation</h2> <p>We&rsquo;re also in the process of updating our local developer documents for help with those who haven&rsquo;t used git before.  In particular, we have a <a href="http://www.bioperl.org/wiki/Using_Git">Using Git</a> page, and have added <a href="http://www.bioperl.org/wiki/Tracking_Git_commits">RSS feeds</a> for our repository commits.</p> <p>Enjoy!</p> <p>chris</p> <p><strong>Update:</strong> SVN version fixed, thanks to DaveMessina++ for pointing it out.</p>https://www.open-bio.org/2010/05/02/obf-google-summer-of-code-accepted-students/Sun, 02 May 2010 19:37:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/05/02/obf-google-summer-of-code-accepted-students/<p>I&rsquo;m pleased to announce the acceptance of <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">OBF&rsquo;s 2010 Google Summer of Code</a> students, listed in alphabetical order with their project titles and primary mentors:</p> <p>Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms</p> <p>Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins</p> <p>Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby</p> <p>Sara Rayburn (PM Christian Zmasek) - Implementing Speciation &amp; Duplication Inference Algorithm for Binary and Non-binary Species Tree</p> <p>Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython&rsquo;s Structural Biology module</p> <p>Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring</p> <p>Congratulations to our accepted students!</p> <p>All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google.  Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate.  We received a lot of really excellent proposals, the decisions were not easy.</p> <p>Thanks very much to all the students who applied, we very much appreciate your hard work.</p> <p>Here&rsquo;s to a great 2010 Summer of Code, I&rsquo;m sure these students will do wonderful work.</p> <p>Rob Buels O|B|F GSoC 2010 Administrator</p>https://www.open-bio.org/2010/04/30/illumina-q2-trim-fastq/Fri, 30 Apr 2010 07:49:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/30/illumina-q2-trim-fastq/<p>In another quirk to the <a href="http://news.open-bio.org/news/2009/12/nar-fastq-format/">FASTQ story</a>, recent Illumina FASTQ files don&rsquo;t actually use the full range of PHRED scores - and a score of 2 has a special meaning, <em>The Read Segment Quality Control Indicator</em> (RSQCI, encoded as &lsquo;B&rsquo;).</p> <p>Hats off to <em>Dr Torsten Seemann</em> for raising awareness of this issue in <a href="http://seqanswers.com/forums/showpost.php?p=17491&amp;postcount=3">his post on the seqanswers.com forum</a>, referring to a presentation by <em>Tobias Mann</em> of Illumina which says:</p> <blockquote> <p><em>The Read Segment Quality Control Indicator:</em></p> <p><em>- At the ends of some reads, quality scores are unreliable. Illumina has an algorithm for identifying these unreliable runs of quality scores, and we use a special indicator to flag these portions of reads</em></p> <p><em>- A quality score of 2, encoded as a &ldquo;B&rdquo;, is used as a special indicator. A quality score of 2 does not imply a specific error rate, but rather implies that the marked region of the read should not be used for downstream analysis.</em></p> <p><em>- Some reads will end with a run of B (or Q2) basecalls, but there will never  be an isolated Q2 basecall.</em></p> </blockquote> <p>So, armed with this knowledge, you might want to apply a simple trimming criteria to any Illumina FASTQ files - remove anything after and including a PHRED quality score of 2 (encoded as ASCII &lsquo;B&rsquo;).</p> <p>We could do this with the rich object orientated <code>SeqRecord</code> based API in Biopython, but when <a href="http://news.open-bio.org/news/2009/09/biopython-fast-fastq/">dealing with massive FASTQ files</a> this overhead matters. Instead we&rsquo;ll stick with plain Python strings:</p> <p><code>from Bio.SeqIO.QualityIO import FastqGeneralIterator handle = open(&quot;B_trimmed.fastq&quot;, &quot;w&quot;) min_length = 10 for title, seq, qual in FastqGeneralIterator(open(&quot;untrimmed.fastq&quot;)) : #Find the location of the first &quot;B&quot; (PHRED quality 2) trim = qual.find(&quot;B&quot;) if trim == -1: #No need to trim handle.write(&quot;@%sn%sn+n%sn&quot; % (title, seq, qual)) elif trim &gt;= min_length: #Take everything up to the first B handle.write(&quot;@%sn%sn+n%sn&quot; % (title, seq[:trim], qual[:trim])) handle.close()</code></p> <p>In practice the above can trim too much - you can still get isolated &ldquo;B&rdquo; characters in the middle of a read, where it is just a low quality score. Instead, we can trim any trailing &ldquo;B&rdquo; characters - which will do the same thing on RSQCI based FASTQ files where the &ldquo;B&rdquo; should only appear at the end:</p> <p><code>from Bio.SeqIO.QualityIO import FastqGeneralIterator handle = open(&quot;B_trimmed.fastq&quot;, &quot;w&quot;) min_length = 10 for title, seq, qual in FastqGeneralIterator(open(&quot;untrimmed.fastq&quot;)) : qual = qual.rstrip(&quot;B&quot;) #Remove any trailing B characters length = len(qual) if length &gt;= min_length: seq = seq[:length] #trim to match handle.write(&quot;@%sn%sn+n%sn&quot; % (title, seq, qual)) handle.close()</code></p> <p>You could easily modify this example to read from stdin and write to stdout (see this <a href="http://www.biopython.org/wiki/Reading_from_unix_pipes">cookbook example</a>), or take filenames as command line arguments to turn this into a general purpose &ldquo;FASTQ B-trimming script&rdquo;.</p>https://www.open-bio.org/2010/04/27/partial-seq-files-biopython/Tue, 27 Apr 2010 13:03:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/27/partial-seq-files-biopython/<p>This is another blog post to highlight one of the neat tricks you&rsquo;ll be able to do with Biopython 1.54 (which you can help test with the <a href="http://news.open-bio.org/news/2010/04/biopython-1-54-beta-released/">Biopython 1.54 beta</a> release).</p> <p>It is often useful to be able to extract a few records from a larger sequence file - for example, some sequences of interest from a full UniProt or GenBank dump. One obvious way to try to do this is to parse the file into an object representation (i.e. <code>SeqRecord</code> objects using <code>Bio.SeqIO.parse(...)</code>), filter to pick out the entries you want, and then write them back to disk (using <code>Bio.SeqIO.write(...)</code>). However, for complex file formats like GenBank this can be lossy ( <code>Bio.SeqIO</code> does not support a 100% identical round trip), and Biopython don&rsquo;t currently support writing out the SwissProt plain text format used by UniProt. So, that approach won&rsquo;t work.</p> <p><a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a> introduced a new <a href="http://news.open-bio.org/news/2009/09/biopython-seqio-index/">indexing function</a>, <code>Bio.SeqIO.index(...)</code>, which allows a large multi-sequence file to be treated like a Python dictionary - parsing requested records on request. This has been enhanced for Biopython 1.54 with a method <code>get_raw(...)</code> to extract the raw for a record as a string.</p> <p>How is this useful? Well, take your large (UniProt) file, index it, then extract the records you want and write them to your output file unmodified:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>from Bio import SeqIO </span></span><span style="display:flex;"><span>uniprot = SeqIO.index(&#34;uniprot_sprot.dat&#34;, &#34;swiss&#34;) </span></span><span style="display:flex;"><span>handle = open(&#34;selected.dat&#34;, &#34;w&#34;) </span></span><span style="display:flex;"><span>for acc in [&#34;P33487&#34;, &#34;P19801&#34;, &#34;P13689&#34;, &#34;Q8JZQ5&#34;, &#34;Q9TRC7&#34;]: </span></span><span style="display:flex;"><span> handle.write(uniprot.get_raw(acc)) </span></span><span style="display:flex;"><span>handle.close() </span></span></code></pre></div><p>Another neat use of this functionality would be to sort entries in a sequential file format, and there is an example of that in the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p>https://www.open-bio.org/2010/04/07/reminder-bosc-abstract-deadline-april-15/Wed, 07 Apr 2010 05:46:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/07/reminder-bosc-abstract-deadline-april-15/<p>Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15.  See the BOSC web site at /wiki/BOSC_2010 for details.  Submissions will only be accepted electronically at <a href="http://events.open-bio.org/BOSC2010/openconf.php">http://events.open-bio.org/BOSC2010/openconf.php</a>.</p> <p>Graduate students, don&rsquo;t forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award.</p> <p>We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. <a href="http://www.sanger.ac.uk/" title="http://www.sanger.ac.uk/">http://www.sanger.ac.uk/</a></p> <p>On behalf of the BOSC 2010 organizing committee, I hope to see you there!</p>https://www.open-bio.org/2010/04/05/biopython-seqio-and-alignio-easier/Mon, 05 Apr 2010 16:37:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/05/biopython-seqio-and-alignio-easier/<p>One of the small changes coming in Biopython 1.54 (which you can try out already using the <a href="http://news.open-bio.org/news/2010/04/biopython-1-54-beta-released/">Biopython 1.54 beta</a>) is to <a href="http://www.biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://www.biopython.org/wiki/AlignIO">Bio.AlignIO</a>. Previously the input and output functions had required file <em>handles</em>, but they will now also accept <em>filenames</em>.</p> <p>This is a case of <em>practicality beats purity</em> (to quote <a href="http://www.python.org/dev/peps/pep-0020/">the Zen of Python</a>), and is particularly handy when doing very short scripts or working at the Python prompt.</p> <p>For example, filtering a FASTA file to take only entries with a minimum length of 100 can be done like this (with handles):</p> <p><code>from Bio import SeqIO in_handle = open(&quot;example.fasta&quot;, &quot;rU&quot;) out_handle = open(&quot;long.fasta&quot;, &quot;w&quot;) records = (rec for rec in SeqIO.parse(in_handle, &quot;fasta&quot;) if len(rec)&gt;100) SeqIO.write(records, out_handle, &quot;fasta&quot;) in_handle.close() out_handle.close()</code></p> <p>Using filenames it becomes much more concise - just three lines:</p> <p><code>from Bio import SeqIO records = (rec for rec in SeqIO.parse(&quot;example.fasta&quot;, &quot;fasta&quot;) if len(rec)&gt;100) SeqIO.write(records, &quot;long.fasta&quot;, &quot;fasta&quot;)</code></p> <p>This also means Python and Biopython beginners can postpone learning about file handles a little longer, although that may not be an entirely good thing ;)</p>https://www.open-bio.org/2010/04/02/biopython-1-54-beta-released/Fri, 02 Apr 2010 17:19:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/02/biopython-1-54-beta-released/<p>A <em>beta</em> release for Biopython 1.54 is now available for download and testing.</p> <p>Since <a href="http://news.open-bio.org/news/2009/12/biopython-release-153/">Biopython 1.53</a> was released at the end of last year, several new features and more documentation have been added, plus the usual bug fixes. For full details see the <a href="http://biopython.open-bio.org/SRC/biopython/NEWS">NEWS file</a>.</p> <p>All the new features have been tested by the dev team but it’s possible there are cases that we haven’t been able to foresee and test, especially for the updated multiple sequence alignment object (which is what you&rsquo;ll now get when parsing alignments with <a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a>), the <a href="http://biopython.org/wiki/Phylo">new Bio.Phylo module</a>, and the <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> support for Standard Flowgram Format (SFF) files.</p> <p>Source distributions and Windows installers are available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the Biopython website ( <a href="http://biopython.org/">biopython.org</a>).</p> <p>We are interested in getting feedback on the beta release as a whole, but especially on the new features and the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p>(At least) 10 people contributed to this release (so far), which includes 4 new people:</p> <ul> <li> <p>Anne Pajon (first contribution)</p> </li> <li> <p>Brad Chapman</p> </li> <li> <p>Christian Zmasek</p> </li> <li> <p>Eric Talevich</p> </li> <li> <p>Jose Blanca (first contribution)</p> </li> <li> <p>Kevin Jacobs (first contribution)</p> </li> <li> <p>Leighton Pritchard</p> </li> <li> <p>Michiel de Hoon</p> </li> <li> <p>Peter Cock</p> </li> <li> <p>Thomas Holder (first contribution)</p> </li> </ul> <p>So, gather your courage, download the release, try it out and please let us know what works and what doesn’t through the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/03/21/obf-in-google-summer-of-code/Sun, 21 Mar 2010 18:26:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/03/21/obf-in-google-summer-of-code/<p>The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer&rsquo;s Google Summer of Code.  Our list of project ideas and mentors is linked from the <a href="http://open-bio.org/wiki/Google_Summer_of_Code" title="O|B|F GSoC">O|B|F GSoC page</a>.</p> <p>Student applications must be submitted to Google by <strong>April 9, 2010,</strong> see the <a href="http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs">official GSoC 2010 FAQ</a>. That is less than three weeks away!</p> <p>Students, have a look at that wiki page, contact the project you&rsquo;re interested in working with, and get rolling on that application post-haste.  A good GSoC application takes quite a bit of thought and effort to put together.  <strong>Students are encouraged to get help from mentors to put together a good application.</strong></p> <p>Current developers on O|B|F projects, have a look through the <a href="http://en.flossmanuals.net/GSoCMentoringGuide">GSoC Mentoring Guide</a>, and if it looks like something you want to do, there&rsquo;s still time to volunteer as a prospective mentor.  Just add your name to the O|B|F and project wiki pages, and contribute your project ideas.  Even if you don&rsquo;t have project ideas of your own, it&rsquo;s good to volunteer.</p> <p>Google Summer of Code is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents).   Students are paid a $5,000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the <a href="http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs">official GSoC 2010 FAQ</a>.</p> <p>Thanks to all who helped make OBF&rsquo;s application to GSoC a success, and let&rsquo;s have a great, productive summer of code!</p> <p>Rob Buels O|B|F GSoC 2010 Administrator</p>https://www.open-bio.org/2010/03/02/bosc-2010-call-for-abstracts/Wed, 03 Mar 2010 01:19:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/03/02/bosc-2010-call-for-abstracts/<p>**Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open.**<strong>At-a-glance</strong> BOSC is an ISMB 2010 Special Interest Group (SIG) Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: <a href="https://www.open-bio.org/wiki/BOSC_2010">/wiki/BOSC_2010</a> Abstract submission via Open Conference System site:  <a href="http://events.open-bio.org/BOSC2010/openconf.php">http://events.open-bio.org/BOSC2010/openconf.php</a> E-mail: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> Bosc-announce list:  <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a> <strong>Important Dates</strong> <strong>April 15: Abstract deadline</strong> May 5:  Notification of accepted abstracts May 28: Early Registration Discount Cut-off date July 8-9:  Codefest 2010 <strong>July 9-10: BOSC 2010</strong> August 15:  Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics</p> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>We have some exciting things planned this year, including:</p> <ul> <li>Codefest 2010 programming session for the two days preceeding BOSC:  See <a href="https://www.open-bio.org/wiki/Codefest_2010">/wiki/Codefest_2010</a> for details.</li> <li>OpenBio Solution Challenge:  See session description below and <a href="https://www.open-bio.org/wiki/SolutionChallenge">/wiki/SolutionChallenge</a> for details.</li> <li>Student Travel Fellowships:  Through generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2010. Each winner will be awarded $250 to defray the costs of travel to BOSC 2010.  See <a href="https://www.open-bio.org/wiki/BOSC_2010#Student_Travel_Awards">/wiki/BOSC_2010#Student_Travel_Awards</a> for details.</li> <li>First-ever BOSC Proceedings will be published in the Open Access journal, BMC Bioinformatics.  Manuscripts will be due after BOSC on August 15.  See <a href="https://www.open-bio.org/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings">/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings</a> for details.</li> <li>Sessions on approaches to analyzing high-throughput &lsquo;omics data, cloud-based approaches to improving software and data accessibility, the semantic web in open source bioinformatics, see below:</li> </ul> <p>We invite abstracts for talks at the following sessions: <strong>OpenBio SolutionChallenge</strong> -- Bioinformatics library providers: please join us in a friendly competition to solve a shared biological problem, demonstrating the utility of your toolkit alongside other developers. Instead of the traditional Bio* updates that we&rsquo;ve had at previous conferences, this year, we&rsquo;re planning to organize these talks around a central theme: the OpenBio Solution Challenge. We start with a biological question of general interest, and the project talks will focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). Specific challenges are being discussed on the SolutionChallenge page and through the various Bio* mailing lists. Alternately, each project could highlight a challenge that they particularly do well, focusing tutorial-style on how to solve a particular problem.</p>https://www.open-bio.org/2010/01/28/openbio-solution-challenge-project-updates-at-bosc-2010/Thu, 28 Jan 2010 20:45:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/01/28/openbio-solution-challenge-project-updates-at-bosc-2010/<p>The BOSC 2010 organizing committee is hard at work getting prepared for this July&rsquo;s meeting in Boston:</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2010">/wiki/BOSC_2010</a></p> <p>One of the items we&rsquo;ve traditionally had at the conference is a project update from each of the OpenBio affiliated groups. This year, we&rsquo;re thinking about organizing these talks around a central theme: the OpenBio solution challenge. We start with a biological question of general interest, and each of the project talks would focus around how you would solve that problem using your toolkit and programming language.</p> <p>This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed).</p> <p>For this to be successful, it of course requires interest and enthusiasm from y&rsquo;all fine folks involved with the projects. Specifically:</p> <ul> <li>Is there interest from your group in participating in the challenge? You&rsquo;ll want at least a few people interesting in working on it, and someone to give a presentation at BOSC.</li> <li>Do you have suggestions on a good theme or specific biological problem to tackle? We&rsquo;ll hope to pick something in a sweet spot that is challenging enough to be of interest, yet reasonable for presentation and preparation.</li> </ul> <p>Let&rsquo;s discuss ideas and get this together. Since the schedule for BOSC is developing rapidly, please give us an idea if you&rsquo;re interested by February 12th, and copy responses to the BOSC mailing list as a central place for discussion.</p> <p><a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></p>https://www.open-bio.org/2010/01/18/bioperl-at-gmod-meeting-2010/Tue, 19 Jan 2010 03:58:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/01/18/bioperl-at-gmod-meeting-2010/<p>BioPerl developers and users attended the <a href="http://www.bioperl.org/wiki/GMOD_2010_Meeting">BioPerl satellite meeting</a> on January 13th, just prior to the <a href="http://gmod.org/wiki/January_2010_GMOD_Meeting">GMOD Meeting</a>.  Several items were covered on the agenda:</p> <ul> <li>In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB backend (i.e. Bio::DB::SeqFeature::Store or similar).  We are also contemplating adding lazy parsing for some parsers, possibly using the Bio::PullParserI methods (or similar) that Sendu Bala created.</li> <li>After a final  1.6 branch point release, we may &lsquo;freeze&rsquo; BioPerl in a maintenance mode, primarily so that we can reorganize core into several more easily installed subdistributions on a branch.  New modules will essentially be additional separate repos that will depend on BioPerl core.  This reorganization has been discussed for a few years now, and as we edge closer to starting this (probably this spring) we&rsquo;ll announce more details.</li> <li>Some initial thoughts on how to handle circular genomes more efficiently.  We essentially do this already, but it isn&rsquo;t full-proof.</li> <li>Need some significant time dedicated towards GFF3-based coding (reimplement FeatureIO but allow some flexibility).  Rob Buels had started the initial run at splitting out FeatureIO, so next step is a true reimplementation.</li> <li>We don&rsquo;t plan on including Moose support for the immediate future, feeling that it would be better to reimplement some of the classes from scratch using Moose and similar as a BioPerl 2.0, or possibly await the impending Rakudo Perl 6 alpha and start afresh using that instead of Moose.</li> </ul> <p>Anything we missed?  Anything you would like to address?  Please add comments and we&rsquo;ll discuss them on list.</p>https://www.open-bio.org/2009/12/29/bioruby-1-4-0-released/Tue, 29 Dec 2009 10:22:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/29/bioruby-1-4-0-released/<p>We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements.</p> <p><strong>PhyloXML support:</strong> Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with the National Evolutionary Synthesis Center (NESCent).</p> <p><strong>FASTQ file format support:</strong> Support for reading and writing FASTQ file format is added. All of the three FASTQ format variants are supported. The code is written by Naohisa Goto, with the help of discussions in the open-bio-l mailing list. The prototype of Bio::Fastq class was first developed during the BioHackathon 2009 held in Okinawa.</p> <p><strong>DNA chromatogram support:</strong> Support for reading DNA chromatogram files are added. SCF and ABIF file formats are supported. The code is developed by Anthony Underwood.</p> <p><strong>MEME (motif-based sequence analysis tools) support:</strong> Support for running MAST (Motif Alignment &amp; Search Tool, part of the MEME Suite, motif-based sequence analysis tools) and parsing its results are added,  developed by Adam Kraut.</p> <p><strong>Improvement of KEGG parser classes:</strong> Some new methods are added to parse new fields added to some KEGG file formats. Unit tests for KEGG parsers are also added and improved. These are contributed by Kozo Nishida.</p> <p><strong>Many sample scripts are added:</strong> Many sample scripts showing demonstrations of usages of classes are added. They were originally primitive test codes written in the &ldquo;if __FILE__ == $0&rdquo; convention.</p> <p><strong>Unit tests can test installed BioRuby:</strong> Mechanism to load library and to find test data in the unit tests are changed, and target library path and test data path can be changed with environment variables.</p> <p><strong>Incompatible change: Bio::NCBI::REST needs email address:</strong> NCBI announced that all Entrez Utilities (E-utilities)  requests must contain email and tool parameters, and requests without them will return error after June 2010. In BioRuby, to set default email address and tool name, following methods are added.</p> <ul> <li>Bio::NCBI.default_email=(email)</li> <li>Bio::NCBI.default_tool=(tool_name)</li> </ul> <p>Note that no default email address is preset in BioRuby. Library users must set their own email address or implement to get user&rsquo;s email address in some way (from input form, configuration file, etc).</p> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="http://github.com/bioruby/bioruby/blob/1.4.0/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.0.tar.gz">http://bioruby.org/archive/bioruby-1.4.0.tar.gz</a></p> <p>Gem file is also available at:  <a href="http://bioruby.org/archive/gems/bio-1.4.0.gem">http://bioruby.org/archive/gems/bio-1.4.0.gem</a></p> <p>We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search &ndash;remote bio and find &ldquo;bio (1.4.0)&rdquo; in the list. Then, % sudo gem install bio</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2009/12/18/bosc-2010-request-for-input/Sat, 19 Dec 2009 01:39:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/18/bosc-2010-request-for-input/<p>BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010.  The BOSC 2010 web site can be accessed here:  <a href="https://www.open-bio.org/wiki/BOSC_2010">/wiki/BOSC_2010</a>.</p> <p>The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community.  You may send your suggestions to the <a href="mailto:bosc@open-bio.org" title="mailto:bosc@open-bio.org">bosc@open-bio.org</a> e-mail address  or add suggestions to the BOSC 2010 talk/discussion wiki page at: <a href="https://www.open-bio.org/wiki/Talk:BOSC_2010.%A0">/wiki/Talk:BOSC_2010.</a> Please respond to any or all of the questions below:</p> <p>1.  For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions.  Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:</p> <ul> <li><strong>Tutorials</strong> where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier.  <strong>Would you be willing to organize/lead such a session for your project?</strong></li> <li><strong>Discussion</strong> following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The &ldquo;speaker&rdquo; would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them.  <strong>Would you be willing to organize/lead such a session for your project?</strong></li> <li><strong>Mini-hackathon</strong> either before, during, or after the 2-day BOSC.  The subject of the hackathon would need to be organized by the individual project leaders/teams.  Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal.  <strong>Would you be willing to organize/lead this type of session?</strong></li> <li>Organizing/creating a <strong>LiveCD</strong> or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community.  <strong>Would you be willing to organize/lead this type of session?</strong></li> <li>What <strong>session topics</strong> would you like to see represented for traditional talks?</li> <li>Who would you like to hear as a <strong>keynote speaker</strong>?</li> </ul> <p>2.  The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC.  If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000?  We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.</p> <p>3.  Call for <strong>volunteers</strong>.  Organizing tutorial/hackathons and such will only be possible if individuals step forward to lead these sessions.  Please let us know if you would be willing to serve in any capacity.  We also need volunteers to review abstracts for the more &ldquo;traditional&rdquo; sessions, please let us know if you are willing to do this as well.</p> <p><strong>Timeline:</strong> We are planning on putting out the Call for Abstracts in mid-January.  To be on track, we would like to receive your input by <strong>Friday, January 8</strong>.  If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.</p> <p>Thanks and Happy Holidays!</p> <p>Kam Dahlquist Chair, BOSC 2010 on behalf of the BOSC 2010 Organizing committee: Brad Chapman, Michael Heur, Darin London, Anton Nekrutenko, Steffen Moeller, Jim Procter And the O|B|F Board: Chris Dagdigian, Nomi Harris, Hilmar Lapp, Jason Stajich</p>https://www.open-bio.org/2009/12/17/nar-fastq-format/Thu, 17 Dec 2009 16:28:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/17/nar-fastq-format/<p>I&rsquo;m delighted to announce an open access publication in <em>Nucleic Acids Research</em> describing the FASTQ file format based on the conventions agreed by the OBF projects:</p> <blockquote> <p><a href="http://dx.doi.org/10.1093/nar/gkp1137">The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants</a> Peter J. A. Cock ( <a href="http://www.biopython.org">Biopython</a>), Christopher J. Fields ( <a href="http://www.bioperl.org">BioPerl</a>), Naohisa Goto ( <a href="http://www.bioruby.org">BioRuby</a>), Michael L. Heuer ( <a href="http://www.biojava.org">BioJava</a>) and Peter M. Rice ( <a href="http://emboss.sourceforge.net/">EMBOSS</a>). Nucleic Acids Research, <a href="http://dx.doi.org/10.1093/nar/gkp1137">doi:10.1093/nar/gkp1137</a></p> </blockquote> <p>This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.</p>https://www.open-bio.org/2009/12/15/biopython-release-153/Tue, 15 Dec 2009 16:57:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/15/biopython-release-153/<p>We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of <a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a>. This is our first release since <a href="http://news.open-bio.org/news/2009/09/biopython-cvs-to-git-migration/">migrating from CVS to git</a> for source code control.</p> <p>There have been some additions to our core objects - the <a href="http://biopython.org/wiki/Seq">Seq</a> (and related UnknownSeq) objects gained upper and lower methods (like the string methods of the same name but alphabet aware) plus a new ungap method. The SeqFeature object now has an extract method to get the region of sequence it describes (useful for getting CDS nucleotide sequences from GenBank files). Also <a href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> objects now support addition, giving a new SeqRecord with the combined sequence, all the SeqFeatures, and any common annotation.</p> <p>SQLite support (built into Python 2.5+) was added to our <a href="http://biopython.org/wiki/BioSQL">BioSQL interface</a> (Brad Chapman). This is still a little experimental as we are using a draft BioSQL SQLite schema, but this should be merged into the next <a href="http://www.biosql.org">BioSQL</a> release.</p> <p>Biopython now includes wrappers for the new NCBI BLAST C++ tools, which will be replacing the old NCBI &ldquo;legacy&rdquo; BLAST tools written in C. The plain text BLAST parser has been updated to cope as well. Nevertheless, we (and the NCBI) still recommend using the XML output for parsing.</p> <p>Bio.Entrez includes the <a href="http://www.nlm.nih.gov/bsd/licensee/announce/2009.html#d09_17">new (Jan 2010) DTD files</a> from the NCBI for parsing MedLine/PubMed data.</p> <p>The NCBI codon tables have been updated from version 3.4 to 3.9, which adds a few extra start codons, and a few new tables (Tables 16, 21, 22 and 23).</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the Nov 2009 release of <a href="http://rebase.neb.com/rebase/rebase.html">REBASE</a>.</p> <p>The Bio.PDB parser and output code has been updated to understand the element column in ATOM and HETATM lines (based on patches contributed by Hongbo Zhu and Frederik Gwinner), and Bio.PDB.PDBList has been updated for recent changes to the PDB FTP site (Paul T. Bathen).</p> <p>Finally, support for running Biopython under <a href="http://www.jython.org">Jython</a> (using the Java Virtual Machine) has been much improved (with input from Kyle Ellrott). Note that Jython does not support C code, and currently Jython does not parse DTD files ( <a href="http://bugs.jython.org/issue1447">Jython Issue 1447</a>; needed for the Bio.Entrez XML parser). However, most of the Biopython modules seem fine from testing with Jython 2.5.0 and 2.5.1.</p> <p>Sources and Windows Installers are available from our <a href="http://www.biopython.org/wiki/Download">downloads</a> page.</p> <p>Thanks to the Biopython development team and to everyone who has reported bugs or contributed patches since our last release.</p> <p>(At least) 12 people contributed to this release, including 3 first timers:</p> <ul> <li>Bartek Wilczynski</li> <li>Brad Chapman</li> <li>Chris Lasher</li> <li>Cymon Cox</li> <li>Frank Kauff</li> <li>Frederik Gwinner (first contribution)</li> <li>Hongbo Zhu (first contribution)</li> <li>Kyle Ellrott</li> <li>Leighton Pritchard</li> <li>Michiel de Hoon</li> <li>Paul Bathen (first contribution)</li> <li>Peter Cock</li> </ul>https://www.open-bio.org/2009/12/14/2009-obf-bod-meeting/Mon, 14 Dec 2009 19:24:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/14/2009-obf-bod-meeting/<p>The official 2009 Board of Directors meeting is taking place today, Monday Dec 14, at 4pm EST (21:00 UTC) via teleconference. If you are an O|B|F member, you will have received the announcement and dial-in information earlier.</p> <p>O|B|F Board of Director meetings are public - anyone interested in O|B|F business can participate, which is one reason we are holding the meeting over teleconference. The dial-in number is +1-518-825-1400, participant code 279610.</p> <p>All you need to participate is a telephone (this is a US toll number, and if you are located international or outside of the area code, pertinent charges from your phone carrier will apply). Or use SkypeOut, which costs a few cents per minute from many locations (check SkypeOut rates).</p> <p>The <a href="https://www.open-bio.org/wiki/Minutes:2009_ConfCall">agenda for the meeting</a> is on the OBF wiki (and minutes will be posted there later).</p>https://www.open-bio.org/2009/12/14/interleaving-paired-fastq-files-with-biopython/Mon, 14 Dec 2009 14:03:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/14/interleaving-paired-fastq-files-with-biopython/<p>This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython&rsquo;s <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> module (see also <a href="http://news.open-bio.org/news/2009/09/biopython-convert-function/">FASTQ conversions</a> &amp; <a href="http://news.open-bio.org/news/2009/09/biopython-fast-fastq/">speeding up FASTQ</a>).</p> <p>There are two main ways of presenting paired end data in FASTA or FASTQ files:</p> <ul> <li>Paired files, with matching entries for the forward and reverse reads (probably the norm with Illumina data)</li> <li>Single files, with alternating entries for the forward and reverse reads (used by Velvet)</li> </ul> <p>Converting between these two is a relatively common operation, and is normally pretty easy. There was a <a href="http://lists.open-bio.org/pipermail/biopython/2009-September/005584.html">short example</a> of how you might do this in Biopython on a recent (September 2009) Velvet users/Biopython mailing list discussion. That script didn&rsquo;t check the record IDs matched up (but neither does the Perl script shuffleSequences_fastq.pl included with Velvet for this task).</p> <p>It would be safer to check the record IDs do match. However, there are several different naming schemes for reads, most typically suffixes of <code>/1</code> and <code>/2</code>, but also things like <code>.f</code> and <code>.r</code> get used. In the case of FASTQ files from the NCBI SRA, the reads have no suffixes, so to feed those into Velvet you may want to check they are equal and then add a suffix as shown below.</p> <p><code> </code></p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-gdscript3" data-lang="gdscript3"><span style="display:flex;"><span><span style="color:#75715e">#This Python script requires Biopython 1.51 or later</span> </span></span><span style="display:flex;"><span>from Bio import SeqIO </span></span><span style="display:flex;"><span>import itertools </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span><span style="color:#75715e">#Setup variables (could parse command line args instead)</span> </span></span><span style="display:flex;"><span>file_f <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;SRR001666_1.fastq&#34;</span> </span></span><span style="display:flex;"><span>file_r <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;SRR001666_2.fastq&#34;</span> </span></span><span style="display:flex;"><span>file_out <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;SRR001666_interleaved.fastq&#34;</span> </span></span><span style="display:flex;"><span>format <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;fastq&#34;</span> <span style="color:#75715e">#or &#34;fastq-illumina&#34;, or &#34;fasta&#34;, or ...</span> </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span><span style="color:#66d9ef">def</span> <span style="color:#a6e22e">interleave</span>(iter1, iter2) : </span></span><span style="display:flex;"><span> <span style="color:#66d9ef">for</span> (forward, reverse) <span style="color:#f92672">in</span> itertools<span style="color:#f92672">.</span>izip(iter1,iter2): </span></span><span style="display:flex;"><span> assert forward<span style="color:#f92672">.</span>id <span style="color:#f92672">==</span> reverse<span style="color:#f92672">.</span>id </span></span><span style="display:flex;"><span> forward<span style="color:#f92672">.</span>id <span style="color:#f92672">+=</span> <span style="color:#e6db74">&#34;/1&#34;</span> </span></span><span style="display:flex;"><span> reverse<span style="color:#f92672">.</span>id <span style="color:#f92672">+=</span> <span style="color:#e6db74">&#34;/2&#34;</span> </span></span><span style="display:flex;"><span> yield forward </span></span><span style="display:flex;"><span> yield reverse </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>records_f <span style="color:#f92672">=</span> SeqIO<span style="color:#f92672">.</span>parse(open(file_f,<span style="color:#e6db74">&#34;rU&#34;</span>), format) </span></span><span style="display:flex;"><span>records_r <span style="color:#f92672">=</span> SeqIO<span style="color:#f92672">.</span>parse(open(file_r,<span style="color:#e6db74">&#34;rU&#34;</span>), format) </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>handle <span style="color:#f92672">=</span> open(file_out, <span style="color:#e6db74">&#34;w&#34;</span>) </span></span><span style="display:flex;"><span>count <span style="color:#f92672">=</span> SeqIO<span style="color:#f92672">.</span>write(interleave(records_f, records_r), handle, format) </span></span><span style="display:flex;"><span>handle<span style="color:#f92672">.</span>close() </span></span><span style="display:flex;"><span>print <span style="color:#e6db74">&#34;</span><span style="color:#e6db74">%i</span><span style="color:#e6db74"> records written to </span><span style="color:#e6db74">%s</span><span style="color:#e6db74">&#34;</span> <span style="color:#f92672">%</span> (count, file_out) </span></span></code></pre></div><p>This example uses the <a href="http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&amp;m=data&amp;s=viewer&amp;run=SRR001666">SRR001666</a> files from the <a href="ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX000/SRX000430/">NCBI SRA FTP site</a>.</p> <p>Now that works fine, and just by changing the filenames and the format name this could be used on FASTA data (or another supported file format). The bad news is it took 14 minutes to produce a 2GB FASTQ. However, going a little more low-level <a href="http://news.open-bio.org/news/2009/09/biopython-fast-fastq/">as discussed before</a> can really pay off. This FASTQ-only version takes just 2 minutes:</p> <p><code> </code></p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-gdscript3" data-lang="gdscript3"><span style="display:flex;"><span><span style="color:#75715e">#This Python script requires Biopython 1.51 or later</span> </span></span><span style="display:flex;"><span>from Bio<span style="color:#f92672">.</span>SeqIO<span style="color:#f92672">.</span>QualityIO import FastqGeneralIterator </span></span><span style="display:flex;"><span>import itertools </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span><span style="color:#75715e">#Setup variables (could parse command line args instead)</span> </span></span><span style="display:flex;"><span>file_f <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;SRR001666_1.fastq&#34;</span> </span></span><span style="display:flex;"><span>file_r <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;SRR001666_2.fastq&#34;</span> </span></span><span style="display:flex;"><span>file_out <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;SRR001666_interleaved.fastq&#34;</span> </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>handle <span style="color:#f92672">=</span> open(file_out, <span style="color:#e6db74">&#34;w&#34;</span>) </span></span><span style="display:flex;"><span>count <span style="color:#f92672">=</span> <span style="color:#ae81ff">0</span> </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>f_iter <span style="color:#f92672">=</span> FastqGeneralIterator(open(file_f,<span style="color:#e6db74">&#34;rU&#34;</span>)) </span></span><span style="display:flex;"><span>r_iter <span style="color:#f92672">=</span> FastqGeneralIterator(open(file_r,<span style="color:#e6db74">&#34;rU&#34;</span>)) </span></span><span style="display:flex;"><span><span style="color:#66d9ef">for</span> (f_id, f_seq, f_q), (r_id, r_seq, r_q) </span></span><span style="display:flex;"><span><span style="color:#f92672">in</span> itertools<span style="color:#f92672">.</span>izip(f_iter,r_iter): </span></span><span style="display:flex;"><span> assert f_id <span style="color:#f92672">==</span> r_id </span></span><span style="display:flex;"><span> count <span style="color:#f92672">+=</span> <span style="color:#ae81ff">2</span> </span></span><span style="display:flex;"><span> <span style="color:#75715e">#Write out both reads with &#34;/1&#34; and &#34;/2&#34; suffix on ID</span> </span></span><span style="display:flex;"><span> handle<span style="color:#f92672">.</span>write(<span style="color:#e6db74">&#34;@</span><span style="color:#e6db74">%s</span><span style="color:#e6db74">/1n</span><span style="color:#e6db74">%s</span><span style="color:#e6db74">n+n</span><span style="color:#e6db74">%s</span><span style="color:#e6db74">n@</span><span style="color:#e6db74">%s</span><span style="color:#e6db74">/2n</span><span style="color:#e6db74">%s</span><span style="color:#e6db74">n+n</span><span style="color:#e6db74">%s</span><span style="color:#e6db74">n&#34;</span> </span></span><span style="display:flex;"><span> <span style="color:#f92672">%</span> (f_id, f_seq, f_q, r_id, r_seq, r_q)) </span></span><span style="display:flex;"><span>handle<span style="color:#f92672">.</span>close() </span></span><span style="display:flex;"><span>print <span style="color:#e6db74">&#34;</span><span style="color:#e6db74">%i</span><span style="color:#e6db74"> records written to </span><span style="color:#e6db74">%s</span><span style="color:#e6db74">&#34;</span> <span style="color:#f92672">%</span> (count, file_out) </span></span></code></pre></div><p>You can make this a little faster still by missing out most of the validation done by the Biopython FASTQ parser - but personally I wouldn&rsquo;t take that risk. I&rsquo;d much rather know about any errors in the data.</p> <p>Peter</p> <p>P.S.</p> <p>Things get more interesting if you want to do quality filtering or trimming. If only one of a pair passes the quality assurance step, then you may want to keep it and treat it as an unpaired read. To give such cleaned up data to Velvet, you would need one file of alternating paired end reads, and a separate file of the orphaned effectively unpaired reads. That deserves another post going into more detail&hellip;</p>https://www.open-bio.org/2009/12/14/minutes2009-confcall/Mon, 14 Dec 2009 05:19:14 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/14/minutes2009-confcall/<h3 id="agenda">Agenda</h3> <ol> <li>Old business <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2008_ConfCall">2008 BoD meeting minutes</a></li> </ul> </li> <li>New business <ol> <li>BOSC <ul> <li>BOSC 2009 (Kam) <ul> <li>Money spent/made attendee number, any other feedback</li> </ul> </li> <li>BOSC 2010 - held with ISMB2010 in Boston, MA, USA</li> </ul> </li> <li>Treasurer&rsquo;s 2009 report (ChrisD) <ul> <li><a href="https://www.open-bio.org/wiki/Minutes:2009_Financial_report">2009 Financial report</a></li> </ul> </li> <li>BoD membership and succession. <ul> <li>Nomination of Nomi Harris for election to the BoD</li> <li>Need plan to elect new BoD members and rotate officers.</li> </ul> </li> <li>OBF Hardware &amp; Sysadmin report (JasonS and ChrisD) <ul> <li>Domain names currently registered, upcoming expirations, newly purchased names</li> <li>Proposal to purchase new hardware - <a href="https://www.open-bio.org/wiki/2009_hardware_purchase_proposal">2009 hardware purchase proposal</a></li> <li>Proposal to purchase box for upstream SPAM filtering</li> <li>System Administration status &amp; coverage report (who, what, issues, future)</li> <li>Consider possibility of moving code mirroring to public (code.google.com; etc) mailling lists to googlegroups?</li> </ul> </li> <li>Hackathons 2010 (Tokyo hackathon in Feb 2010) will involve some OBF projects/developers</li> <li>Additional topics proposed by community</li> </ol> </li> </ol> <h3 id="minutes-from-the-meeting">Minutes from the meeting</h3> <p><strong>Venue:</strong> held by conference call, scheduled for 4pm EST (21:00 UTC).</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Kam Dahlquist, Jason Stajich, Chris Dagdigian, Hilmar Lapp</li> <li>Directors nominee: Nomi Harris</li> <li>Guests: Darin London, Scott Markel, Peter Cock (joined later)</li> </ul> <p><strong>Minutes:</strong></p> <h4 id="hilmar-calls-meeting-to-order-at-404pm-est">Hilmar calls meeting to order at 4.04pm EST.</h4> <ul> <li>Approval of previous meeting minutes. <ul> <li>Hilmar moves to approve, Kam, Jason, and Chris second. 2008 minutes approved by unanimous consent.</li> </ul> </li> </ul> <h4 id="bosc-2009">BOSC 2009:</h4> <ul> <li>97 registrants</li> <li>have spreadsheet on accounting from Stephen Leard, only one keynote speaker is showing, needs to be investigated and possibly fixed</li> <li>Currently the balance of the escrow account is $12,553. This hasn&rsquo;t changed very much over the years. <ul> <li>Need to further digest the accounting spreadsheet to figure out the exact surplus amount for BOSC 2009.</li> </ul> </li> <li>Our registrant count has held relatively steady.</li> </ul> <h4 id="bosc-2010">BOSC 2010:</h4> <ul> <li>The full proposal is waived for SIGs in good standing (which we are). <ul> <li>Instead a letter of intent is required, which Kam submitted in time. We should hear back from the SIG committee on Dec 18.</li> <li>Kam is contacting 2009 committee members. Two have so far responded positively.</li> </ul> </li> <li>We will be using the Open Conference System again for 2010. Call for abstracts is targeted to go out after the holiday break in January.</li> <li>Received a generous sponsorship from Eagle Genomics that would support keynote speaker expenses and student travel fellowships.</li> <li>Signed an agreement for Proceedings in BMC Bioinformatics for the 2009 conference, which we ended up not pursuing. Planning to revive this though and pursue this in earnest for the 2010 conference. <ul> <li>Would anticipate up to 20 papers of 4-5 pages each. Quote that we received from BMC amounts to around 500GBP in page charges per paper.</li> <li>Should talk with the folks of the BioLINK SIG, specifically Lynette Hirschman. They planned to organize a proceedings for 2009 in Lecture Notes for Bioinformatics.</li> </ul> </li> <li>In terms of publicity, could aim for a published meeting report (e.g., Briefings in Bioinformatics, or even a more scholarly journal).</li> <li>Press release could also be effective to generate more publicity. Nomi has done this before and offers to help.</li> <li>Chris offers to help with organization as a local. Are there plans to expand the conference agenda? <ul> <li>We did not have any free time at the end of the days really. The plan is to pretty much go with the same outline of the conference as last year.</li> <li>Still very open to hear suggestions for how to expand or change the meeting outline.</li> <li>Could consider sponsoring a mini-hackathon, where we can sponsor travel (airfare? or hotel?) out of BOSC escrow funds. This seems like a really good idea and make the trip worth for more people. <ul> <li>Brad Chapman (Biopython) is local (to BOSC 2010) and indicated earlier that he would be willing to help with this and may be in a position to take a lead on finding rooms.</li> <li>ACTION: Kam will look into policies governing what we can sponsor from the escrow account.</li> <li>ACTION: Kam will contact project leaders and see whether possible leaders self-emerge that would be willing to organize all this.</li> </ul> </li> </ul> </li> <li>Can we make an agreement with ISMB to fix a ceiling for the escrow amount, and pay out to us funds above that. <ul> <li>Need to review the agreements that govern this currently. Not even clear whether we are allowed to move money out. Kam will look into this.</li> </ul> </li> </ul> <h4 id="2009-financial-report">2009 Financial Report</h4> <ul> <li>Chris presents 2009 Financial Report. We have about $31k in funds sitting in the bank.</li> <li>The 2009 donation is not yet deposited. ACTION: Chris will deposit by the end of the 2009 calendar year.</li> <li>Travel reimbursements for BOSC 2009 organizers have not been made, and have not been requested. <ul> <li>The principle (discussed at an earlier Board meeting) is to assume the organizers&rsquo; sponsoring organizations will sponsor their BOSC attendance. If not, they should request sponsorship from OBF.</li> </ul> </li> <li>Hilmar moves to approve the 2009 Financial Report. Kam and Jason second, approved by unanimous consent.</li> </ul> <h4 id="board-of-directors-membership">Board of Directors membership</h4> <ul> <li>On behalf of the Nominating Committee, Hilmar nominates Nomi Harris for election to the Board of Directors. <ul> <li>Nomi introduces herself. She has been in Bioinformatics since 1986, worked in a variety of well-known large genome informatics projects, on the ISMB organizing committee once, and many times on the BOSC committee. Would like to promote open-source, and help extend what OBF does to reach out into the larger bioinformatics community, help foster collaboration, help OBF be a more central part of the evolution of bioinformatics as a field. She is also particularly interested in medical informatics, and how to bring that into the OBF community. Is interested in social mechanisms to encourage and incentivize open-source development and contribution.</li> <li>Held secret vote on election. Results: 4/4 votes for, 0/4 votes against, and 0/4 votes abstain. Nomi Harris is elected to the O|B|F Board of Directors.</li> </ul> </li> <li>Jason presents the question of needing a timeline for rotation of officers, and to get new members onto the BoD. <ul> <li>Successful recruiting should be improved on by identifying people who we want on the BoD and the approach those people.</li> <li>Could be more active on this at the BOSC-located BoD business meetings.</li> <li>The Nominating Committee should ask project leaders for suggestions, and whether they would be willing to serve.</li> <li>Should also look beyond our own member projects to identify people who advocate and promote open-source, specifically in bioinformatics.</li> <li>Should we plan and hold a Board meeting that is specifically for BoD membership. In the same vein, ask member projects what they need from the OBF as an umbrella that is currently not provided.</li> <li>Could integrate this into the BOSC agenda as a panel discussion with OBF directors as the panel members.</li> <li>Could try to connect with organizations and people who use open-source in teaching, and teach open-source reusing and contributing. Kam has identified contacts. Should we also connect with the ISMB Student Council. <ul> <li>Having distributed open-source project contribution on the CV is valuable.</li> <li>Should try to get into the Google Summer of Code program again in 2010. Hilmar is very interested in orchestrating that, but will need help in advertising, publicizing, and recruiting mentors.</li> <li>Should we also have something less formal, simply encouraging mentorship. OBF as the umbrella could use some its funds to reward the most prolific contributors in different areas.</li> </ul> </li> <li>In general, we need to embrace more the social aspects of recruiting new members.</li> </ul> </li> <li>Jason would like to be able to rotate off the President position in 2010. Chris is happy to continue serving. Hilmar is happy to continue serving in his current capacity, too. Kam is willing to serve as an officer, but is not comfortable serving as president yet.</li> </ul> <h4 id="obf-hardware-and-domain-name-assets">OBF hardware and domain name assets</h4> <ul> <li>Part of our identity is still owning the code repository and support infrastructure for open-source development. Going forward though, the volunteer manpower seems insufficient to sustain the required maintenance burden.</li> <li>Is hosting the infrastructure ourselves still the best way to invest our resources? Would moving mailing lists and wikis to other hosts (such as SourceForge, Google Code &amp; Groups) be the better direction?</li> <li>Our hardware is donated and old. They are difficult to distribute administrative control over.</li> <li>If restructuring our hardware, the goal would be virtualization, based on current, upgraded, 64bit hardware.</li> <li>Spam moderation on OBF mailing lists is highly insufficient, yet still consumes a major amount of volunteer time. <ul> <li>BioTeam has been using an out-sourced solution for spam-detection and deflection that Chris reports to have been highly effective for BioTeam.</li> </ul> </li> <li>How could projects become OBF-affiliated when they have hosting etc already in place, externally to OBF-controlled hardware? <ul> <li>The OBF infrastructure was not designed for being able to add projects as easily as possible. Instead we have focused on projects that seemed to have sufficient critical mass behind them to withstand the test of time.</li> <li>Our biggest asset is the community. Our mailing lists and wikis are branded, and it is important to keep that. How transparent can these be sourced out?</li> </ul> </li> <li>There are some bad experiences over time with some of the most prominent providers of open-source development infrastructure. Would need to see a lot more data and experience on envisioned hosting provider candidates.</li> <li>For Biopython, having website and branding available under the OBF infrastructure is really valuable.</li> <li>The intent here isn&rsquo;t really to move away from having our own hardware, but to advocate why we have it, and that it takes effort to maintain and administer it. <ul> <li>Some of the member projects run some of their stuff externally, which can give an odd impression.</li> <li>ACTION: Jason and Chris to articulate and publicize this among member projects. Identify and delegate training of new root admin volunteers.</li> </ul> </li> <li>No actual decision on the hardware purchase proposal made. We first need to hear more input from our member projects, and some evidence for how the necessary system administration resources will be provided through volunteers and continued training.</li> </ul> <p>Meeting is adjourned at 6.12pm EST.</p> <h3 id="project-reports-filed">Project reports filed</h3> <p>Any reports that need to be recorded for 2009 can be lined here. Summary of O|B|F supported projects: projects are active(?), need more support (?), have had releases(?)</p> <ul> <li>BioPerl <ul> <li>1.6.0 released in Jan 2009, 1.6.1 released Nov 2009</li> </ul> </li> <li>BioJava</li> <li>BioPython <ul> <li>Biopython 1.50 released Apr 2009, 1.51 released Aug 2009, 1.52 released Sep 2009</li> </ul> </li> <li>BioSQL</li> <li>BioMOBY</li> <li>BioDAS</li> <li>EMBOSS</li> <li>BioRuby?</li> <li>BioLib?</li> </ul>https://www.open-bio.org/2009/11/22/bioperl-interview-for-floss-weekly/Sun, 22 Nov 2009 20:27:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/11/22/bioperl-interview-for-floss-weekly/<p>Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.  The interview is now available <a href="http://www.podtrac.com/pts/redirect.mp3/twit.cachefly.net/floss0096.mp3">as an MP3</a> on the <a href="http://twit.tv/floss96">FLOSS Weekly</a> website; several streaming versions (including podcast) are also available.</p>https://www.open-bio.org/2009/10/10/bioperl-core-1-6-1-ppm-available/Sat, 10 Oct 2009 05:18:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/10/10/bioperl-core-1-6-1-ppm-available/<p>BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the <a href="http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows">BioPerl wiki</a>. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.</p>https://www.open-bio.org/2009/10/01/first-alphas-of-bioperl-run-bioperl-db-bioperl-network/Thu, 01 Oct 2009 16:40:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/10/01/first-alphas-of-bioperl-run-bioperl-db-bioperl-network/<p>Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN:</p> <ul> <li><a href="http://search.cpan.org/~cjfields/BioPerl-Run-1.6.1_001/">BioPerl-Run</a></li> <li><a href="http://search.cpan.org/~cjfields/BioPerl-DB-1.6.0_001/">BioPerl-DB</a></li> <li><a href="http://search.cpan.org/~cjfields/BioPerl-Network-1.6.0_001/">BioPerl-Network</a></li> </ul> <p>They can also be downloaded from the BioPerl website:</p> <p><a href="http://bioperl.org/DIST/RC/">http://bioperl.org/DIST/RC/</a></p> <p>This is the first run where we&rsquo;ve switched to a regular Module::Build installation, so expect some initial bumps! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). The other, more serious one, is that the Build.PL script checks for DBI but isn&rsquo;t checking for any compatible DBD::* adaptors for BioPerl-DB (so it fails tests if DBI is installed). We have code in core to check for DBI drivers, so I may adapt that for BioPerl-DB.</p> <p>Enjoy!</p> <p>chris</p>https://www.open-bio.org/2009/09/29/bioperl-1-6-1-released/Tue, 29 Sep 2009 17:55:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/29/bioperl-1-6-1-released/<p>We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl&rsquo;s core code. You can grab it here:</p> <p>Via CPAN:</p> <p><a href="http://search.cpan.org/~cjfields/BioPerl-1.6.1/">http://search.cpan.org/~cjfields/BioPerl-1.6.1/</a></p> <p>Via the BioPerl website:</p> <p><a href="http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2">http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2</a> <a href="http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz">http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz</a> <a href="http://bioperl.org/DIST/BioPerl-1.6.1.zip">http://bioperl.org/DIST/BioPerl-1.6.1.zip</a></p> <p>The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).</p> <p>Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the &lsquo;Changes&rsquo; file included with the distribution.</p> <p>A few highlights:</p> <ul> <li>FASTQ parsing and interconversion of the three FASTQ variants (Sanger, Illumina, Solexa) now works (a concerted OBF effort!)</li> <li>Significant refactoring of Bio::Restriction methods</li> <li>Complete refactoring of Bio::Search-related tiling code, including HOWTO documentation</li> <li>GBrowse-related fixes:</li> <li>- <em>berkeleydb database now autoindexes wig files and locks correctly</em></li> <li>- <em>add Pg, SQLite, and faster BerkeleyDB implementations</em></li> <li>Infernal 1.0 output is now parsed</li> <li>New SearchIO-based parser for gmap -f9 output</li> <li>BLAST XML parsing essentially complete</li> <li>Installation via CPANPLUS should now work</li> <li>For those using Strawberry Perl on Windows, the latest build is expected to pass all tests.</li> <li>&lsquo;raw&rsquo; sequence format now parsed by line or optionally as a single sequence</li> <li>SCF parsing/writing now round-trips</li> <li>Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast</li> <li>Bio::Tools::SeqPattern now has a backtranslate() method</li> <li>Bio::Tree::Statistics now has methods to calculate Fitch-based score, internal trait values, statratio(), sum of leaf distances</li> <li>Scripts</li> <li><em>- update to bp_seqfeature_load for SQLite</em></li> <li><em>- hivq.pl - commmand-line interface to Bio::DB::HIV</em></li> <li><em>- fastam9_to_table - fix for MPI output</em></li> <li><em>- gccalc - total stats</em></li> <li><em>- einfo - simple script to find up-to-date NCBI databases, list field and link values for a specific database</em></li> </ul> <p>We will shortly release updates for BioPerl-db, BioPerl-run, and BioPerl-network. Enjoy!</p> <p>chris</p>https://www.open-bio.org/2009/09/25/biopython-fast-fastq/Fri, 25 Sep 2009 11:49:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/25/biopython-fast-fastq/<p><a href="http://news.open-bio.org/news/2009/08/biopython-1-51-released/">Biopython 1.51</a> onward includes support for Sanger, Solexa and Illumina 1.3+ FASTQ files in <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a>, which allows a lot of neat tricks very concisely. For example, the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">tutorial</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>) has examples finding and removing primer or adaptor sequences.</p> <p>However, because the Bio.SeqIO interface revolves around <a href="http://biopython.org/wiki/SeqRecord">SeqRecord objects</a> there is often a speed penalty. For example for <a href="http://en.wikipedia.org/wiki/FASTQ_format">FASTQ files</a>, the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing.</p> <p>The new <a href="http://news.open-bio.org/news/2009/09/biopython-convert-function/">Bio.SeqIO.convert(&hellip;)</a> function in <a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a> onwards makes converting from FASTQ to FASTA, or between the FASTQ variants about five times faster. It can do this because it doesn&rsquo;t bother with creating any objects - it just uses Python strings.</p> <p>You can use the same approach in your own scripts. For example, suppose you have a Solexa FASTQ file where you want to trim all the reads, taking just the first 21 bases (say). Why might you want to do this? Well, in Solexa/Illumina there is a general decline in read quality along the sequence, so it can make sense to trim, and some algorithms like to have all the input reads the same length. Here is how I would write this using the standard Bio.SeqIO functions:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>from Bio import SeqIO </span></span><span style="display:flex;"><span>records = (rec[:21] for rec in SeqIO.parse(open(&#34;untrimmed.fastq&#34;), &#34;fastq-solexa&#34;)) </span></span><span style="display:flex;"><span>handle = open(&#34;trimmed21.fastq&#34;, &#34;w&#34;) </span></span><span style="display:flex;"><span>count = SeqIO.write(records, handle, &#34;fastq-solexa&#34;) </span></span><span style="display:flex;"><span>handle.close() </span></span><span style="display:flex;"><span>print &#34;Trimmed %i FASTQ records&#34; % count </span></span></code></pre></div><p>This works, and is very simple and general. The same template can be used on any file formats supported by <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a>. However, it might be a bit slow for large next generation sequence files.</p> <p>Instead, we can get a little more low level - and work directly with strings. This requires you to know more about the details of the FASTQ file format. Parsing FASTQ files is surprising complicated (with nasty things like line wrapping technically allowed), so we&rsquo;ll still get Biopython to do that bit - but not bother with constructing SeqRecord objects and decoding the FASTQ quality strings. On the other hand, doing the FASTQ output explicitly isn&rsquo;t actually too bad once you know how things work:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>from Bio.SeqIO.QualityIO import FastqGeneralIterator </span></span><span style="display:flex;"><span>trim = 21 </span></span><span style="display:flex;"><span>handle = open(&#34;trimmed21.fastq&#34;, &#34;w&#34;) </span></span><span style="display:flex;"><span>for title, seq, qual in FastqGeneralIterator(open(&#34;untrimmed.fastq&#34;)) : </span></span><span style="display:flex;"><span>    handle.write(&#34;@%sn%sn+n%sn&#34; % (title, seq[:trim], qual[:trim])) </span></span><span style="display:flex;"><span>handle.close() </span></span></code></pre></div><p>Again, the solution is a very short script - but this time it is much less flexible, and not nearly as clear what is going on. On the bright side, it is many times faster. Deciding on this trade-off is down to you, but I hope this blog post has highlighted the potential usefulness of the FastqGeneralIterator function in Bio.SeqIO.QualityIO, which you might otherwise have overlooked. To find out more, please read the built in documentation (also available <a href="http://biopython.org/DIST/docs/api/Bio.SeqIO.QualityIO-module.html#FastqGeneralIterator" title="Documentation for Bio.SeqIO.QualityIO function FastqGeneralIterator">online</a>):</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>from Bio.SeqIO.QualityIO import FastqGeneralIterator </span></span><span style="display:flex;"><span>&gt;&gt;&gt; help(FastqGeneralIterator) </span></span><span style="display:flex;"><span>... </span></span></code></pre></div><p>Please sign up to the <a href="http://biopython.org/wiki/Mailing_lists">Biopython mailing list</a> if you want to discuss this topic further.</p> <p>Peter</p> <p><em>Update</em>: A similar parser for FASTA files for looping over the records as strings was added in Biopython 1.61,</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>&gt;&gt;&gt; from Bio.SeqIO.FastaIO import SimpleFastaParser </span></span><span style="display:flex;"><span>&gt;&gt;&gt; help(SimpleFastaParser) </span></span><span style="display:flex;"><span>... </span></span></code></pre></div>https://www.open-bio.org/2009/09/24/biopython-cvs-to-git-migration/Thu, 24 Sep 2009 13:00:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/24/biopython-cvs-to-git-migration/<p>The release of <a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a> earlier this week marked the end of an era, it was our last release using CVS for source code control.</p> <p>As of now, Biopython is using a <a href="http://github.com/biopython/biopython" title="Biopython on github">git repository</a>, hosted on <a href="http://github.com">github.com</a> who kindly provide git hosting for open source projects free of charge. The <a href="http://bioruby.org">BioRuby project</a> have been <a href="http://github.com/bioruby/bioruby" title="BioRuby on github">using github</a> for some time, so we are in good company.</p> <p>Our existing OBF hosted CVS repository will be maintained in the short to medium term as a backup, but will not be updated.</p> <p>Although many people have been involved in this move, we&rsquo;d like to thank Bartek Wilczynski in particular for handling the CVS to git conversion, and the mirroring our CVS updates to git during the transition period. In the next few weeks hopefully we&rsquo;ll get our <a href="http://biopython.org/wiki/GitUsage">git usage wiki pages</a> perfected, as we start using git for real.</p>https://www.open-bio.org/2009/09/22/biopython-release-152/Tue, 22 Sep 2009 16:26:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/22/biopython-release-152/<p>We are pleased to announce the availability of Biopython 1.52, a new stable release of the <a href="http://biopython.org">Biopython</a> library.</p> <p>It may only have been one month since <a href="http://news.open-bio.org/news/2009/08/biopython-1-51-released/" title="Biopython 1.51">the last release</a>, but in that time we&rsquo;ve added enough useful features to warrant a new release. In particular, Biopython 1.52 includes more substantial support for population genetics, and adds new functions that will be useful for people working with next generation sequencing.</p> <p>Tiago Antao&rsquo;s work on the Population Genetics module brings a command line wrapper for GenePop which allows the estimation of <a href="http://en.wikipedia.org/wiki/F-statistics">F-statistics</a>, null allele frequencies and migration rates as well as tests for isolation by distance (IBD) and deviation from Hardy-Weinberg equilibrium.</p> <p>Bio.SeqIO and Bio.AlignIO both now have a <a href="http://news.open-bio.org/news/2009/09/biopython-convert-function/">new <strong>convert()</strong> function</a> that allows for simple (and potentially optimized) conversion between file formats. Bio.SeqIO also gets a <a href="http://news.open-bio.org/news/2009/09/biopython-seqio-index/" title="Indexing sequence files with Biopython">new <strong>index()</strong> function</a> which allows random access to sequences in a file without reading every record in that file into memory.</p> <p>The new release also adds command line wrappers for the <a href="http://emboss.sourceforge.net/embassy/#PHYLIP" title="Emboss Embassy packages">EMBOSS versions</a> of the <a href="http://evolution.genetics.washington.edu/phylip.html" title="Joe Felsenstein's Phylip page">PHYLIP phylogeny programs</a> and the <a href="http://www.novocraft.com/products.html#novoalign">Novoalign assembler from NovaCraft</a> - plus squashes a few minor bugs reported since 1.51 was released.</p> <p>Biopython 1.52 will be the last release to use the CVS server as the main repository for code in development. From now on the <a href="http://github.com/biopython/biopython" title="Biopython on github">official development branch will be on github</a>, would-be developers can see our wiki page on <a href="http://www.biopython.org/wiki/GitUsage" title="Biopython wiki article on git usage">git usage</a> to see the benefits on this system.</p> <p>Sources and Windows Installers are available from the <a href="http://www.biopython.org/wiki/Download" title="Download Biopython">downloads page</a>.</p> <p>Thanks to the Biopython development team and to everyone who has reported bugs since our last release.</p>https://www.open-bio.org/2009/09/22/biopython-convert-function/Tue, 22 Sep 2009 10:24:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/22/biopython-convert-function/<p>As per <a href="http://news.open-bio.org/news/2009/09/biopython-seqio-index/" title="Indexing sequence files with Biopython">Peter&rsquo;s recent post</a> we are using this space to show of a couple of the new features in <a href="http://biopython.org">Biopython</a> 1.52 before it is released. In this post we&rsquo;ll look at the new <strong>convert()</strong> function that both <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a> will get in Biopython 1.52.</p> <p>No one has ever complained that bioinformatics just doesn&rsquo;t have enough file formats - you probably frequently find yourself converting sequence files to suit particular applications with <strong>Bio.SeqIO</strong>. At the moment this is usually a two step process, something like this:</p> <p>`&raquo;&gt; records = SeqIO.parse(in_handle &ldquo;genbank&rdquo;)</p> <blockquote> <blockquote> <blockquote> <p>SeqIO.write(records, out_handle, &ldquo;fasta&rdquo;)`</p> </blockquote> </blockquote> </blockquote> <p>As of Biopython 1.52, you&rsquo;ll be able to achieve the same result in a single step:</p> <p><code>&gt;&gt;&gt; SeqIO.convert(in_handle, &quot;genbank&quot;, out_handle, &quot;fasta&quot;)</code></p> <p>In fact, it&rsquo;s even easier than that because the convert function will accept filename strings as well as file handles for both input and output.</p> <p>Adding the convert function to <strong>Bio.SeqIO</strong> and <strong>Bio.AlignIO</strong> will make your scripts more readable and might even save you a couple of lines of code, but perhaps more importantly it allows for the conversion process to be optimized for the two formats being used. In most cases the same old parse and write functions are called internally, however some key conversions are much faster&hellip;</p> <p>In the above example we are moving from a GenBank file, which probably includes multiple features for each sequence, to a FASTA file, which doesn&rsquo;t include features. If we used the two step process above we&rsquo;d be spending time reading each sequence&rsquo;s features into memory just to skip them when they get passed to the write function. <strong>Bio.SeqIO.convert()</strong> knows that the sequences in the input file are destined to be written to a FASTA file so it can skip over the features and save a bit of time in doing the conversion.</p> <p>Obviously, any optimization is most important when its used on very large files, like those produced in next generation sequencing projects. For example, when converting between each of the FASTQ file formats variants with the &ldquo;SeqIO two step&rdquo; a significant amount of time is taken creating <a href="http://biopython.org/wiki/SeqRecord">SeqRecord objects</a> for each record in the input file and decoding the quality scores into numbers. However, none of the attributes or methods of the SeqRecord object are required to do the conversion. For this reason <strong>Bio.SeqIO.convert()</strong> deals with each record as simple strings. This makes it about five times faster - on a par with converters written in C.</p> <p>The Biopython 1.52 edition of the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial &amp; Cookbook</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>) will cover these new convert functions in more detail.</p>https://www.open-bio.org/2009/09/21/biopython-seqio-index/Mon, 21 Sep 2009 17:37:12 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/21/biopython-seqio-index/<p>The forthcoming release of <a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a> will include a couple of nice improvements to the <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO module</a>, and here we&rsquo;re going to introduce the new <strong>index</strong> function. This will of course be covered in the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial &amp; Cookbook</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>) once this code is released.</p> <p>Suppose you have a <em>large</em> sequence file with many many individual sequences in it. This could be next generation sequence data for example, maybe a FASTQ, FASTA or QUAL file. Or, it might be a big annotation rich file, such as the whole of UniProt, or a chunk of GenBank.</p> <p>The <strong>Bio.SeqIO.parse(&hellip;)</strong> function lets you iterate over all the records in a file, one by one. This allows you to process each sequence in turn, keeping only one in memory at a time. This approach is <em>very</em> valuable for dealing with big files.</p> <p>However, sometimes you can&rsquo;t just loop over the records in the order found in the file. You may <em>require</em> random access. In Python, the natural API here is a dictionary - for example looking up the records via their ID string. This is how the existing <strong>Bio.SeqIO.to_dict(&hellip;)</strong> function works. It is just a helper function to build an <em>in memory</em> dictionary of a collection of SeqRecord objects. However, because everything is kept in memory (RAM), this only works on small or medium sized files. :(</p> <p>So, what should you do when you have a very large file, and it is no longer possible to load everything into memory at once? Well, you might consider using a <a href="http://biosql.org">BioSQL</a> database - this is probably quite a sensible option for something like GenBank data. However, for next generation sequencing data this is probably overkill. This is where the new <strong>Bio.SeqIO.index(&hellip;)</strong> function comes in. It behaves like a Python dictionary, but doesn&rsquo;t keep everything in memory at once!</p> <p>What <strong>Bio.SeqIO.index(&hellip;)</strong> does is first quickly scan the file looking for the position of each new record, and records this information against the record ID string. This still requires a reasonable amount of memory, but works fine even for millions of entries in a file. Then, when you ask for a particular record, it jumps to the relevant part of the file, and then parses the data into a SeqRecord.</p> <p>For example, consider the FASTQ file SRR014849.fastq (available <a href="ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX003/SRX003639/SRR014849.fastq.gz">compressed at the NCBI</a>). The <strong>Bio.SeqIO.index(&hellip;)</strong> function takes a minimum of two arguments, the filename and the file format:</p> <p>`</p> <blockquote> <blockquote> <blockquote> <p>from Bio import SeqIO data = SeqIO.index(&ldquo;SRR014849.fastq&rdquo;, &ldquo;fastq&rdquo;) len(data) 94696 data.keys()[:3] [&lsquo;SRR014849.80961&rsquo;, &lsquo;SRR014849.80960&rsquo;, &lsquo;SRR014849.80963&rsquo;] print data[&ldquo;SRR014849.290838&rdquo;].seq TGAGAATTTTTATTTTCAAGGGTTGGAACCGAAGGGTTTGAATTCAAACCCTTTCGGTTCCAACCCGACAAGTCATCGATGTTG print data[&ldquo;SRR014849.290838&rdquo;].letter_annotations[&ldquo;phred_quality&rdquo;] [20, 18, 24, 25, 33, 26, 37, 33, 22, 11, 1, 22, 37, 33, 22, 10, 25, 31, 26, 36, 32, 16, 33, 26, 31, 25, 33, 25, 31, 25, 22, 33, 26, 35, 30, 12, 35, 31, 17, 19, 30, 20, 33, 26, 27, 31, 27, 6, 36, 32, 15, 33, 29, 10, 27, 32, 24, 30, 25, 30, 20, 24, 13, 35, 31, 13, 27, 26, 28, 32, 24, 28, 28, 27, 22, 22, 26, 28, 26, 24, 27, 30, 22, 27]`</p> </blockquote> </blockquote> </blockquote> <p>In this case the FASTQ file is only 24MB (so the example is easy to try at home), but the same approach works just as well on a 1GB FASTQ file :)</p> <p>This will be covered in more detail by the new edition of the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial &amp; Cookbook</a>, and once you have Biopython 1.52 or later installed don&rsquo;t forget about the built in help:</p> <p>`&raquo;&gt; from Bio import SeqIO</p> <blockquote> <blockquote> <blockquote> <p>help(SeqIO.index) &hellip; `</p> </blockquote> </blockquote> </blockquote> <p>Biopython 1.52 will index most of the file formats that can already be parsed with the SeqIO library - but not any multiple alignment formats. There is a table on the <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO wiki page</a>.</p> <p>Enjoy!</p> <p>Peter</p> <p>P.S. Note that random access to all the records in a sequence file isn&rsquo;t the only potential benefit of using <strong>Bio.SeqIO.index(&hellip;)</strong>. Suppose you are only interested in a few entries in a large file. You could use a for loop with <strong>Bio.SeqIO.parse(&hellip;)</strong>, but this will mean every single record gets parsed and turned into a SeqRecord. If instead you used <strong>Bio.SeqIO.index(&hellip;)</strong> then only the few records you care about get parsed and turned into SeqRecord objects. This can save a lot of time, especially for an annotation rich format like SwissProt or GenBank.</p>https://www.open-bio.org/2009/09/02/bioruby-1-3-1-released/Wed, 02 Sep 2009 13:47:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/02/bioruby-1-3-1-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/" title="BioRuby">BioRuby</a> 1.3.1. This new release fixes many bugs existed in 1.3.0.</p> <p>Here is a brief summary of changes.</p> <ul> <li>Refactoring of BioSQL support.</li> <li>Bio::PubMed bug fixes.</li> <li>Bio::NCBI::REST bug fixes.</li> <li>Bio::GCG::Msf bug fixes.</li> <li>Bio::Fasta::Report bug fixes and added support for multiple query sequences.</li> <li>Bio::Sim4::Report bug fixes.</li> <li>Added unit tests for Bio::GCG::Msf and Bio::Sim4::Report.</li> <li>License of BioRuby is clarified.</li> </ul> <p>In addition, many changes have been made, mainly bug fixes. For more information, you can see <a href="http://github.com/bioruby/bioruby/blob/e731c6e52bc9a672e4546eeca4f2d2d968bdba09/ChangeLog" title="ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.3.1.tar.gz" title="http://bioruby.org/archive/bioruby-1.3.1.tar.gz">http://bioruby.org/archive/bioruby-1.3.1.tar.gz</a></p> <p>We also put RubyGems pacakge at RubyForge as always. You can easily install by using RubyGems. % sudo gem install bio</p> <p>You can also obtain bioruby gem file from <a href="http://bioruby.org/" title="bioruby.org">bioruby.org</a>. <a href="http://bioruby.org/archive/gems/bio-1.3.1.gem" title="http://bioruby.org/archive/gems/bio-1.3.1.gem">http://bioruby.org/archive/gems/bio-1.3.1.gem</a></p> <p>Hope you enjoy.</p>https://www.open-bio.org/2009/08/17/biopython-1-51-released/Mon, 17 Aug 2009 11:52:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/08/17/biopython-1-51-released/<p>We are pleased to announce the release of Biopython 1.51.This new stable release enhances <a href="http://news.open-bio.org/news/2009/04/biopython-release-150/" title="1.50 announcement">version 1.50</a> (released in April) by extending the functionality of existing modules, adding a set of application wrappers for popular alignment programs and fixing a number of minor bugs.</p> <p>In particular, the SeqIO module can now write Genbank files that include features, and deal with FASTQ files created by Illumina 1.3+. Support for this format allows interconversion between FASTQ files using Solexa, Sanger and Ilumina variants using conventions agreed upon with the <a href="http://www.bioperl.org/wiki/Main_Page" title="BioPerl main page">BioPerl</a> and <a href="http://emboss.sourceforge.net/" title="EMBOSS page">EMBOSS</a> projects.</p> <p>Biopython 1.51 is the first stable release to include the Align.Applications module which allows users to define command line wrappers for popular alignment programs including <a href="http://www.clustal.org/" title="Clustal Hompage">ClustalW</a>, <a href="http://www.drive5.com/muscle/" title="Muscle homepage">Muscle</a> and <a href="//www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" title="T-Coffe Hompage">T-Coffee</a>.</p> <p>Bio.Fasta and the application tools ApplicationResult and generic_run() have been marked as <a href="http://biopython.org/wiki/Deprecation_policy" title="Deprecation Policy">deprecated</a> - Bio.Fasta has been superseded by SeqIO&rsquo;s support for the Fasta format and we provide ducumentation for using the <a href="http://docs.python.org/library/subprocess.html" title="subprocess documentation">subprocess</a> module from the Python Standard Library as a more flexible approach to calling applications.</p> <p>As always the <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.html" title="Biopython Tutorial">Tutorial and Cookbook</a> has been updated to document all the changes.</p> <p>Thank you to everyone who tested our 1.51 beta or submitted bugs since out last stable release and to all our contributors</p> <p>Sources and Windows Installer are available from the <a href="http://biopython.org/wiki/Download" title="Biopython Downloads">downloads page</a>.</p>https://www.open-bio.org/2009/06/27/minutes2009-bosc-meeting/Sat, 27 Jun 2009 05:11:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/06/27/minutes2009-bosc-meeting/<p><em>Note: this is preliminary and needs some editing.</em></p> <h3 id="obf-business-meeting-at-bosc-2009">OBF Business Meeting at BOSC 2009</h3> <ul> <li><strong>Location:</strong> Rica Talk Hotel, Restaurant 2nd floor</li> <li><strong>Present:</strong> <ul> <li>current BoD members: Hilmar Lapp, Kam Dahlquist</li> <li>Guests:</li> </ul> </li> </ul> <h4 id="called-meeting-to-order-at-705pm">Called meeting to order at 7.05pm.</h4> <ul> <li>Explained business meeting purpose and distinction to conference call that will make decisions</li> <li>Introductions: Hilmar, Kam, everyone else around the table (see guests)</li> </ul> <h4 id="discussion">Discussion:</h4> <ul> <li>OBF does a very good job in servicing its member project</li> <li>could look at open source projects more globally; specifically could come up with an open source policy statement that is global</li> <li>Kam: in agreement, we are overdue with coming up with a broader vision statement <ul> <li>should maybe open this up and do it in an open and transparent manner</li> </ul> </li> <li>Location of incorporation issue <ul> <li>Has not been pursued further since the last conference call.</li> <li>Issue of being under US export restrictions, and the open question of whether we can legally accept membership applications from citizens of countries under US trade sanctions.</li> <li>Incorporating in Canada would be an option. Generally, need to look carefully at the local laws as to what they permit in terms of transferring funds.</li> </ul> </li> <li>Open-source hosting portals: what are the benefits of the various sites? <ul> <li>Github: very much focused on the code, working with other people.</li> <li>SourceForge: temporary inaccessibility problems and interface changes can be nasty, especially for web hosting. They also</li> </ul> </li> <li>Shouldn&rsquo;t OBF take a more outspoken role in software development best practices, patterns, and standards? <ul> <li>OBF history has provided a forum for such practice recommendations to be promulgated and to foster the community to converge among common practices, but has otherwise remained neutral.</li> <li>Is that maybe a role the member projects could fill out? For example, EMBOSS or Biojava have done this in their communities.</li> <li>Some mistakes are often repeated. Maybe create a repository of organizational knowledge about practices that have proven efficient, and anti-patterns.</li> <li>What makes a project an Open Bio project? Could formalize some recommendations based on empirical experiences and lessons learned.</li> <li>We may be easily duplicating efforts - there are many other organizations and fields defining design patterns and recommended practices.</li> <li>There are still many new people coming into Bioinformatics that come from a different background. They shouldn&rsquo;t have to learn by the hard way how not to do things. <ul> <li>Once people are into it they really need to make the first step of looking beyond their own little sphere themselves.</li> <li>However, training and education needs to be built into the undergrad and graduate curricula.</li> <li>Can and should the OBF play a role in this, for example by compiling and providing resources, information, and tutorial material?</li> <li>ISCB actually has an education committee, and it takes simply showing up to participate. Members come from any different perspectives and backgrounds. A subgroup (which seems invitation-only) is working on</li> <li>Should OBF maybe initiate an open resource (as opposed to a purchased book) for education and training? Really needs a critical mass of people to push it forward.</li> <li>OBF could provide a coordination or point of contact or counselor role to help potential authors retain copyright when they publish a book.</li> </ul> </li> <li>caBIG infratructure increasingly mature and required to be built upon or in a compliant way by NIH grant applicants.</li> <li>Everyone reinventing the wheel continues to be an issue. Need to reach local partnerships between faculty members to break down further the &ldquo;do it on our own attitude).</li> <li>caBIG had to dole out money for &ldquo;early adopters&rdquo;.</li> <li>Biologists can be highly biased purely due to the application domain.</li> </ul> </li> <li>People may have odd preconceptions to open-source projects solely because they haven&rsquo;t looked at the supporting community yet.</li> <li>Bioinformaticists often are trying to solve a specific problem, only to move on to something else immediately afterwards.</li> <li>BOSC conference: <ul> <li>Should keep requiring abstract submissions (rather than just title, for example), but should not require full papers to remain sufficiently inclusive.</li> <li>Tutorials could be held in a session concurrent with the main ISMB conference. <ul> <li>These parallel tracks are separate submissions to ISCB. Lonnie and Peter volunteer to work out a proposal for 2010.</li> </ul> </li> </ul> </li> <li>OBF remit: Should keep existing, support its member projects, and promote open-source software among biologists.</li> <li>Conference proceedings: <ul> <li>Open source software work</li> </ul> </li> </ul>https://www.open-bio.org/2009/06/23/biopython-151-beta-released/Tue, 23 Jun 2009 15:42:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/06/23/biopython-151-beta-released/<p>A <em>beta</em> release for Biopython 1.51 is now available for download and testing.</p> <p>In the two months since <a href="http://news.open-bio.org/news/2009/04/biopython-release-150/">Biopython 1.50</a> was released, we have introduced support for writing features in GenBank files using <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a>, extended <a href="http://news.open-bio.org/news/2009/03/biopython-next-gen-sequencing/">SeqIO&rsquo;s support for the FASTQ format</a> to include files created by Illumina 1.3+, and added a new set of application wrappers for alignment programs, and made numerous tweaks and bug fixes.</p> <p>All the new features have been tested by the dev team but it&rsquo;s possible there are cases that we haven&rsquo;t been able to foresee and test, especially for the GenBank feature writer (as there as just so many possible odd fuzzy feature locations).</p> <p>Note that as previously announced, Biopython no longer supports <a href="http://news.open-bio.org/news/2009/05/dropping-python23-support/">Python 2.3</a>, and our deprecated parsing infrastructure (Martel and Bio.Mindy) has been removed.</p> <p>Source distributions and Windows installers are available from the <a href="http://biopython.org/wiki/Download">downloads</a> page on the <a href="http://biopython.org">Biopython website (biopython.org)</a>.</p> <p>We are interested in getting feedback on the beta release as a whole, but especially on the new features and the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p>So, gather your courage, download the release, try it out and let us know what works and what doesn&rsquo;t through the <a href="http://www.biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2009/06/21/ncbi-einfo-biopython/Sun, 21 Jun 2009 21:42:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/06/21/ncbi-einfo-biopython/<p>Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/eutils_help.html">Entrez Programming Utilities</a> called <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/einfo_help.html">Entrez EInfo</a> can help.</p> <p>For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the <a href="http://www.ncbi.nlm.nih.gov/sites/entrez" title="NCBI Entrez">Entrez web interface</a>, for use in a script with <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/esearch_help.html%3EESearch%3C/a%3E" title="where you might also download them with &lt;a href=">EFetch</a>.</p> <p>I knew from past experience about using <code>name[ORGN]</code> in Entrez to search for an organism name - but how would you specify just mitochondria? I actually worked this out from the NCBI help and exploring the Entrez website&rsquo;s advanced search - but it took a while.</p> <p>There is an easier way to find out the search fields available in Entrez! Just recently I came across an interesting <a href="http://nsaunders.wordpress.com/2009/05/27/querying-ncbi-entrez-database-fields-using-ruby/">blog post from Neil Saunders</a> (written a couple of weeks ago) showing how Entrez EInfo provides information about the search fields in XML format, and how you can use Ruby to process this.</p> <p><a href="http://biopython.org">Biopython</a> can do this too of course - using <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#chapter:entrez">Bio.Entrez</a> this took just a few lines of Python:</p> <p>`&raquo;&gt; from Bio import Entrez</p> <blockquote> <blockquote> <blockquote> <p>data = Entrez.read(Entrez.einfo(db=&ldquo;genome&rdquo;)) for field in data[&ldquo;DbInfo&rdquo;][&ldquo;FieldList&rdquo;] : &hellip; print &ldquo;%(Name)s, %(FullName)s, %(Description)s&rdquo; % field &hellip; ALL, All Fields, All terms from all searchable fields UID, UID, Unique number assigned to each sequence FILT, Filter, Limits the records WORD, Text Word, Free text associated with record TITL, Title, Words in definition line KYWD, Keyword, Nonstandardized terms provided by submitter AUTH, Author, Author(s) of publication JOUR, Journal, Journal abbreviation of publication VOL, Volume, Volume number of publication ISS, Issue, Issue number of publication PAGE, Page Number, Page number(s) of publication ORGN, Organism, Scientific and common names of organism, and all higher levels of taxonomy ACCN, Accession, Accession number of sequence PACC, Primary Accession, Does not include retired secondary accessions GENE, Gene Name, Name of gene associated with sequence PROT, Protein Name, Name of protein associated with sequence ECNO, EC/RN Number, EC number for enzyme or CAS registry number PDAT, Publication Date, Date sequence added to GenBank MDAT, Modification Date, Date of last update SUBS, Substance Name, CAS chemical name or MEDLINE Substance Name PROP, Properties, Classification by source qualifiers and molecule type SQID, SeqID String, String identifier for sequence GPRJ, Genome Project, Genome Project SLEN, Sequence Length, Length of sequence FKEY, Feature key, Feature annotated on sequence RTYP, Replicon type, Replicon type RNAM, Replicon name, Replicon name ORGL, Organelle, Organelle `</p> </blockquote> </blockquote> </blockquote> <p>That gives us a list of all the fields we can currently search on in the Genome database (and you could use the same code for any of the other NCBI databases in Entrez - they probably all have different searchable fields). Very handy! The ones in bold are discussed below.</p> <p>So for my particular search, using &ldquo;ORGL&rdquo; to filter on organelle looks sensible, and after a bit of trial and error on the website I ended up with <code>mitochondrion[ORGL]</code> as a useful filter (not mitochondrial, or mitochondria).</p> <p>I already knew about using &ldquo;ORGN&rdquo; to filter on the organism, either by species name or with a suitably formatted NCBI taxon ID (which you can get by searching or browsing the Entrez taxonomy database), e.g. <code>txid9443[ORGN]</code> gives <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9443">primates</a>.</p> <p>Putting these together, to get <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&amp;term=txid9443%5BORGN%5D%20AND%20mitochondrion%5BORGL%5D">all the primate mitochondria in the Entrez genome database</a> you could use:</p> <blockquote> <p>txid9443[ORGN] AND mitochondrion[ORGL]</p> </blockquote> <p>Note that you have to use &ldquo;AND&rdquo; in upper case.</p> <p>I think we&rsquo;ll have to add something along these lines to the <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> ( <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>)&hellip; <em>Update: That&rsquo;s done now and will be included with our next release</em> :)</p> <p>Entrez rocks! (although their documentation could use a few more examples).</p> <p>Peter</p>https://www.open-bio.org/2009/06/01/bosc-schedule-posted-2/Tue, 02 Jun 2009 02:09:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/06/01/bosc-schedule-posted-2/<p>The BOSC 2009 schedule of speakers with links to abstracts has been posted at <a href="https://www.open-bio.org/wiki/BOSC_2009_Schedule">/wiki/BOSC_2009_Schedule</a>.</p>https://www.open-bio.org/2009/05/13/bosc-update-ruttenberg-hanmer-confirmed-as-keynotes-early-registration-deadline-friday/Thu, 14 May 2009 01:12:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/05/13/bosc-update-ruttenberg-hanmer-confirmed-as-keynotes-early-registration-deadline-friday/<p>Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC 2009.  For more information, see the BOSC 2009 web site at <a href="https://www.open-bio.org/wiki/BOSC_2009">/wiki/BOSC_2009</a>.</p> <p>Abstract acceptances went out today&ndash;stay tuned for the schedule, which will be posted once the speakers have confirmed their invitations.</p> <p>The early registration deadline for BOSC is Friday, May 15; don&rsquo;t forget to take advantage of the discounted fee for early registrants at <a href="http://www.iscb.org/ismbeccb2009/registration.php">http://www.iscb.org/ismbeccb2009/registration.php</a>.</p>https://www.open-bio.org/2009/05/06/dropping-python23-support/Wed, 06 May 2009 08:22:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/05/06/dropping-python23-support/<p>As announced <a href="http://lists.open-bio.org/pipermail/biopython/2009-May/005148.html" title="Biopython discussion archive">here</a>, any last minute requests to postpone dropping support for Python 2.3 from the next release of <a href="http://biopython.org">Biopython</a> must be posted to the <a href="http://www.biopython.org/wiki/Mailing_lists" title="Biopython mailing lists">main Biopython mailing list</a> no later than Friday, May 8.</p>https://www.open-bio.org/2009/04/29/biopython-cookbook-wiki/Thu, 30 Apr 2009 01:36:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/29/biopython-cookbook-wiki/<p>Hi all,</p> <p>You may have noticed we&rsquo;re trying out using the wiki for <a href="http://biopython.org/wiki/Category:Cookbook">Biopython cookbook entries</a>. It&rsquo;s a new idea so at the moment there are only a few &lsquo;recipes&rsquo; on offer. If you have some tricks you find yourself using time and again to solve a problem why not share them? Similarly, if you find yourself coming up against a problem you can&rsquo;t seem to solve easily with Biopython&rsquo;s tools send a message to one of the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> proposing it as a cookbook example and someone just might solve it for you!</p> <p>There are also several short examples in the main &quot; <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a>&quot; ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">pdf version</a>) which might be worth copying/moving to the wiki. What would you pick from here?</p> <p>Feedback from <a href="http://www.biopython.org">Biopython</a> newcomers would be especially valuable! :)</p>https://www.open-bio.org/2009/04/27/biopython-projects-chosen-for-google-summer-of-code/Mon, 27 Apr 2009 09:14:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/27/biopython-projects-chosen-for-google-summer-of-code/<p>Congratulations to Nick Matzke and Eric Talevich who have had <a href="http://www.biopython.org">Biopython</a> projects accepted for this year&rsquo;s <a href="http://code.google.com/soc/">Google Summer of Code</a>. Both projects were accepted as part of <a href="http://www.nescent.org/index.php">The National Evolutionary Synthesis Center&rsquo;s (NESCent)</a> involvement as a mentoring organisation with the program.</p> <p>Nick will spend his summer working on modules that access locality data from biodiversity databases and incorporate this information in biogeographical and phylogenetic analyses ( <a href="http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250">Nick&rsquo;s abstract</a>) while Eric will be building a parser for the emerging PhyloXML format for storing and sharing phylogenetic trees ( <a href="http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798969">Eric&rsquo;s abstract</a>).</p> <p>Congratulations to Nick and Eric and to their mentors Stephen Smith and Brad Chapman (who has [his own post on this topic](<a href="http://bcbio.wordpress.com/2009/04/20/biopython-projects-for-google-">http://bcbio.wordpress.com/2009/04/20/biopython-projects-for-google-</a> summer-of-code/)) and thanks to Google and NESCent for their support of these projects.</p>https://www.open-bio.org/2009/04/20/biopython-release-150/Mon, 20 Apr 2009 18:58:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/20/biopython-release-150/<p>We are pleased to announce Biopython release 1.50, featuring some significant additions since <a href="http://news.open-bio.org/news/2008/09/biopython-release-148/">Biopython 1.49</a> was released late last year.</p> <p><a href="http://bioinf.scri.ac.uk/lp/programs.php#genomediagram">GenomeDiagram</a> by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.</p> <p>A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.SwissProt and Bio.ExPASy and their revised parsers.</p> <p>As noted in a previous news posting, <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> can now read and write <a href="http://news.open-bio.org/news/2009/03/biopython-next-gen-sequencing/">FASTQ and QUAL files</a> used in second generation sequencing work. In connection with this, our <a href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> object has a new dictionary attribute, letter_annotations, for per-letter-annotation information like sequence quality scores or secondary structure predictions. Also, the SeqRecord object can now be sliced to give a new SeqRecord covering just part of the sequence.</p> <p>Biopython 1.50 supports Python 2.3, 2.4, 2.5 and 2.6. However, this is expected to be the final version to support Python 2.3 (see this <a href="http://news.open-bio.org/news/2009/04/2008/11/biopython-and-python-26-and-python-23/">previous announcement</a>). Also, Biopython 1.50 should be the last release to include our old deprecated parsing infrastructure (Martel and Bio.Mindy).</p> <p>We’ve also updated the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html" title="Biopython Tutorial and Cookbook (HTML)">Biopython Tutorial and Cookbook</a> (also available in <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf" title="Biopython Tutorial and Cookbook (PDF)">PDF</a>), and not just by adding <a href="http://biopython.org/wiki/Logo" title="About the Biopython logo">our logo</a> to the cover ;)</p> <p>Thank you to everyone who tested the <a href="http://news.open-bio.org/news/2009/04/biopython-150-beta-released/">Biopython 1.50 beta release</a>, and to all our contributors.</p> <p>Source distributions and Windows installers are available from the <a href="http://biopython.org/wiki/Download">downloads</a> page on the <a href="http://biopython.org/">Biopython website (biopython.org)</a>.</p> <p>-Peter, on behalf of the Biopython developers</p>https://www.open-bio.org/2009/04/10/reminder-abstracts-for-bosc-2009-due-april-13/Fri, 10 Apr 2009 20:41:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/10/reminder-abstracts-for-bosc-2009-due-april-13/<p>This is a reminder from the BOSC 2009 Organizing committee that abstracts for BOSC are due on Monday, April 13.</p>https://www.open-bio.org/2009/04/03/biopython-150-beta-released/Fri, 03 Apr 2009 21:08:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/03/biopython-150-beta-released/<p>We are pleased to announce a beta release of Biopython 1.50 for public testing. There have been some significant changes since <a href="http://news.open-bio.org/news/2008/11/biopython-release-149/">Biopython 1.49</a> was released late last year.</p> <p><a href="http://bioinf.scri.ac.uk/lp/programs.php#genomediagram">GenomeDiagram</a> by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.</p> <p>A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.ExPASy and the revised Prosite and Enzyme parsers.</p> <p>As noted in a previous news posting, <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> can now read and write <a href="http://news.open-bio.org/news/2009/03/biopython-next-gen-sequencing/">FASTQ and QUAL files</a> used in second generation sequencing work. In connection with this, our <a href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> object has a new dictionary attribute, letter_annotations, for per-letter-annotation information like sequence quality scores or secondary structure predictions. Also, the SeqRecord object can now be sliced to give a new SeqRecord covering just part of the sequence.</p> <p>As in the previous release, Biopython 1.50 beta supports Python 2.3, 2.4, 2.5 and 2.6. However, Biopython 1.50 is expected to be the final version to support Python 2.3 (see this <a href="../2008/11/biopython-and-python-26-and-python-23/">previous announcement</a>). Also, Biopython 1.50 should be the last release to include our old deprecated parsing infrastructure (Martel and Bio.Mindy).</p> <p>So, if you are feeling brave, please try out Biopython 1.50 beta, and let us know on the <a href="http://www.biopython.org/wiki/Mailing_lists">mailing lists</a> if it works, or more importantly if something doesn’t. Comments on the new code are particularly welcome.</p> <p>We’d also like feedback on the updated <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> (also available in <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p>Source distributions and Windows installers are available from the Biopython website: <a href="http://biopython.org/">biopython.org</a>.</p> <p>Thanks!</p> <p>-Peter on behalf of the Biopython developers</p>https://www.open-bio.org/2009/03/27/biopython-on-twitter/Fri, 27 Mar 2009 11:19:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/27/biopython-on-twitter/<p>Just to let you all know, <a href="http://twitter.com/Biopython">Biopython is now on twitter</a>. And in case you missed the <a href="https://www.open-bio.org/news/2009/02/hello-twitter-world/">OBF announcement</a> last month, so is the <a href="http://twitter.com/obf_news">O|B|F News feed</a> (and <a href="http://twitter.com/bioperl">BioPerl</a>). You are welcome to follow us (all) on <a href="http://twitter.com/">twitter</a>.</p> <p>I&rsquo;d also like to remind people there are news feeds for the <a href="http://news.open-bio.org/news/category/obf-projects/biopython/">Biopython news posts</a> (as <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/rdf">RDF</a>, <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss/">RSS</a>, <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss2/">RSS2</a>, or <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/atom">Atom</a> format). We&rsquo;re planning to have these automatically echoed onto twitter in future&hellip; <em>(update)</em> &hellip;and that seems to be working now :)</p>https://www.open-bio.org/2009/03/26/biopython-next-gen-sequencing/Thu, 26 Mar 2009 16:13:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/26/biopython-next-gen-sequencing/<p>Those of you doing next generation sequencing may be pleased to know that the next release of <a href="http://www.biopython.org">Biopython</a> is expected to include support for reading and writing <a href="http://bioperl.org/wiki/FASTQ_sequence_format">FASTQ</a> and <a href="http://bioperl.org/wiki/Qual_sequence_format">QUAL</a> files within our <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> interface. These formats are used for traditional Sanger capillary sequencing, and Roche 454 sequencing (Roche provide tools to convert from their binary SFF files) with PHRED quality scores. Solexa/Illumina sequencers produce a FASTQ variant where the quality scores are encoded differently, and this is also supported.</p> <p>As part of this work, the <a href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> has a new attribute holding a dictionary of per-letter-annotation (e.g. PHRED quality scores, Solexa quality scores, or for proteins secondary structure predictions), and the SeqRecord object can be sliced to give a new SeqRecord covering just part of the sequence, with the per-letter-annotation cropped to match.</p> <p>The code is in our <a href="http://biopython.org/wiki/CVS">CVS tree</a>, and <a href="http://github.com/biopython/biopython/tree/master">mirrored on github</a>, so those of you happy to install Biopython from source and help test it can grab the code now, and give it a go - feedback on the development <a href="http://biopython.org/wiki/Mailing_lists">mailing list</a> please. Alternatively, sit back and await the forthcoming Biopython 1.50 (beta) release, which should allow more widespread testing&hellip;</p> <p><em>Update:</em> This new functionality was included in <a href="http://news.open-bio.org/news/2009/04/biopython-release-150/" title="Biopython 1.50">Biopython 1.50</a>, including both Sanger standard FASTQ files and the original Solexa/Illumina FASTQ variant using Solexa scores. This did not cover the new FASTQ variant used on Solexa/Illumina 1.3+ but that is now supported in our development code, and will be included in Biopython 1.51. Peter, 2009/06/16</p>https://www.open-bio.org/2009/03/22/biopython-paper-published/Sun, 22 Mar 2009 18:45:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/22/biopython-paper-published/<p>An Application Note describing Biopython has recently been accepted for publication in the <a href="http://bioinformatics.oxfordjournals.org/">Oxford Journal <em>Bioinformatics</em></a>. An advance copy of the Open Access article is available online:</p> <blockquote> <p>P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M.J.L. de Hoon (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. <em>Bioinformatics</em>, <a href="http://dx.doi.org/10.1093/bioinformatics/btp163">doi:10.1093/bioinformatics/btp163</a></p> </blockquote>https://www.open-bio.org/2009/03/17/biopython-and-version-control-systems/Tue, 17 Mar 2009 14:52:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/17/biopython-and-version-control-systems/<p>Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of <a href="http://github.com/biopython/">Biopython on GitHub</a>, which is automatically updated from the OBF hosted <a href="http://www.biopython.org/wiki/CVS">Biopython CVS repository</a>. See our <a href="http://biopython.org/wiki/GitMigration">git migration wiki page</a> for details. If this is favorably received, then moving Biopython from CVS to git seems likely at some point this year.</p> <p>Originally, all the OBF hosted projects used <a href="http://www.nongnu.org/cvs/">CVS</a> for their source code repositories. At the start of 2008, <a href="http://www.bioperl.org">BioPerl</a> and <a href="http://www.biojava.org">BioJava</a> moved over to <a href="http://subversion.tigris.org/">Subversion (SVN)</a>, followed by <a href="http://www.biosql.org">BioSQL</a>. <a href="http://www.biopython.org">Biopython</a> was originally going to do the same, but this didn&rsquo;t actually happen. Having all the Bio* projects using the same version control system would have simplified server administration for the OBF, but using SVN wouldn&rsquo;t really have made that much difference to Biopython development. Discussion on the <a href="http://biopython.org/pipermail/biopython-dev/">Biopython development mailing list</a> has since shifted towards next-generation distributed version control systems like <a href="http://git-scm.com/">git</a> or <a href="http://bazaar-vcs.org/">Bazaar</a>.</p> <p>Quote from Linus Torvalds,</p> <blockquote> <p>The slogan of Subversion for a while was ‘CVS done right’, or something like that, and if you start with that kind of slogan, there&rsquo;s nowhere you can go. There is no way to do CVS right.</p> </blockquote> <p>In addition to creating the Linux kernel, Linus Torvalds more recently wrote <a href="http://git-scm.com/">git</a>, a prominent example of a distributed version control system. Rather than switching from CVS to SVN, the <a href="http://www.bioruby.org">BioRuby</a> project choose instead to use git, hosted on <a href="http://github.com">github</a> (see the <a href="http://github.com/bioruby/bioruby/tree/master">BioRuby repository</a>). Biopython is considering doing something similar - using a <em>distributed</em> version control system like git should make it easier for potential Biopython contributors to manage their own local copies of Biopython under version control.</p> <p>Peter, on behalf of the Biopython developers</p>https://www.open-bio.org/2009/03/10/google-summer-of-code-project-ideas-page/Tue, 10 Mar 2009 05:56:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/10/google-summer-of-code-project-ideas-page/<p>A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup:</p> <p><a href="http://open-bio.org/wiki/Google_Summer_Code_2009">http://open-bio.org/wiki/Google_Summer_Code_2009</a></p>https://www.open-bio.org/2009/02/26/release-16-of-bioperl-run-bioperl-db-bioperl-network/Thu, 26 Feb 2009 05:18:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/26/release-16-of-bioperl-run-bioperl-db-bioperl-network/<p>All,</p> <p>I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000).</p> <p>FIXED:</p> <ol> <li>Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names</li> <li>Bio::Tools::Run::Vista tests now pass if Vista.jar is installed.</li> <li>bug fix in bioperl-network</li> </ol> <p>What remains for the 1.6 release series:</p> <p>\* Documentation, Documentation, and Documentation. I haven&rsquo;t had much time unfortunately to work on documentation, primarily for BUGS/ INSTALL/README etc within db/run/network (the latter has been mainly updated by Brian O.) I will attempt to update these for the next point release, tentatively scheduled for mid-April.</p> <p>NOTE (so there is no confusion): the BioPerl-run archive is designated as BioPerl-1.6.1.tar.gz. This is due to a small off-by-one bug in the test suite that passed for me locally but fails if primer3 isn&rsquo;t installed. This unfortunately required a reupload to PAUSE. However, the minimal core version version required is still 1.006000.</p> <p>Related to the above, I will sort out the versioning issues for the next point release as we arrive closer to it. If needed we can bump the point release up to 1.6.2 to bring everything in sync.</p> <p>Here they are!</p> <p>BioPerl-run:</p> <p><a href="http://bioperl.org/DIST/BioPerl-run-1.6.1.tar.bz2">http://bioperl.org/DIST/BioPerl-run-1.6.1.tar.bz2</a> <a href="http://bioperl.org/DIST/BioPerl-run-1.6.1.tar.gz">http://bioperl.org/DIST/BioPerl-run-1.6.1.tar.gz</a> <a href="http://bioperl.org/DIST/BioPerl-run-1.6.1.zip">http://bioperl.org/DIST/BioPerl-run-1.6.1.zip</a></p> <p>BioPerl-db:</p> <p><a href="http://bioperl.org/DIST/BioPerl-db-1.6.0.tar.bz2">http://bioperl.org/DIST/BioPerl-db-1.6.0.tar.bz2</a> <a href="http://bioperl.org/DIST/BioPerl-db-1.6.0.tar.gz">http://bioperl.org/DIST/BioPerl-db-1.6.0.tar.gz</a> <a href="http://bioperl.org/DIST/BioPerl-db-1.6.0.zip">http://bioperl.org/DIST/BioPerl-db-1.6.0.zip</a></p> <p>BioPerl-network:</p> <p><a href="http://bioperl.org/DIST/BioPerl-network-1.6.0.tar.bz2">http://bioperl.org/DIST/BioPerl-network-1.6.0.tar.bz2</a> <a href="http://bioperl.org/DIST/BioPerl-network-1.6.0.tar.gz">http://bioperl.org/DIST/BioPerl-network-1.6.0.tar.gz</a> <a href="http://bioperl.org/DIST/BioPerl-network-1.6.0.zip">http://bioperl.org/DIST/BioPerl-network-1.6.0.zip</a></p> <p>SIGNATURES:</p> <p><a href="http://bioperl.org/DIST/SIGNATURES.md5">http://bioperl.org/DIST/SIGNATURES.md5</a></p> <p>Cheers!</p> <p>chris</p>https://www.open-bio.org/2009/02/24/bosc-2009-call-for-abstracts/Tue, 24 Feb 2009 22:09:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/24/bosc-2009-call-for-abstracts/<p>Please forward as appropriate and forgive multiple postings.</p> <p>Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009</p> <p>An ISMB 2009 Special Interest Group (SIG) Date: June 27-28, 2009 Location: Stockholm, Sweden URL: <a href="https://www.open-bio.org/wiki/BOSC_2009">/wiki/BOSC_2009</a> Abstract submission via EasyChair: <a href="https://www.easychair.org/login.cgi?conf=bosc2009">https://www.easychair.org/login.cgi?conf=bosc2009</a></p> <p>Important Dates Monday, April 13: Abstract deadline May 1, 2009: Notification of accepted abstracts May 15, 2009: Early Registration Discount Cut-off date June 27-28, 2009: BOSC 2009</p> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.</p> <p>This year’s conference will mark the 10th anniversary of BOSC. To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead: Open Source Solutions to Grand Challenges in Bioinformatics.” We are inviting abstracts for two different types of talks:</p> <p>1. Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.</p> <p>2. Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.</p> <p>In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session. This year’s topics include: Topics Design Patterns in Bioinformatics Regulatory Genomics Multicore and GPGPU computing Data &amp; Analysis Management (shared session with DAM SIG) Computational Grids Visualization There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.</p> <p>To contact the organizing committee, e-mail <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">bosc at open-bio.org.</a></p> <p>To sign up for BOSC-related announcements, subscribe to the Bosc-announce list ( <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a>).</p> <p>BOSC 2009 Organizing Committee Kam D. Dahlquist (Chair) Lonnie R. Welch (Co-chair) Hilmar Lapp Jens Lichtenberg Frank Drews Andrew Dalke Jim Procter Seán I. O&rsquo; Donoghue Anton Nekrutenko Steffen Moeller</p>https://www.open-bio.org/2009/02/13/google-summer-of-code-call-for-bio-volunteers/Fri, 13 Feb 2009 21:01:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/13/google-summer-of-code-call-for-bio-volunteers/<p>Google is committed to run the <a href="http://code.google.com/soc/2008">Summer of Code program</a> again this year. It will be for the 5th time.</p> <p>In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project. Projects (or umbrella organizations) wishing to participate in the program apply during the organization application period (March 9-13 in 2009). Those accepted into the program provide project ideas and supply mentors that guide the work on those. Students apply to a project within the program with specific project ideas, based on those suggested or based on their own idea, get ranked by the mentors of the project, and those accepted into the program get paired up with mentors. Projects are chiefly about programming, the coding period is 3 months (Jun-Aug), and there is no travel required by either student or mentor. The program is global; other than the US trade restrictions that Google is under, there are no restrictions as to where student or mentor reside. The main motivations behind the program are to recruit new contributors to open-source projects, and to produce more open-source code. See the <a href="http://code.google.com/opensource/gsoc/2009/faqs.html">program FAQs</a> for more information.</p> <p>I&rsquo;ve had the honor of being part of the program for the last two years, administering <a href="http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2007">NESCent&rsquo;s participation as an organization in 2007</a> and <a href="http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2008">2008</a> and in 2007 mentoring a student. I have to say I find it the most awesome open-source program since sliced bread (or the invention of BLAST if that means more to you). Despite that and sadly enough, there has been a dearth of participating bioinformatics projects (though some notable ones, such as CytoScape have participated).</p> <p>There have been two Bio* Summer of Code projects under the NESCent umbrella, <a href="http://biojava.org/wiki/BioJava:PhyloSOC07">one in 2007</a> and <a href="http://bioperl.org/wiki/PhyloXML_support_in_BioPerl">one in 2008</a>. I would be willing to volunteer to take the lead on and administer a full-blown participation of O|B|F as a Bio* umbrella organization, provided 1) at least one Bio* person volunteers to serve as backup administrator, and 2) enough Bio* contributors volunteer to serve as prospective mentors. (Note that if we apply as an organization, there is no guarantee that we would be accepted. In fact, in the past up to 2/3 of applying organizations have been rejected.)</p> <p>Mentoring involves participating in creating the page of project ideas (I&rsquo;d provide template and guidance), corresponding with applicants who have questions, participating in student application ranking, and for primary mentors (those directly assigned to a student) based on empirical evidence at least 5hrs/week of time spent with the student to help him/her get over obstacles or avoid wrong paths.</p> <p>I think almost all mentors would concur that the experience was very gratifying, but as a mentor you will be spending a non-negligible amount of time with the student. I think it is the student-mentor pairing and interaction, not the stipend, that in the end makes the participation for students uniquely productive in terms of learning, and different from simply contributing to the project of choice (which they could always do).</p> <p>For a personal impression for how the program is from a mentor perspective, I&rsquo;ll let Chris Fields speak who was the mentor for the 2008 phyloXML in BioPerl project. From a student&rsquo;s perspective, I&rsquo;ll leave it to the 2007 Biojava student Bohyun Lee (blee34-at-mail.gatech.edu) and the 2008 BioPerl student Mira Han (mirhan-at-indiana.edu) to comment (if they are still on the list).</p> <p>So if you think this is a good idea for Bio* to be part of, if you would like to help in some way, if you can see yourself as a mentor, or if you are a lurking would-be student, please let yourself be heard. Email either to the developer list of your Bio* project or to me.</p>https://www.open-bio.org/2009/02/11/hello-twitter-world/Wed, 11 Feb 2009 21:27:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/11/hello-twitter-world/<p>O|B|F News feed is now available in <a href="http://twitter.com/">Twitter</a>! You are welcome to <a href="http://twitter.com/obf_news">follow us</a>.</p> <p>Cheers, The O|B|F Admins.</p>https://www.open-bio.org/2009/01/25/bioperl-16-released/Mon, 26 Jan 2009 00:56:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/01/25/bioperl-16-released/<p>Release Pumpkin <a href="http://bioperl.org/wiki/User:Cjfields">Chris Fields</a> has announced the <a href="http://bioperl.org/wiki/Getting_BioPerl#BioPerl_Releases">release of BioPerl 1.6</a> - the first stable release in a several years containing many significant improvements and bug fixes.</p> <blockquote> <p>I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available.  This is the first BioPerl core release in the 1.6 series and is considered a &lsquo;stable&rsquo; (non-developer) release.  The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours.  A direct CPAN link is here:</p> <p><a href="http://search.cpan.org/~cjfields/BioPerl-1.6.0/">http://search.cpan.org/~cjfields/BioPerl-1.6.0/</a></p> <p>The release can also be directly downloaded here:</p> <p><a href="http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2">http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2</a> <a href="http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz">http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz</a> <a href="http://bioperl.org/DIST/BioPerl-1.6.0.zip">http://bioperl.org/DIST/BioPerl-1.6.0.zip</a></p> <p>Signature file: <a href="http://bioperl.org/DIST/SIGNATURES.md5">http://bioperl.org/DIST/SIGNATURES.md5</a></p> <p>Please feel free to report issues with testing, installation, etc. on the mail list, on this page:</p> <p><a href="http://www.bioperl.org/wiki/Release_1.6_Testing">http://www.bioperl.org/wiki/Release_1.6_Testing</a></p> <p>or via Bugzilla:</p> <p><a href="http://bugzilla.open-bio.org/">http://bugzilla.open-bio.org/</a></p> <p>We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days.  These will likely go through a short alpha release cycle depending on any problems that arise.  A PPM release for all distributions (including BioPerl core) will also be announced in the near future.</p> <p>Thanks to everyone for chipping in on getting this release out the door!  It&rsquo;s been a looooong wait&hellip;</p> <p>Enjoy!</p> <p>chris</p> </blockquote>https://www.open-bio.org/2009/01/23/bioperl-16-rc4/Fri, 23 Jan 2009 19:20:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/01/23/bioperl-16-rc4/<p><a href="http://lists.open-bio.org/pipermail/bioperl-l/2009-January/029000.html">RC4 is up</a>, we are days away from final release&hellip;</p>https://www.open-bio.org/2009/01/07/bosc-2009-accepted-by-ismb/Wed, 07 Jan 2009 17:07:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/01/07/bosc-2009-accepted-by-ismb/<p>Belated, and probably most of you knew already, but just in case you didn&rsquo;t, the <a href="http://open-bio.org/wiki/BOSC_2009">2009 Bioinformatics Open Source Conference</a> (BOSC) was accepted on Dec 16 as a Special Interest Group (SIG) meeting by the respective <a href="http://www.iscb.org/ismbeccb2009/">ISMB 2009</a> review committee. Special thanks and congratulations to Kam Dahlquist, who agreed again this year to chair the conference, and who pulled the proposal together.</p> <p>You can follow the organization and the conference taking shape at the <a href="http://open-bio.org/wiki/BOSC_2009">BOSC 2009 wiki page</a>. Ideas, preliminary schedules, etc are discussed  on the <a href="http://open-bio.org/wiki/Talk:BOSC_2009">associated talk page</a>. You are welcome and encouraged to join us there. The blurb for publicizing the event on the ISMB website is due on January 16, in a little more than 1 week. If you have ideas or would like to help, do let us know.</p>https://www.open-bio.org/2009/01/07/kam-dahlquist-elected-to-board-of-directors/Wed, 07 Jan 2009 16:51:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/01/07/kam-dahlquist-elected-to-board-of-directors/<p>The <a href="https://www.open-bio.org/wiki/Minutes:2008_ConfCall#Minutes" title="2008 BoD meeting minutes">minutes of the November 2008 O|B|F Board of Directors meeting</a> have been posted. The most important result of that meeting is that <a href="http://myweb.lmu.edu/kdahlqui/">Kam Dahlquist</a> was elected to the Board, bringing the number of <a href="https://www.open-bio.org/wiki/Board">Board members</a> back to four. Please join us in extending a warm welcome to Kam!</p> <p>We aim to elect additional Directors this year, please contact the <a href="https://www.open-bio.org/wiki/Board#Nominating_Committee">Nominating Committee</a> if you are interested in serving, or if you know people who might be. Suggestions of people we should tap to serve are also welcome and appreciated.</p> <p>Among the other topics discussed the more important ones were the preparations for BOSC 2009, the hosting offer from the Ohio Supercomputer Center (OSC), and possibilities for obtaining 501(c)3 tax exempt status. See the minutes for details.</p>https://www.open-bio.org/2008/12/26/bioperl-branched-for-16-rc1-is-up/Sat, 27 Dec 2008 01:07:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/12/26/bioperl-branched-for-16-rc1-is-up/<p>BioPerl has <a href="http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/branches/branch-1-6">branched for 1.6</a> and the RC1 is up for testing as <a href="http://lists.open-bio.org/pipermail/bioperl-l/2008-December/028791.html">Chris announced</a>.</p>https://www.open-bio.org/2008/12/09/bioperl-16-preparations/Tue, 09 Dec 2008 19:49:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/12/09/bioperl-16-preparations/<p><a href="http://bioperl.org/">BioPerl</a> is preparing for version 1.6 release in the coming months. As part of this some restructuring and simplification of the packaging is occurring.</p> <ul> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2008-December/028597.html">Bio-Graphics has been split off</a> into its own package back on <a href="http://gmod.cvs.sourceforge.net/viewvc/gmod/Bio-Graphics">Sourceforge</a> to allow for a separate release schedule. It will be uploaded to CPAN as a separate package. In the future other small groups of modules will also be split off from the Core.  Eventually the Core will constitute components that will be the main parsers and data objects while less-common use cases or tightly related modules (like bioperl-network) will be released to CPAN on their own.</li> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2008-December/028590.html">Tests have been split off</a> into smaller chunks.</li> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2008-December/028655.html">Anyone who has contributed to the code</a> and feels their name should be included in the authors&rsquo; list needs to either add it or email the mailing list or Chris Fields.</li> <li>S <a href="http://lists.open-bio.org/pipermail/bioperl-l/2008-December/028649.html">endu has moved</a> ModuleBuildBioperl and BioperlTest into Bio::Root</li> <li>Bugs are being triaged at <a href="http://bugzilla.open-bio.org">bugzilla</a> so if you have any opinions you can vote on the bugs in the queue.</li> </ul>https://www.open-bio.org/2008/11/21/biopython-release-149/Fri, 21 Nov 2008 16:51:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/21/biopython-release-149/<p>We are pleased to announce the release of Biopython 1.49. There have been some significant changes since <a href="http://news.open-bio.org/news/2008/09/biopython-release-148/">Biopython 1.48</a> was released a few months ago, which is why we initially <a href="http://news.open-bio.org/news/2008/11/biopython-149-beta-released/">released a beta</a> for wider testing. Thank you to all those who tried this and reported the minor problems uncovered.</p> <p><a href="http://news.open-bio.org/news/2008/09/biopython-numeric-and-numpy/">As previously announced</a>, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).</p> <p>As in the previous releases, Biopython 1.49 supports Python 2.3, 2.4 and 2.5 but should now also work fine on Python 2.6. Please note that we intend to drop support for Python 2.3 in a couple of releases time (see <a href="http://news.open-bio.org/news/2008/11/biopython-and-python-26-and-python-23/">previous news article</a>).</p> <p>We also have some new functionality, starting with the basic sequence object (the Seq class) which now has more methods. This encourages a more object orientated coding style, and makes basic biological operations like transcription and translation more accessible and discoverable.</p> <p>Our <a href="http://www.biopython.org/wiki/BioSQL">BioSQL interface</a> can now optionally fetch the NCBI taxonomy on demand when loading sequences (via Bio.Entrez) allowing you to populate the taxon/taxon_name tables gradually. Also, BioSQL should now work with the psycopg2 driver for PostgreSQL (as well as the older psycopg driver), and the handling of feature locations has also been improved.</p> <p>We&rsquo;ve also updated the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> (also available in <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p>Finally, our old parsing infrastructure (Martel and Bio.Mindy) is now considered to be deprecated, meaning mxTextTools is no longer required to use Biopython. This should not affect any of the typically used parsers (e.g. <a href="http://www.biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://www.biopython.org/wiki/SeqIO">Bio.AlignIO</a>).</p> <p>Given there have been more changes than in recent Biopython releases, please do check your old scripts still work fine, and let us know on the <a href="http://www.biopython.org/wiki/Mailing_lists" title="Biopython ailing lists">mailing list</a> or file a bug if there is anything wrong.</p> <p>Source distributions and Windows installers are available from the Biopython website: <a href="http://biopython.org/" title="Biopython website">biopython.org</a></p> <p>Thanks!</p> <p>-Peter on behalf of the Biopython developers</p>https://www.open-bio.org/2008/11/19/minutes2008-confcall/Wed, 19 Nov 2008 05:09:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/19/minutes2008-confcall/<p>Scheduled for Nov 19, 12:30 - 2PM PST via Conference call. Please email <a href="mailto:board@open-bio.org">board@open-bio.org</a> to receive call-in information so we will know how many callers there will be.</p> <h3 id="agenda">Agenda</h3> <h4 id="old-business">Old Business</h4> <ol> <li>Approve <a href="https://www.open-bio.org/wiki/Minutes:2008_BOSC_Meeting#Minutes">minutes from BOSC 2008 Meeting</a></li> </ol> <h4 id="new-business">New Business</h4> <ol> <li>To vote on a new member to the board, Kam Dahlquist</li> <li>Discuss leadership changes and plan how Board membership will be expanded in the next year</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2009">BOSC 2009</a>: planning is underway by BOSC committee, will discuss any input needed by BoD</li> <li><a href="https://www.open-bio.org/w/images/4/4c/2008-OBF-Treasurer-Report_Ammended2.pdf">Treasurer&rsquo;s financial report</a> from summer 2008, with accounts updated to be current for</li> <li>Any purchase or server hosting decisions <ul> <li>I put some thoughts regarding the OSC hosting offer on my talk page: <a href="https://www.open-bio.org/wiki/User:Dag">User:Dag</a> &ndash; <a href="https://www.open-bio.org/wiki/User:Dag">Dag</a> 20:34, 19 November 2008 (UTC)</li> </ul> </li> </ol> <h3 id="minutes">Minutes</h3> <p><strong>Venue:</strong> held by conference call, starting 12.30pm Pacific Time (US).</p> <p><strong>Attending:</strong></p> <ul> <li>Directors: Jason Stajich, Hilmar Lapp, Chris Dagdigian</li> <li>Director nominee: Kam Dahlquist</li> <li>Guests: Andrew McSweeny, Lonnie Welch, Steve Chervitz, Mauricio Herrera Cuadra</li> </ul> <p><strong>Minutes:</strong></p> <p>Hilmar calls meeting to order. All 3 current BoD members are present, so quorum for elections and decisions is reached. Brief introductions of the BoD members follow.</p> <ul> <li>Jason moves to approve the minutes from BOSC 2008, Chris seconds. Motion unanimously approved.</li> <li>Proceeded to vote on Kam Dahlquist&rsquo;s candidacy to the Board of Directors. Jason and Hilmar express their excitement about Kam volunteering to serve and gratitude about her patience with the amount of time it took to make this vote happen. Kam states her motivations and teaching and research interests, and how serving on the Board fits into that. <ul> <li>Votes cast as electronic ballots, using SurveyMonkey (with settings no IP logging, 3 votes max, one vote per computer).</li> <li>Result: Kam Dahlquist is unanimously elected to the Board of Directors with 3 votes in favor, none against, and none abstaining. We warmly welcome Kam to the Board.</li> </ul> </li> </ul> <h4 id="leadership-changes-board-expansion">Leadership changes, Board expansion</h4> <ul> <li>Kam suggests to use BOSC, in particular BOSC 2009 which is currently being planned, as a vehicle to direct a membership and leadership volunteering drive <ul> <li>We could create a mailing list of people to target</li> <li>Compile avenues for advertising.</li> <li>ISCB student council, ISCB education committee would be good allies for recruitment of members and exchange of ideas and information</li> <li>PLoS at ISMB 2008 has offered up ideas of mutual linking to each other on the respective websites. Kam would be willing to follow up on that if agreed upon.</li> </ul> </li> <li>What is the advantage of being a member, being a part of the organization? <ul> <li>Should create a concise statement of what those benefits are.</li> </ul> </li> <li>Should expand our mission statement to be broader about the support of open source software in bioinformatics, to better explain what the OBF stands for. <ul> <li>Pointer to and explicit support of OSI, lobby journals to encourage authors to use open-source licenses, promoting open source software to granting agencies</li> <li>Education is another aspect.</li> <li>We get interviewed on occasion by reporters. It would be great to have a statement of principles to point reporters and others to.</li> </ul> </li> <li>As an organization, we have oscillated between narrow project support and broader vision statement. <ul> <li>Have discussed pro-bono education activities to institutions that don&rsquo;t have the means to provide it.</li> <li>However, the reality is that most people are brought to the organization through the software being developed under the OBF umbrella. The manpower on the Board is very limited at this point, and it is not clear whether the membership would actually support (resource-wise) a wider mission.</li> </ul> </li> <li>Kam suggests to draft a vision statement, which could then be approved by the Board and serve as a reference. <ul> <li>Jason motions to revisit the vision statement and to draft an updated statement, which would then be invited for feedback and input by the membership. Hilmar seconds, and motion passes with unanimous consent.</li> <li>Suggested timeline is to have a draft up for people to look at one month in advance of the BOSC 2009 conference.</li> </ul> </li> </ul> <h4 id="bosc-2009">BOSC 2009</h4> <ul> <li>Kam as the organizing chair reports that the proposal is due today and will be submitted by her later today. <ul> <li>We will try something a bit unusual: the afternoon of the second day will feature an overlapping session with the Post-genomic Grand Challenges SIG (f.k.a. Post-ENCODE SIG), organized by Lonnie Welch.</li> <li>We plan to recruit 2 keynote speakers.</li> <li>Traditional sessions (Bio* updates, OSS, BoF, lightning talks) remain.</li> <li>We will try to actively recruit people to submit abstracts to the theme sessions.</li> <li>Authors presenting software will be asked to come prepared to give tutorials.</li> <li>Regular genomics hackathon being planned concurrent with the tutorials, led by Lonnie Welch and some work of his group.</li> <li>Kam is overseer and chair, Lonnie Welch will be co-chair and help with coordinating between the different theme sessions.</li> <li>ISCB&rsquo;s approval is due Dec 17, plan is to hit the ground running from that point on forward. We will be setting up OCS or EasyChair to manage the conference submissions.</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2009">BOSC 2009</a> page and <a href="https://www.open-bio.org/wiki/Talk:BOSC_2009">its discussion page</a> have dates and links.</li> </ul> </li> <li>Lonnie invites ideas and input to the regulatory genomics software and design patterns themes.</li> <li>Kam plans to subscribe all past conference participants to the BOSC-announce list, which is deemed fine unanimously.</li> <li>Plan is to make the submitted planning document public after submission.</li> </ul> <h4 id="osc-hosting-offer">OSC Hosting Offer</h4> <ul> <li>Ashok Krishnamurthy joins the meeting. He is Director of Research at the Ohio Supercomputer Center (OSC). <ul> <li>State-funded agency to provide computing services to the entire Ohio higher education community</li> <li>Hosting OBF seems much in keeping with the long-term charge of the OSC</li> <li>Would like to gather information on what would be involved in requirements and needed resources to take this back to his stakeholder community so they can decide.</li> </ul> </li> <li>Chris reports that currently we have 2 physical servers owned by the OBF, several virtual servers, located in a colocation cage with industry-standard security and network connection with several layers of redundancy. The source code server code.open-bio.org is hosted as a virtual server on BioTeam hardware. <ul> <li>Network bandwidth and colocation is donated by BioTeam.</li> <li>Due to the BioTeam contract, network bandwidth is limited to 11MB. OBF services don&rsquo;t come anywhere near to this at present.</li> <li>Most of the load originates from email.</li> <li>We have most of the system administration done by volunteers, for example mailing list administration.</li> </ul> </li> <li>Chris suggests that the limited system administration resources may have been one of the factors in being rather careful about starting up new projects under the umbrella.</li> <li>Maintenance and system administration is all run by volunteers.</li> <li>There has been a long-standing discussion about deploying test installations of various OBF umbrella-related services (such as DAS) and databases (such as GBrowse, BioSQL), as testbeds for developers.</li> <li>Lonnie&rsquo;s motivation was that the Ohio Bioinformatics Consortium is building infrastructure at present, which could synergize very well with the needs or goals of OBF. <ul> <li>Computing infrastructure for biologists, state-of-the-art turnkey solution for scientists.</li> </ul> </li> <li>Our current need doesn&rsquo;t really seem to be additional hardware, rather system administration resources. <ul> <li>Prebuilding ready-to-install images of the bioinformatics toolkits could be a unique service that OSC can provide.</li> </ul> </li> <li>Hardware and bandwidth to support OBF services: what are our current limitations? <ul> <li>Examples are databases for testing (BioSQL, GMOD, GBrowse), web-services (LSID, DAS, etc).</li> <li>OSC would need a concrete proposal of what they would provide, and how it would be used and by whom. <ul> <li>Biggest limitation is human resources, hardware resrouces are less limited.</li> <li>Ashok would work with Lonnie to create a value proposition.</li> </ul> </li> <li>Setup at BioTeam is tailored towards and focused on making the developers&rsquo; life easy. Possibility for OSC to provide value on the computing environment, such as web services and other software installations, protected shell accounts, etc. Could be a learning resource for building the software developed within the umbrella. <ul> <li>Could also have good synergy with the Bioinformatics fellowship program at Ohio, students are always in search of thesis projects. Could also tie in with a Summer of Code participation.</li> <li>Ashok states that would fall very well in line with the Ohio Bioinformatics Consortium&rsquo;s mission.</li> </ul> </li> <li>Steve Chervitz comments that this would likely create great interest in the DAS community, which has recently become quite active again. The community could also contribute to mentoring trainees, such as Summer of Code students or Ohio bioinformatics students. <ul> <li>IGB could also be hosted by OBF (is presently hosted at SourceForge, which has had problems).</li> </ul> </li> </ul> </li> <li>Jason motions to draft a proposal to the Ohio Bioinformatics Consortium about which hardware resources the OSC could uniquely contribute, and what formal mentorship relationships could be developed for developer trainees. <ul> <li>Hilmar seconds. Approved by unanimous consent.</li> <li>Jason is willing to provide ideas, Chris volunteers to help with fleshing out and write. Hilmar would also be willing to help. Aiming for 1st quarter in 2009.</li> <li>Lonnie says that the Bioinformatics Scholarship program of OBC is just coming online, so having something in Q1 2009 would be good. Suggests to have a brainstorming call even before Xmas.</li> </ul> </li> <li>Hardware purchase decisions are postponed for when the proposal is written. <ul> <li>Our current systems are 32-bit, need to upgrade in 2009.</li> </ul> </li> </ul> <h4 id="financial-report">Financial report</h4> <ul> <li>Cash balance gets swept into a money market account and earns very little interest ($125).</li> <li>The current balance stems nearly entirely from the early BOSC conferences, and was hence earned several years ago. <ul> <li>Our revenue from BOSC has completely dried up due to ISCB handling the BOSC budget and finances.</li> </ul> </li> <li>Received two donations at BOSC 2008 ($1,000 from Helicos, $250 from an anonymous donor) <ul> <li>The $250 donation was awarded to two student presenters as travel support. Still need to send those checks.</li> <li>The $1000 check has been deposited. The funds will be used to pay the keynote speaker expenses.</li> </ul> </li> <li>Minor expenses (primarily domain purchases or extensions) are mostly donated by Chris.</li> <li>Kam repors that the current balance of the escrow account with ISCB is $14,847.25. This increased from 2007 because we made a surplus at the 2008 conference and did not pay expenses out of escrow. <ul> <li>Keynote speaker expenses and compensation will be reimbursed from bank account, not the ISCB escrow. This still needs to be completed.</li> </ul> </li> <li>Comment from Andrew that the cost of attending BOSC is too high and that that was the main reason for him not to attend in 2008. <ul> <li>We have no control over how ISCB sets the registration fee. We could try to influence the amount, but past experience shows that this is not likely going to affect much if anything.</li> <li>But we can institute a student scholarship program. Need to investigate how we can award scholarships out of the ISCB escrow; this will likely need to be tied to reimbursing travel costs.</li> <li>Should assess how many students we have had in 2008, and see whether a scholarship program can change this.</li> <li>Postponing an actual motion on this until we have the numbers on the table on costs, how much we can afford, and how much impact we could make.</li> </ul> </li> <li>Chris apologizes for having dropped the ball several times on the course to re-establish the corporation in good standing, and to becoming 501(c)3 approved. <ul> <li>Chris offers his resignation if requested by the Board. None of the Directors motions to request this, so the offer is dismissed.</li> <li>Reminds us that the 501(c)3 process takes a non-negligible amount of work, and we should be sure that the effort is worth the benefits and in line with our future mission. Cost would be up to $4,000 one-time for the IRS paperwork, and annual expenses for financial and accounting compliance could be $1,500-2000.</li> <li>Incorporated as a Delaware not-for-profit fraternal organization. We are back in good standing with the State of Delaware (which requires $75 in fees annually).</li> </ul> </li> <li>Conclusion is to revisit this question when we draft the extended mission statement. It is deemed critical that we know what we would spend the money for if we are going down the route of fund-raising.</li> </ul> <h3 id="final-remarks">Final remarks:</h3> <ul> <li>Phone conference worked pretty well, and could work well going forward in helping us make decisions when we need to rather than being stalled due to quorum issues.</li> <li>Chris suggests to integrate Webex or a Webex-like service to have more interactivity.</li> </ul> <p>Meeting adjourns at 2.40pm Pacific Time (US).</p> <p><strong>Note added in proof</strong></p> <p>After the meeting Steve Trutane (f.k.a. Chervitz), and in response Hilmar, provided additional information and comments on the 501(c)3 status alternatives. Specifically, there is mechanism called <a href="http://en.wikipedia.org/wiki/Fiscal_sponsorship"><em>Fiscal Sponsorship</em></a> (see also <a href="http://www.publiccounsel.org/cdp/fiscal_sponsor.pdf">http://www.publiccounsel.org/cdp/fiscal_sponsor.pdf</a>) which may offer a promising alternative that avoids the hassle and costs of gaining and maintaining 501(c)3 status ourselves, yet would retain the benefits for donors. It turns out that the <a href="http://conservancy.softwarefreedom.org/">Software Freedom Conservancy</a> mentioned during the meeting is exactly such a Fiscal Sponsorship offering entity with a focus on open-source software projects. For the purposes of becoming a Conservancy member, the core OBF activities (such as providing project infrastructure and running BOSC) might then become their own sub-project.</p>https://www.open-bio.org/2008/11/18/obf-conference-call-board-meeting/Tue, 18 Nov 2008 19:46:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/18/obf-conference-call-board-meeting/<p>The OBF Conference call is scheduled for 12:30PM to 2PM PST on Wednesday Nov 19, 2008.  Members of the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a> and those interested in the decisions are invited to listen in and participate.  A brief agenda is available <a href="https://www.open-bio.org/wiki/Minutes:2008_ConfCall">here</a>.</p> <p>Please email Hilmar Lapp at hlapp _AT_ gmx.net for call in number and codes if you wish to participate or listen to the discussion.  Those official members should have gotten an email via the  OBF members email list.</p>https://www.open-bio.org/2008/11/17/minutes2008-bosc-meeting/Mon, 17 Nov 2008 05:07:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/17/minutes2008-bosc-meeting/<h3 id="agenda">Agenda</h3> <ul> <li>Old Business <ol> <li>Approval of <a href="https://www.open-bio.org/wiki/Minutes:2007_BOSC_Meeting">minutes from 2007</a></li> </ol> </li> <li>New Business <ol> <li>Current Board <ul> <li>Confirm past term expirations of those who did not run again for the Board.</li> <li>What to do about the Secretary seat?</li> <li>Some of the items on the agenda here need a legitimate vote by the Board (with prior notification and quorum satisfied). Should plan for a (presumably virtual) voting Board meeting soon afterwards.</li> <li>How can we better ensure quorum?</li> </ul> </li> <li>Voting on the board appointments <ul> <li>Kam Dalhquist has already served as a major organizer for BOSC and is interested in helping lead the OBF to achieve more outreach and education.</li> <li>Darin London has served as BOSC chair for the past 4 years</li> <li>Strengthen connection with O|B|J</li> <li>Procedure for appointment of additional BOD members</li> </ul> </li> <li>Financial report (Treasurer) <ul> <li>Account standing, reserves</li> <li>501(c)3 accounting and filing status</li> <li>Sponsorship accounting</li> </ul> </li> <li><a href="https://www.open-bio.org/wiki/BOSC">BOSC</a> <ul> <li>Short 2007 report (attendance, talk highlights)</li> <li>BOSC 2008 summary (attendance, talk hightlights)</li> <li>Should BOSC 2009 to be held in conjuction with ISMB2009?</li> <li>Possibilities for including submitted papers for a publication.</li> </ul> </li> <li>OBF Membership accounting and drive to register more members <ul> <li>Membership forms physical records</li> <li>Members who are citizens of trade-restricted countries - legal advice, file for exemption?</li> <li>Form doesn&rsquo;t give date, need to amend</li> </ul> </li> <li>OBF future directions</li> <li>Review of By-Laws (Parliamentarian) <ul> <li>10-days prior notice of Board meeting requirement: need to change or have a standing Board meeting (BoF) on day 1 or 2 of BOSC</li> <li>Not clear who elects officers - members may, but not a requirement, Directors can elect officers too. Leave as is or change?</li> </ul> </li> </ol> </li> </ul> <h3 id="minutes">Minutes</h3> <p><strong>Location:</strong> Radisson Harbourfront, 5th floor poolside, July 18, 2008</p> <p><strong>Present:</strong></p> <ul> <li>current BoD members: Jason Stajich, Hilmar Lapp</li> <li>Director nominee: Kam Dahlquist</li> <li>Guests: Aaron Mackey, Mauricio Herrera Cuadro, Michael Heuer, Paul Gordon, Andrew Jenkinson, Saravanabamuttu Gnaneshan</li> </ul> <p><strong>Meeting minutes:</strong></p> <p>Approval of 2007 meeting notes</p> <ul> <li>unanimously approved</li> </ul> <p>Introductions of present BoD members and guests</p> <h4 id="obf-board">OBF Board</h4> <ul> <li>Term expirations confirmed.</li> <li>Board currently consists of Jason Stajich, Hilmar Lapp, and Chris Dagdigian.</li> <li>How to ensure Board meetings to meet bylaw requirements? <ul> <li>Teleconference over the phone</li> <li>IRC not favored, might pose undue burden, also identification might be problematic</li> <li>multi-jabber would be a possibility but also disfavored as creating a barrier (and technical issues)</li> <li>Teleconference will be our future modus for binding vote-entitled Board meetings, meetings at BOSC will have BoF/membership discussion character</li> </ul> </li> <li>Soliciting new leadership contribution <ul> <li>OBF is a volunteer effort.</li> <li>Ability of people to commit time may depend on their institution&rsquo;s or employer&rsquo;s commitment to support this.</li> <li>Frequent observation of volunteer projects is that there is a small group of people doing everything, getting burned out, and then moving on, requiring a new leadership to be recruited.</li> <li>One can only encourage people to join if there is critical mass, professional conduct.</li> <li>Consider projects and organizations that weren&rsquo;t presenting (Cytoscape and Ensembl as examples).</li> </ul> </li> <li>Size of Board: bylaws doesn&rsquo;t make a stipulation.</li> <li>Election procedure <ul> <li>Explained procedure laid out by the bylaws.</li> <li>Nominating committee should network and advertise broadly to obtain a pool of Director candidates.</li> <li>Aaron Mackey volunteers to serve on the Nominating Committee.</li> <li>Set ourselves a deadline of Sep 15 to have the nomination process complete and hold the BoD meeting the elects them.</li> <li>Will approach members and consituents for suggestions of whom to approach.</li> <li>Should aim for electing at least two new Directors, possibly 3.</li> <li>Kam is on slate to be nominated for Director, and is committed to serve.</li> <li>Should invite Darin London whether we would be interested in serving.</li> <li>Should invite Toshiaki Katayama, or someone else he suggests from OBJ, to serve.</li> <li>Would we want to be exclusionary to anyone? Only to people or organizations who would want to commercialize the organization, in whatever aspect.</li> </ul> </li> <li>Secretary officer will temporarily held by Parliamentarian.</li> </ul> <h4 id="financial-report">Financial report</h4> <ul> <li>No update from Chris Dagdigian.</li> <li>Haven&rsquo;t lost any money, still have about $30,000 in two accounts.</li> <li>Kam will get ISMB account straightened out.</li> </ul> <h4 id="bosc">BOSC</h4> <ul> <li>Bad catering for the meeting (only coffee, less-than-great lunch)</li> <li>No computer support for presentation.</li> <li>Need to resign ourselves to the fact that ISCB is factually no longer accountable to the SIGs since they absorb the losses and keep the profits.</li> <li>Concern that ISCB will factor the accounting such so that our historical surplus drops to zero, and may cut BOSC then.</li> <li>Is there an alternative venue for people to present instead of at BOSC? <ul> <li>Possibly OSCON, but who would attend / be able to attend OSCON?</li> <li>ISMB covers many of the areas that motivates our constituency to come.</li> <li>Should we hold the meeting at the same place at ISMB but organize it separately?</li> <li>Conclusion: Hold BOSC 2009 in conjunction with ISMB. <ul> <li>But don&rsquo;t want to end up with the same situation as in Brisbane.</li> <li>Supporting organizing committee attendance; OBF needs to be prepared to absorb the travel of the BOSC organizing committee chair (if the person&rsquo;s attempts to secure funding from elsewhere fail).</li> </ul> </li> </ul> </li> <li>Structure of BOSC: <ul> <li>Balance between demonstrations and presentations should be improved.</li> <li>Could be very useful to fold OBF project tutorials (or others) into BOSC.</li> <li>Software could be subject of talks on the first and of tutorials on the second day. Should presenters come prepared to give tutorials?</li> <li>Content seems to work though for user-developers in terms of getting the information that they were looking for?</li> </ul> </li> <li>Marketing the conference can be improved upon a lot. <ul> <li>Professional review with for the first time got feedback to the submitters.</li> <li>Open source requirements were pretty rigorously enforced.</li> <li>Emphasis on quality should help with marketing in the future.</li> </ul> </li> <li>BOSC 2007 attendance was 97 (registered) <ul> <li>Have 77 primary sign-ups this year.</li> </ul> </li> </ul> <h4 id="bosc-proceedings">BOSC proceedings:</h4> <ul> <li>Page charges from BMC are very high (BP850 normally, BP500 in bulk (BP10,000 for 20 papers) but then we have to do all the work ourselves).</li> <li>Authors may not have the incentive to use this venue because they may want to publish a full paper in a higher-impact venue.</li> <li>Should BOSC have Proceedings? <ul> <li>People should have the possibility to present at BOSC.</li> <li>We are not at the level of quality as ISMB is.</li> <li>The main thing that comes out of BOSC is code, presentations don&rsquo;t really add the main value.</li> <li>We&rsquo;re not ready for having</li> </ul> </li> <li>Looks like this is a non-issue?</li> </ul> <h4 id="obf-fund-drive">OBF fund drive</h4> <ul> <li>Using training to gain funds?</li> <li>Having more people on the Board should give us more possibilities to explore opportunities to raise funds.</li> <li>Sponsorship <ul> <li>BioTeam donates bandwidth, colocation space, domain purchases. Should acknowledge that appropriately on the OBF website.</li> <li>Have sponsorship for BOSC from Helicos ($1000) and an anonymous donor ($250). The latter will fund the student travel fellowship and the former will subsidize the keynote speaker. <ul> <li>Possibly remaining funds will be used towards travel fellowships in 2009.</li> </ul> </li> <li>May in the future need to secure sponsorship to fund organizer travel.</li> </ul> </li> </ul> <h4 id="membership">Membership</h4> <ul> <li>Trade restrictions: <ul> <li>Can we re-incorporate in Canada?</li> <li>Should we seek legal advice? Yes, pro-bono if possible.</li> </ul> </li> <li>Should chang the form to include date, having that is useful.</li> </ul>https://www.open-bio.org/2008/11/08/obf-board-meeting/Sat, 08 Nov 2008 13:30:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/08/obf-board-meeting/<p>The OBF board meeting will be held via conference call on Nov 19, from 12:30PM to 2PM PST.  Agenda items and information about participating is available on the <a href="http://open-bio.org/wiki/Minutes:2008_ConfCall">agenda webpage</a>. We anticipate this call primarily to manage administrative tasks for the foundation. We welcome input on including more members in the OBF leadership and helping set the direction for the foundation.</p>https://www.open-bio.org/2008/11/07/biopython-149-beta-released/Fri, 07 Nov 2008 16:45:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/07/biopython-149-beta-released/<p>We are pleased to announce a beta release of Biopython 1.49. There are been some significant changes since <a href="http://news.open-bio.org/news/2008/09/biopython-release-148/">Biopython 1.48</a> was released two months ago, which is why we are initially releasing a beta for wider testing.</p> <p>As <a href="http://news.open-bio.org/news/2008/09/biopython-numeric-and-numpy/">previously announced</a>, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).</p> <p>As in the previous releases, Biopython 1.49 beta supports Python 2.3, 2.4 and 2.5 but should now also work fine on <a href="http://www.python.org/download/releases/2.6/">Python 2.6</a>. Please note that we intend to drop support for Python 2.3 in a couple of releases time (see <a href="http://news.open-bio.org/news/2008/11/biopython-and-python-26-and-python-23/">previous news article</a>).</p> <p>We also have some new functionality, starting with the basic sequence object (the Seq class) which now has more methods. This encourages a more object orientated coding style, and makes basic biological operations like transcription and translation more accessible and discoverable.</p> <p>Our <a href="http://www.biopython.org/wiki/BioSQL">BioSQL interface</a> can now optionally fetch the NCBI taxonomy on demand when loading sequences (via Bio.Entrez) allowing you to populate the taxon/taxon_name tables gradually. Also, BioSQL should now work with the psycopg2 driver for PostgreSQL (as well as the older psycopg driver).</p> <p>Finally, our old parsing infrastructure (Martel and Bio.Mindy) is now considered to be deprecated, meaning mxTextTools is no longer required to use Biopython. This should not affect any of the typically used parsers (e.g. <a href="http://www.biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://www.biopython.org/wiki/AlignIO">Bio.AlignIO</a>).</p> <p>So, if you are feeling brave and know the risks, please try out Biopython 1.49 beta, and let us know on the <a href="http://www.biopython.org/wiki/Mailing_lists">mailing lists</a> if it works, or more importantly if something doesn&rsquo;t.</p> <p>We&rsquo;d also like feedback on the updated <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> (also available in <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p>Source distributions and Windows installers are available from the Biopython website: <a href="http://biopython.org">biopython.org</a></p> <p>Thanks!</p> <p>-Peter on behalf of the Biopython developers</p>https://www.open-bio.org/2008/11/02/biopython-and-python-26-and-python-23/Sun, 02 Nov 2008 11:54:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/02/biopython-and-python-26-and-python-23/<p>Many of you will be aware that <a href="http://www.python.org/download/releases/2.6/">Python 2.6</a> was released a month ago (October 1st, 2008). This supports a lot of new syntax and functionality, but also deprecates some old modules (e.g. the sets module).</p> <p>While <a href="http://news.open-bio.org/news/2008/09/biopython-release-148/">Biopython 1.48</a> does mostly work with Python 2.6, we&rsquo;ve been testing with Python 2.6 and have fixed a number of deprecations or breakages in <a href="http://www.biopython.org/wiki/CVS">our CVS repository</a>. If using Biopython with Python 2.6 is important to you, please help out by testing the CVS code (which needs <a href="http://news.open-bio.org/news/2008/09/biopython-numeric-and-numpy/">NumPy and not Numeric</a>) and letting us know on the <a href="http://www.biopython.org/wiki/Mailing_lists">mailing list</a> or <a href="http://bugzilla.open-bio.org/">bugzilla</a> if we&rsquo;ve missed anything.</p> <p>The next release of Biopython <em>should</em> support Python 2.3 to 2.6 inclusive :)</p> <p>However, the bad news is that we are considering dropping support for Python 2.3 after only a couple more releases - please get in touch via the <a href="http://www.biopython.org/wiki/Mailing_lists">mailing list</a> ASAP if this will cause you problems.</p>https://www.open-bio.org/2008/09/22/biopython-numeric-and-numpy/Mon, 22 Sep 2008 15:06:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/09/22/biopython-numeric-and-numpy/<p>To date, <a href="http://biopython.org">Biopython</a> releases have relied on the original numerical python library, <strong>Numeric</strong> (used in python with &ldquo;import Numeric&rdquo;).  In the next release we will at last be moving to its successor, <strong>NumPy</strong> (used in python with &ldquo;import numpy&rdquo;).</p> <p>This transition is already under way in the Biopython source code repository.  For further details, or to voice your opinion or enthusiasm, please join the <a href="http://biopython.org/wiki/Mailing_lists">Biopython Mailing List(s)</a>.</p> <p>Finally, for anyone interested in the background story, the SciPy project has a page describing the <a href="http://www.scipy.org/History_of_SciPy">history of the numerical python libraries</a>.</p>https://www.open-bio.org/2008/09/09/biopython-release-148/Tue, 09 Sep 2008 10:03:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/09/09/biopython-release-148/<p>We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete).</p> <p>The following additional file formats are now supported in <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a>:</p> <ul> <li>reading and writing &ldquo;tab&rdquo; format (simple tab separated)</li> <li>writing &ldquo;nexus&rdquo; files</li> <li>reading &ldquo;pir&rdquo; files (NBRF/PIR)</li> <li>basic support for writing &ldquo;genbank&rdquo; files (GenBank plain text)</li> </ul> <p>This release also fixes some problems reading Clustal alignments (introduced in Biopython 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers.</p> <p>The SeqRecord and Alignment objects have a new method to get the object as a string in a given file format (handled via Bio.SeqIO and Bio.AlignIO).</p> <p>Bio.PubMed and the online code in Bio.GenBank are now considered obsolete, and we intend to deprecate them after the next release. For accessing PubMed and GenBank, please use Bio.Entrez instead. Martel and Bio.Mindy are now considered to be obsolete, and are likely to be deprecated and removed in a future release, at which point we will drop the optional dependency on mxTextTools. Bio.Fasta is also considered to be obsolete, please use Bio.SeqIO instead. We do intend to deprecate this module eventually, however, for several years this was the primary FASTA parsing module in Biopython and is likely to be in use in many existing scripts.</p> <p>In addition a number of other modules have been deprecated, including: Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics - see the DEPRECATED file for full details.</p> <p>Source distributions and Windows installers are available from the Biopython website: <a href="http://biopython.org/">biopython.org</a></p> <p>My thanks to all bug reporters, code contributors and others who made this new release possible.</p> <p>&ndash;Peter on behalf of the Biopython developers</p>https://www.open-bio.org/2008/08/13/biosql-v101-released/Wed, 13 Aug 2008 11:38:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/08/13/biosql-v101-released/<p>This is a belated news entry announcing the second BioSQL v1.0 (code-named Tokyo) release, v1.0.1, which was made on August 2, 2008. It is available from the <a href="http://www.biosql.org/wiki/Downloads">BioSQL downloads</a> page.</p> <p>This version of the schema should be fully backwards compatible with the v1.0.0 schema for nearly all software and queries. The only change is relaxing a column width constraint. Migration scripts are for those who want to simply upgrade their existing database.</p> <p>In addition, the script load_ncbi_taxonomy.pl has been fixed to no longer require the taxon primary key and the NCBI taxon ID to be identical. The Bio* language bindings should not be affected by this change.</p> <p>For full details, see <a href="http://lists.open-bio.org/pipermail/biosql-l/2008-August/001311.html">Hilmar&rsquo;s official announcement</a> on the BioSQL mailing list</p>https://www.open-bio.org/2008/07/05/biopython-release-147/Sat, 05 Jul 2008 23:50:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/07/05/biopython-release-147/<p>We are pleased to announce the release of Biopython 1.47.</p> <p>This release includes a new <a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a> module, updates to Bio.Blast, parsers for NCBI&rsquo;s Entrez E-Utilities, numerous other code improvements and fixes, and an extended and updated documentation. In particular if you use Biopython to access NCBI&rsquo;s E-Utilities, we encourage you to download and install this release to ensure full compliance with NCBI&rsquo;s access rules.</p> <p>Source distributions and Windows installers are available from the Biopython website at <a href="http://biopython.org">http://biopython.org</a>. My thanks to all code contributors who made this new release possible.</p> <p>&ndash;Michiel on behalf of the Biopython developers</p>https://www.open-bio.org/2008/05/18/julian-lombardi-will-present-keynote-at-bosc-2008/Sun, 18 May 2008 19:23:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/05/18/julian-lombardi-will-present-keynote-at-bosc-2008/<p>The BOSC 2008 Organizing Committee is pleased to announce that Julian Lombardi will be giving the keynote address this year. Dr. Lombardi is one of the original architects of the open-source, peer-to-peer OpenCroquet platform for creating and deploying deeply collaborative multi-user online applications and virtual worlds.</p> <p>For further information about Dr. Lombardi, see the <a href="http://en.wikipedia.org/wiki/Julian_Lombardi">Wikipedia entry about him</a>, <a href="http://jlombardi.blogspot.com/">his blog</a>, and the <a href="http://www.opencroquet.org">OpenCroquet website</a>.</p>https://www.open-bio.org/2008/03/22/biopython-release-145/Sat, 22 Mar 2008 10:55:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/03/22/biopython-release-145/<p>We are pleased to announce the release of Biopython 1.45.</p> <p>This release includes numerous code improvements and fixes, including in Bio.Seq, Bio.SeqIO, Bio.Entrez, Bio.PopGen, Bio.SwissProt, Bio.Cluster, Bio.SCOP, Bio.InterPro, Bio.GenBank, Bio.ExPASy, BioSQL, and the Biopython documentation. Too many to list them all here!</p> <p>Source distributions and Windows installers are available from the Biopython website at <a href="http://biopython.org">http://biopython.org</a>. My thanks to all code contributers who made this new release possible.</p> <p>&ndash;Michiel on behalf of the Biopython developers</p>https://www.open-bio.org/2008/03/06/biosql-v100-released/Fri, 07 Mar 2008 01:04:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/03/06/biosql-v100-released/<p>After a long wait and several earlier attempts, version 1.0.0 (code-named Tokyo, see below) of BioSQL has finally been released. The release can be downloaded at <a href="http://biosql.org/DIST/">http://biosql.org/DIST/</a> as .tar.gz, .tar.bz, and Zip (which also has Windows-style end-of-line characters) archives. The <a href="http://lists.open-bio.org/pipermail/biosql-l/2008-March/001190.html">full release announcement</a> can be found in the BioSQL mailing list archives, and in the distribution itself.</p> <p>This version of the schema has essentially been the same since November 2004. Software that worked with schema versions downloaded from CVS (or, as of lately, svn) after November 2004 should work with all 1.0.x releases. The release contains the core BioSQL schema for several RDBMSs (MySQL, PostgreSQL, Oracle, HSQLDB, and Apache Derby), accompanying documentation, and a Perl script to preload or update the NCBI taxonomy.</p> <p>BioSQL is a generic, extensible relational model for sequences, sequence features, their annotation, and ontology terms. It is also designed as the interoperable persistence interface between the Bio* projects. Additional information regarding BioSQL, including links to language bindings, a roadmap to future releases and enhancements, and possible local optimizations is available from the <a href="http://biosql.org/">BioSQL website</a>.</p> <p>This release and the accompanying work was irreversibly set in motion at the BioHackathon 2008 in Tokyo, and would not have happened without the active encouragement from several hackathon participants, especially Heikki Lehvähslaiho, Mark Schreiber, Richard Holland, and Raoul Bonnal. In recognition of this, and in keeping with an informal tradition held up since the first BioHackathon, I am code-naming the 1.0.x release series the Tokyo release series of BioSQL.</p> <p>Enjoy!</p>https://www.open-bio.org/2008/02/18/bosc-2008-is-on/Mon, 18 Feb 2008 15:35:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/02/18/bosc-2008-is-on/<p>Our application to hold BOSC as a two-day SIG (Special Interest Group) meeting in conjunction with ISMB has been accepted for this year. BOSC will take place July 18 and 19 in Toronto, Canada.</p> <p>For the first time this year, the second conference day will overlap with the ISMB tutorial day, in an attempt to make the overall stay shorter for those who want to attend both BOSC and ISMB. The other upside of this is that BOSC attendees who stay on for ISMB can reflect on the event at the ISMB Opening Reception, which will be held the same night as BOSC concludes.</p> <p>In our outline we propose a more structured agenda with several sessions dedicated to specific challenging topics in our field, for example on currently intractable (or very hard) problems in bioinformatics, emerging technologies, best practices, and - of course - bioinformatics open source software. Over the next couple of weeks we&rsquo;ll flesh those out as needed, and put up calls for submissions.</p> <p>Hence, if you were thinking about submitting, don&rsquo;t hold off preparing until the official call, and if you weren&rsquo;t, think again. It&rsquo;s going to be a really interesting conference. Also, if you have any suggestions for session topics, please come forward and email us as soon as possible at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a>.</p>https://www.open-bio.org/2007/10/28/biopython-release-144/Sun, 28 Oct 2007 06:19:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/10/28/biopython-release-144/<p>We are pleased to announce the release of Biopython 1.44.</p> <p>This release includes lots of code improvements and fixes in the Blast interface and parsers, sequence input/output, the SwissProt parser, the clustering routines, as well as a brand new module for population genetics. For reasons of compatibility, some radical changes were necessary in some parts of the code; please let us know if you find some functionality missing.</p> <p>Source distributions and Windows installers are available from the Biopython website at <a href="http://biopython.org">http://biopython.org</a>. My thanks to all code contributers who made this new release possible.</p> <p>&ndash;Michiel on behalf of the Biopython developers</p>https://www.open-bio.org/2007/07/21/minutes2007-bosc-meeting/Sat, 21 Jul 2007 15:58:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/07/21/minutes2007-bosc-meeting/<p><strong>Venue:</strong> Cafe Prückl, Vienna <strong>Date:</strong> 7/21/2007, 5.30pm <strong>Attending:</strong> Jason Stajich (OBF President), Hilmar Lapp (OBF Parliamentarian), Darin London, Kam Dahlquist</p> <h3 id="bosc">BOSC</h3> <ul> <li>Had 94 attendees registered specifically for BOSC as of July 9th</li> <li>Do we have an audience? Is there a niche that BOSC continues to fill? The numbers seem to speak a clear voice.</li> <li>Show-and-tell was received positively, but didn&rsquo;t play as big a role anymore</li> <li>Want to continue running the conference</li> <li>Venue: <ul> <li>Seems much favorable to associate with an existing major event</li> <li>One model could be to associate with different events on an alternating basis, such as IMSB every other year and a different conference every other year</li> </ul> </li> <li>Need a new Organizing Committee, several people volunteered to help organizing <ul> <li>Committee should decide on sessions, timetable, outreach venues</li> <li>Session chairs who are also charged to identify the most desirable speakers</li> <li>Should have budget to reimburse travel for key speakers who otherwise wouldn&rsquo;t be able to come</li> <li>Need to look into venue and procedure for publishing the talks</li> <li>Include a hackathon?</li> </ul> </li> </ul> <p><strong>Action items:</strong></p> <ul> <li>Darin to craft on-line feedback survey for BOSC</li> <li>Darin to draft initial call for nomination to the BOSC Organizing Committee (BOC)</li> <li>Darin to collate required responsibilities for the BOC in the run up to the conference</li> </ul> <h3 id="open-bio-board">Open-Bio Board</h3> <ul> <li>Membership of the BOD <ul> <li>Current members are technically Jason Stajich, Chris Dagdigian, Andrew Dalke, Ewan Birney, Hilmar Lapp</li> <li>Steven Brenner resigned in 2006.</li> </ul> </li> <li>Financial report: <ul> <li>Have $15k in the bank.</li> <li>Have not filed a tax report since incorporation.</li> <li>Need to hire an accountant (for filing tax reports), lawyer (re-incorporate).</li> <li>(Paste points from Chris&rsquo; letter here)</li> </ul> </li> </ul> <h3 id="mission-of-the-organization">Mission of the organization</h3> <ul> <li>Want do continue what we do right now, i.e., infrastructure support for the projects <ul> <li>Should ask project leaders for what they need</li> </ul> </li> <li>Should we take a more active role? <ul> <li>Public opinion forming on open source software?</li> <li>Should be present at the open-source panel</li> <li>Outreach and education?</li> </ul> </li> <li>Advertising and outreach for BOSC is also advertising for OBF <ul> <li>Makes us appear on people&rsquo;s minds, something that people want to be a part of</li> <li>Regular letters about news of BOSC</li> <li>OBF official blog?</li> </ul> </li> <li>Community building: <ul> <li>Creating ways for people to reach others</li> <li>Providing a forum for people to engage in discourse about how to advance the state of open source in bioinformatics</li> <li>Connect possibly &ldquo;competing&rdquo; projects to make an attempt at advancing the quality and availability of software</li> <li>Coordinate meet-ups of people at other events (other than BOSC)</li> <li>Must not be exclusive or ideologic</li> </ul> </li> <li>Create a year-long plan leading up to BOSC 2008 <ul> <li>Generate excitement</li> <li>Need mechanism to identify who is currently on the board</li> <li>Need mechanism to identify those who aren&rsquo;t contributing, and remove them from board</li> <li>Need to identify new treasurer</li> <li>Need to identify candidates who would like to serve on the board</li> <li>Revitalize and reform the board</li> </ul> </li> </ul> <p><strong>Action items:</strong></p> <ul> <li>Jason to identify a lawyer</li> <li>Jason to investigate and identify mailing address</li> <li>Will hold follow-up conference call (phone or skype or IRC) in August</li> </ul>https://www.open-bio.org/2007/07/09/are-you-going-to-ismbbosc-2007/Tue, 10 Jul 2007 01:33:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/07/09/are-you-going-to-ismbbosc-2007/<p><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="">If you&rsquo;ll be at BOSC or ISMB - please see this page and sign your name if you would like to try and meet up.  We&rsquo;ll do a developer&rsquo;s dinner as well as have a BoF.</p> <p><a href="http://bioperl.org/wiki/BOSC2007_Meetup">http://bioperl.org/wiki/BOSC2007_Meetup</a></p>https://www.open-bio.org/2007/07/09/hey-whats-happening/Tue, 10 Jul 2007 01:30:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/07/09/hey-whats-happening/<p>So <a href="http://bioperl.org/wiki/Mailing_list_summaries">Mailing list summaries</a> have stopped because we need someone else to help post these summaries. Not a light job unfortunately. If you are interested, please post to the mailing list or contact Jason, Sendu, or Chris for more details. This is one way you can help BioPerl without contributing code if you aren&rsquo;t comfortable with that type of commitment.</p> <p>Two things that have been discussed on the mailing list lately are:</p> <ul> <li>Converting from CVS to SVN for code repository</li> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2007-July/026057.html">Splitting</a> BioPerl core code ( <a href="http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/">bioperl-live</a> CVS repository) into separate pieces to reduce the number of modules in the &ldquo;Core&rdquo; code base.</li> </ul> <p>If you have an opinion about this - please join the discussion on the mailing list.</p>https://www.open-bio.org/2007/06/15/howto-automate-tree-drawing/Fri, 15 Jun 2007 18:01:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/06/15/howto-automate-tree-drawing/<p>I updated the <a href="http://bioperl.org/wiki/HOWTO:Trees#Making_Images_of_Trees">Trees HowTo</a> with some code demonstrating how to automatically generate postscript trees from newick or nexus tree files. This uses the <code>Bio::Tree::Draw::Cladogram</code> module that will draw Phylograms or Cladograms. With a few unix tools ( <a href="http://search.cpan.org/dist/eps2png/">eps2png</a> and epstopdf [part of <a href="http://ctan.org/">TeX</a>]) you can generate png and pdf files automatically making this an easy addition to phylogenetic pipelines that generate webpages as well as stand alone applications.</p>https://www.open-bio.org/2007/06/14/mediawiki-updated-2/Thu, 14 Jun 2007 06:09:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/06/14/mediawiki-updated-2/<p>Updated mediawiki to 1.10</p> <p>Did a bulk creation of a number of modules wiki pages for modules that had been previously created but not added to the wiki. Added them with default module templates.</p>https://www.open-bio.org/2007/03/17/biopython-release-143/Sat, 17 Mar 2007 23:15:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2007/03/17/biopython-release-143/<p>We are pleased to announce the release of Biopython 1.43.</p> <p>This release includes a brand-new set of parsers in <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> by Peter Cock for reading biological sequence files in various formats, an updated Blast XML parser in Bio.Blast.NCBIXML, a new UniGene flat-file parser by Sean Davis, and numerous improvements and bug fixes in Bio.PDB, Bio.SwissProt, Bio.Nexus, BioSQL, and others. Believe it or not, even the documentation was updated.</p> <p>Source distributions and Windows installers are available from the Biopython website at <a href="http://biopython.org">http://biopython.org</a>. My thanks to all code contributers who made this new release possible.</p> <p>&ndash;Michiel on behalf of the Biopython developers</p>https://www.open-bio.org/2006/12/06/bioperl-152-release-2/Wed, 06 Dec 2006 23:03:31 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/12/06/bioperl-152-release-2/<p>I&rsquo;m proud to announce the final release of Bioperl 1.5.2. Full details are available at <a href="http://www.bioperl.org/wiki/Release_1.5.2">http://www.bioperl.org/wiki/Release_1.5.2</a></p>https://www.open-bio.org/2006/12/06/bioperl-152-release/Wed, 06 Dec 2006 22:46:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/12/06/bioperl-152-release/<p>I&rsquo;m proud to announce the final release of Bioperl 1.5.2. Full details are available at <a href="http://www.bioperl.org/wiki/Release_1.5.2">http://www.bioperl.org/wiki/Release_1.5.2</a></p>https://www.open-bio.org/2006/11/27/rc5-for-152/Mon, 27 Nov 2006 08:19:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/11/27/rc5-for-152/<p>Sendu has posted <a href="http://lists.open-bio.org/pipermail/bioperl-l/2006-November/024217.html">1.5.2 RC5</a>. There may be a few more kinks to work out, so try this release and report if there are problems with the tests.</p>https://www.open-bio.org/2006/11/09/rc-153/Thu, 09 Nov 2006 22:31:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/11/09/rc-153/<p>Sendu has <a href="http://lists.open-bio.org/pipermail/bioperl-l/2006-November/023916.html">announced</a> that <a href="http://www.bioperl.org/wiki/Release_1.5.2">Release Candidate 3</a> is available for download and testing. This may be the last RC before the 1.5.2 release so give it a whirl and speak up with any problems or concerns.</p>https://www.open-bio.org/2006/11/09/mediawiki-updated/Thu, 09 Nov 2006 22:28:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/11/09/mediawiki-updated/<p>Bioperl wiki is now running Mediawiki 1.8.2. nothing too different under the hood at this point, the <a href="http://www.mediawiki.org/wiki/MediaWiki">mediawiki</a> people probably have more to say in the <a href="http://svn.wikimedia.org/viewvc/mediawiki/tags/REL1_8_0/phase3/RELEASE-NOTES?view=markup">release-notes</a>.</p>https://www.open-bio.org/2006/08/10/next-bioperl-release/Thu, 10 Aug 2006 23:53:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/08/10/next-bioperl-release/<p>We are currently planning a timetable for the next few Bioperl releases, including the next developer release (v1.5.2), the next stable release (1.6) and beyond. Users are welcome to add requests (within reason!), donate code, etc. Lots of changes in store!</p> <p>The release schedule can be found <a href="http://www.bioperl.org/wiki/Bioperl_Release">here</a>. In order to add comments, you will be required to sign up for an account on the <a href="http://www.bioperl.org/wiki/Main_Page">BioPerl wiki</a>.</p>https://www.open-bio.org/2006/07/16/biopython-release-142/Sun, 16 Jul 2006 23:54:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/07/16/biopython-release-142/<p>Dear biopythoneers,</p> <p>We are pleased to announce the release of Biopython 1.42. This release includes a brand-new Genbank parser in Bio.GenBank by Peter Cock, numerous updates to Bio.Nexus by Frank Kauff and to Bio.Geo by Peter, lots of bug fixes by scores of contributors through BugZilla, and Bio.Cluster became object-oriented.</p> <p>Source distributions and Windows installers are available from our spiffy new Wiki-based website at <a href="http://biopython.org">http://biopython.org</a>. My thanks to all code contributors who made this new release possible.</p> <p>&ndash;Michiel on behalf of the Biopython developers</p>https://www.open-bio.org/2006/06/26/updated-pdoc-software/Mon, 26 Jun 2006 20:36:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/06/26/updated-pdoc-software/<p><a href="http://www.scmbb.ulb.ac.be/~raphael/">Raphaël Leplae</a> has updated the <a href="http://pdoc.sourceforge.net/">Pdoc</a> software to have an improved stylesheet and fix several bugs including problems rendering <a href="http://bioperl.org/wiki/Module:Bio::DB::Fasta">Bio::DB::Fasta</a>. Thanks a lot Raphaël and Patrick Meidl for getting the bugs reported and fixed for this nice POD to HTML converter.</p> <p>You can see the Pdoc for Bioperl packages in action at the <a href="http://doc.bioperl.org">doc.bioperl.org</a> site. See the bottom links which are for live code, the frozen version for releases remains, well, frozen.</p>https://www.open-bio.org/2006/06/07/mediawiki-167/Wed, 07 Jun 2006 19:12:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/06/07/mediawiki-167/<p><a href="http://www.mediawiki.org/wiki/Download">Upgraded</a> MW install for some bugfixes and security fixes.</p>https://www.open-bio.org/2006/06/06/bioperl-network-added-to-pdoc/Wed, 07 Jun 2006 01:30:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/06/06/bioperl-network-added-to-pdoc/<p>Bioperl <a href="http://bioperl.org/wiki/Network_package">Network</a> package <a href="http://doc.bioperl.org/releases/bioperl-current/bioperl-network/">documentation</a> added to the <a href="http://doc.bioperl.org">Pdoc site</a> and is automaticly updated daily.</p>https://www.open-bio.org/2006/06/03/mediawiki-upgraded/Sat, 03 Jun 2006 20:06:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/06/03/mediawiki-upgraded/<p>Upgraded BioPerl mediawiki to <a href="http://www.mediawiki.org/wiki/Important_Release_Notes">1.6.6</a>.</p>https://www.open-bio.org/2006/05/18/modware-a-bioperl-based-api-for-chado/Thu, 18 May 2006 18:00:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/05/18/modware-a-bioperl-based-api-for-chado/<p>We are announcing a new Sourceforge Project called Modware. It is an object-oriented API written in Perl that creates BioPerl object representations of biological features stored in a Chado database. It basically creates a Bio::Seq object for chromosomes in Chado and creates Bio::SeqFeature::Gene objects for protein coding transcripts stored in Chado. Things like contigs are represented as Bio::SeqFeature::Generic objects. We also provide many methods for manipulating these objects once they are in memory.</p> <p>For download please visit our Sourceforge project page: <a href="http://sourceforge.net/projects/gmod-ware">http://sourceforge.net/projects/gmod-ware</a></p> <p>For API documentation and some short examples of selected use cases visit our project home page: <a href="http://gmod-ware.sourceforge.net/">http://gmod-ware.sourceforge.net/</a></p>https://www.open-bio.org/2006/05/14/deobfuscator-interface-now-available/Sun, 14 May 2006 04:08:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/05/14/deobfuscator-interface-now-available/<p>I&rsquo;m glad to announce the availability of the <a href="http://bioperl.org/wiki/Deobfuscator">Deobfuscator</a> interface at the BioPerl website. You can use it at the following URL:</p> <p><a href="http://bioperl.org/cgi-bin/deob_interface.cgi">http://bioperl.org/cgi-bin/deob_interface.cgi</a></p> <p>Many thanks to Laura Kavanaugh and David Messina for this great contribution to the BioPerl project!</p>https://www.open-bio.org/2006/05/10/listsummaries-for-april-26-may-9/Wed, 10 May 2006 18:58:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/05/10/listsummaries-for-april-26-may-9/<p>ListSummaries for April 26-May 9 are up at the usual place:</p> <p><a href="http://www.bioperl.org/wiki/Mailing_list_summaries">http://www.bioperl.org/wiki/Mailing_list_summaries</a></p> <p>Direct link:</p> <p><a href="http://www.bioperl.org/wiki/ListSummary:April_26-May_9%2C2006">http://www.bioperl.org/wiki/ListSummary:April_26-May_9%2C2006</a></p> <p>It’s a bit of a hurried one so don’t be surprised to find a few spelling errors here and there. I’m getting ready for a conference in a couple weeks so I may be off the radar a bit here and there. The next ListSummary won’t be posted until May 26. Enjoy!</p>https://www.open-bio.org/2006/05/02/bioperl-run-in-freebsd/Tue, 02 May 2006 21:59:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/05/02/bioperl-run-in-freebsd/<p>It&rsquo;s my great pleasure to announce the availability of the <a href="http://bioperl.org/wiki/Run_package">BioPerl-run</a> packages (stable &amp; developer releases) for the <a href="http://www.freebsd.org/">FreeBSD</a> operating system.</p> <p>For instructions on how to install BioPerl ports in FreeBSD, please take a look into the <a href="https://www.open-bio.org/wiki/Getting_BioPerl">Getting Bioperl</a> section of the <a href="https://www.open-bio.org/wiki/Main_Page">BioPerl Wiki</a>.</p>https://www.open-bio.org/2006/04/27/rss-feeds/Fri, 28 Apr 2006 03:26:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/04/27/rss-feeds/<p>I&rsquo;ve added a page about <a href="https://www.open-bio.org/wiki/BioPerl:RSS_feeds">RSS feeds</a> in BioPerl. These include links to CVS commits as a RSS feed. This a bit of a hack using cvs2rss and cvs2cl and I have hardcoded it to show the last 30 commits only.</p> <p>In addition RSS news is now embedded on the <a href="https://www.open-bio.org/">main BioPerl</a> and <a href="https://www.open-bio.org/wiki/Tracking_CVS_commits">Tracking CVS commits</a> webpages to make for better interlinking between the news and wiki site ( <em>you might even be reading this there</em>).</p>https://www.open-bio.org/2006/04/25/bioperl-listsummaries-for-april-12-25/Tue, 25 Apr 2006 14:28:19 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/04/25/bioperl-listsummaries-for-april-12-25/<p>The newest summary of the BioPerl mailing lists has been posted to the wiki:</p> <ul> <li><a href="http://www.bioperl.org/wiki/ListSummary:April_12-25%2C2006">April 12-25</a></li> </ul> <p>Post gripes, harrassments, and faint praises at the regular places.</p>https://www.open-bio.org/2006/04/11/bioperl-mailing-list-summaries/Tue, 11 Apr 2006 12:48:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/04/11/bioperl-mailing-list-summaries/<p>The first of a biweekly summary of BioPerl mailing list summaries has been posted to the wiki:</p> <ul> <li><a href="http://www.bioperl.org/wiki/BioPerl_Mailing_List_Summaries_for_April_1-11">April 1-11</a></li> </ul> <p>These will likely be archived <a href="http://www.bioperl.org/wiki/Mailing_list_summaries">on the wiki</a> but may be moved to a more suitable location in the future (maybe to this blog?).</p>https://www.open-bio.org/2006/04/05/weekly-mailing-list-traffic-summaries/Wed, 05 Apr 2006 19:18:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/04/05/weekly-mailing-list-traffic-summaries/<p>I plan on starting a weekly, possibly biweekly, summary of mailing list traffic. These will be somewhat in the same vein as the <a href="http://dev.perl.org/perl5/list-summaries/">Perl5</a> or <a href="http://dev.perl.org/perl6/list-summaries/">Perl6</a> summaries and will be posted on the blog here and sent to the bioperl-l mail list. Barring another <a href="http://edition.cnn.com/2006/WEATHER/04/02/midwest.tornadoes/">natural disaster here</a>, these should start up next week (covering mail list traffic starting from April 1). The summaries will cover traffic mainly from <a href="http://bioperl.org/mailman/listinfo/bioperl-l">bioperl-l</a> (the main mail list) but will include <a href="http://bioperl.org/mailman/listinfo/biosql-l">biosql-l</a>, since it&rsquo;s fairly low traffic, and bugs/module updates from <a href="http://bioperl.org/mailman/listinfo/bioperl-guts-l">bioperl-guts-l.</a></p> <p>Drop a comment on the list to let me know if there are any requests/questions/gripes/etc.</p>https://www.open-bio.org/2006/04/05/mailing-list-reading-with-gmane/Wed, 05 Apr 2006 17:25:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/04/05/mailing-list-reading-with-gmane/<p><a href="http://gmane.org">GMANE</a> has been tracking BioPerl traffic for a few years now.</p> <p>You can see the page <a href="http://dir.gmane.org/gmane.comp.lang.perl.bio.general">here</a> There are several interfaces there including <a href="http://news.gmane.org/gmane.comp.lang.perl.bio.general">threaded</a> and <a href="http://blog.gmane.org/gmane.comp.lang.perl.bio.general">BLOG-like</a>.</p> <p>Those interested in tracking the mailing list in RSS readers should grab this <a href="http://rss.gmane.org/gmane.comp.lang.perl.bio.general">link</a>.</p> <p>There is also a search option for the archives. Try to <a href="http://search.gmane.org/?query=BLAST&amp;group=gmane.comp.lang.perl.bio.general">search GMANE for BLAST</a></p>https://www.open-bio.org/2006/03/25/cvs-server-move/Sat, 25 Mar 2006 17:10:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/03/25/cvs-server-move/<p>The CVS repository is migrating from &lsquo;pub&rsquo; to a new host called &lsquo;dev&rsquo; and requires us to re-issue accounts. This will be a good opportunity to verify email addresses and remove unused accounts.</p> <p>You should have received an email from Chris D requesting specific information and you will get a new password in the response. If not you will need to send a note to the helpdesk at support_AT_open-bio.org. The changover will happen around March 25th.</p>https://www.open-bio.org/2006/03/23/developer-accounts-re-issued/Fri, 24 Mar 2006 00:28:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/03/23/developer-accounts-re-issued/<p>We are moving developer repository to a new server which will require you to get a new developer account. To fix your local repository you should be able to run this on your local repository:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> $ find bioperl -name &#39;Root&#39; | xargs perl -i.backup -p -e &#39;s/pub.open/dev.open/&#39; </span></span></code></pre></div><p>or just check out a clean version.</p> <p>Note that before (and sometime ON) the 25th of March anything that is committed to the dev machine CVS repository will likely get wiped out so it is best to either hold off commits on the 25th or keep copies of stuff around.</p> <p>If you are a developer and did NOT get an email from Chris Dagdigian about server stuff you need to email the helpdesk with your existing login to pub.open-bio.org at <a href="mailto:support-AT-open-bio.org">support-AT-open-bio.org</a>.</p>https://www.open-bio.org/2006/02/18/gallery-updated/Sat, 18 Feb 2006 18:23:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/02/18/gallery-updated/<p>The BOSC 2002 pictures have been migrated to the O|B|F gallery site <a href="http://gallery.open-bio.org/gallery2/v/hackathon2002/">hackathon2002</a>.</p> <p>Thanks to Nat Torkington and his continual hosting of the <a href="http://prometheus.frii.com/gallery/">original site</a>.</p>https://www.open-bio.org/2006/02/16/installation-files-added-to-website/Thu, 16 Feb 2006 17:31:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/02/16/installation-files-added-to-website/<p>Installation instructions for Bioperl have been added to the main Bioperl website. They have been updated with links and tags for the wiki. Currently, both pages are accessible through links from <a href="http://www.bioperl.org/wiki/Getting_BioPerl">Getting Bioperl</a> and <a href="http://www.bioperl.org/wiki/Installing_BioPerl">Installing Bioperl</a>; these links will be subject to change. Please correct lins/tags/information as necessary.</p> <ul> <li><a href="http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix">Installing Bioperl for Unix</a></li> <li><a href="http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows">Installing Bioperl on Windows</a></li> </ul>https://www.open-bio.org/2006/02/13/more-website-updates/Mon, 13 Feb 2006 04:11:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/02/13/more-website-updates/<p>Wordpress 2.0.1 installed. Presumably no major differences to be seen but some bug fixes installed.</p> <p>A Wiki spam filter was installed, we&rsquo;ll see how well it performs but trying to cut down on spammers.</p> <p>We also will try and setup a RSS feed on the wiki main page so that news feeds from this site (and perhaps other open-bio sites) will be scrolled on the main BioPerl website. There are nice plugins for this in wikimedia we just need to find the time to do the install and testing.</p>https://www.open-bio.org/2006/02/07/discussions-about-modules-which-run-blast/Tue, 07 Feb 2006 17:55:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/02/07/discussions-about-modules-which-run-blast/<p>Some <a href="http://lists.open-bio.org/pipermail/bioperl-l/2006-February/020739.html">discussion</a> about changing how the <a href="http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast">RemoteBlast</a> module behaves. If you have feedback respond to Roger&rsquo;s post.</p> <p>Also see these posts</p> <ul> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2006-January/020665.html">Chris Field&rsquo;s post (1)</a></li> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2006-February/020721.html">Chris Field&rsquo;s post (2)</a></li> <li><a href="http://lists.open-bio.org/pipermail/bioperl-l/2006-January/020698.html">Roger volunteering to take on maintenance</a></li> </ul>https://www.open-bio.org/2006/01/30/bioperl-on-mac-os-x-using-fink/Mon, 30 Jan 2006 18:55:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/01/30/bioperl-on-mac-os-x-using-fink/<p>Instructions on how to install BioPerl on Mac OS X have been added to the <a href="https://www.open-bio.org/wiki/Main_Page">Wiki</a>, specifically at the <a href="https://www.open-bio.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink">Getting Bioperl</a> section. Thanks to Koen van der Drift for contributing with this info.</p> <p>We continue to encourage people who is taking care of creating packages for other platforms (specific Linux distributions, Windows, etc.) to put in the wiki the necessary documentation about <a href="https://www.open-bio.org/wiki/Getting_BioPerl">installing BioPerl</a> and <a href="https://www.open-bio.org/wiki/Tutorial:Installing_Perl_modules">Perl modules</a> in your favorite OS/distributions.</p>https://www.open-bio.org/2006/01/25/website-is-live/Wed, 25 Jan 2006 20:33:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/01/25/website-is-live/<p>(reposting this news from <a href="http://news.open-bio.org/archives/2006_01.html#000086">O|B|F News</a>)</p> <p>I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.</p> <p>The website continues to be at the URL <a href="http://www.bioperl.org">http://www.bioperl.org</a>. The DNS updates may take up to 24 hours to reach everyone.</p> <p>The initial content of the site is result of the work of myself, Mauricio Herrera Cuadra, Brian Osborne, and Torsten Seemann. We encourage you to contribute to the site&rsquo;s content by signing up for an account.</p> <p>There are several guides for style of the site. One in particular is how to link to Modules which can contain additional information from the POD <a href="http://bioperl.org/wiki/Module:Bio::SeqIO">http://bioperl.org/wiki/Module:Bio::SeqIO</a>.</p> <p>You&rsquo;ll notice that many of the paths have changed but the DIST and SRC continues to be available at <a href="http://bioperl.org/DIST">http://bioperl.org/DIST</a> and <a href="http://bioperl.org/SRC">http://bioperl.org/SRC</a>. The HOWTOs are now available from <a href="http://bioperl.org/wiki/HOWTOs">http://bioperl.org/wiki/HOWTOs</a> (although we should be forwarding the old URL links to the correct place).</p> <p>The FAQ is available at <a href="http://bioperl.org/wiki/FAQ">http://bioperl.org/wiki/FAQ</a> and I encourage you to add your questions to it so they can be properly archived and addressed.</p> <p>We also have initiated a News site for Bioperl for posting announcements regarding development and software. I would like to see if there are volunteers to post weekly or monthly summaries of mailing list traffic and development. <a href="http://www.bioperl.org/news/">(this server)</a>.</p> <p>Jason Stajich on behalf of Mauricio Herrera Cuadra, Brian Osborne, Torsten Seemann.</p>https://www.open-bio.org/2006/01/25/new-bioperl-website/Wed, 25 Jan 2006 19:00:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/01/25/new-bioperl-website/<p>I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the <a href="http://www.wikipedia.org">wikipedia</a> project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.</p> <p>The website continues to be at the URL <a href="http://www.bioperl.org">http://www.bioperl.org</a>. The DNS updates may take up to 24 hours to reach everyone.</p> <p>The initial content of the site is result of the work of myself, Mauricio Herrera Cuadra, Brian Osborne, and Torsten Seemann. We encourage you to contribute to the site&rsquo;s content by signing up for an account.</p> <p>There are several guides for style of the site. One in particular is how to link to Modules which can contain additional information from the POD <a href="http://bioperl.org/wiki/Module:Bio::SeqIO">http://bioperl.org/wiki/Module:Bio::SeqIO</a></p> <p>You&rsquo;ll notice that many of the paths have changed but the DIST and SRC continues to be available at <a href="http://bioperl.org/DIST">http://bioperl.org/DIST</a> and <a href="http://bioperl.org/SRC">http://bioperl.org/SRC</a>. The HOWTOs are now available from <a href="http://bioperl.org/wiki/HOWTOs">http://bioperl.org/wiki/HOWTOs</a>.</p> <p>The FAQ is available at <a href="http://bioperl.org/wiki/FAQ">http://bioperl.org/wiki/FAQ</a> and I encourage you to add your questions to it so they can be properly archived and addressed.</p> <p>We also have initiated a News site for Bioperl for posting announcements regarding development and software. I would like to see if there are volunteers to post weekly or monthly summaries of mailing list traffic and development. <a href="http://www.bioperl.org/news/">http://www.bioperl.org/news/</a></p> <p>Jason Stajich on behalf of Mauricio Herrera Cuadra, Brian Osborne, Torsten Seemann.</p>https://www.open-bio.org/2006/01/17/publications-and-projects-which-reference-bioperl/Wed, 18 Jan 2006 02:24:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/01/17/publications-and-projects-which-reference-bioperl/<p>I&rsquo;ve been updating the <a href="http://bioperl.open-bio.org/wiki/BioPerl_publications" title="pubs">Publications page</a> on the wiki to keep track of the number of pubs and projects which use BioPerl. <a href="http://scholar.google.com">Google scholar</a> seems to get a lot of these correct, sometimes there are redundancies, but generally has been a good place to find this list. The other way is to go to each of the journal&rsquo;s home pages, and search for &ldquo;BioPerl&rdquo; in the content, that can be tedious though&hellip;.</p>https://www.open-bio.org/2006/01/17/new-theme/Wed, 18 Jan 2006 02:22:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/01/17/new-theme/<p>I installed the new Regulus theme, comments are welcome as to whether or not you like it.</p> <p>It is possible to customize the color scheme and top-image as well if there are suggestions - perhaps we&rsquo;ll build a header which incorporates our logo once that is <a href="http://bioperl.open-bio.org/wiki/Potential_Logos" title="_logos">decided</a>.</p>https://www.open-bio.org/2006/01/11/site-software-updated/Wed, 11 Jan 2006 16:58:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2006/01/11/site-software-updated/<p>I&rsquo;ve updated the wordpress install to <a href="http://wordpress.org/development/2005/12/wp2/">2.0</a> which has a lot more features and seems to be better setup for permissions and what not.</p> <p>I also upgraded the <a href="https://www.open-bio.org/wiki">wiki</a> to <a href="http://www.mediawiki.org/wiki/MediaWiki">1.5.5</a> to deal with some <a href="http://en.wikipedia.org/wiki/Windows_Metafile_vulnerability">potential security holes</a> with <a href="http://en.wikipedia.org/wiki/Windows_Metafile">WMF</a> files.</p> <p>I also changed the permalink structure so that the links are informative by date and post-slug. I like this much more.</p>https://www.open-bio.org/2005/12/08/developer-release-in-freebsd/Thu, 08 Dec 2005 19:41:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/12/08/developer-release-in-freebsd/<p>The Developer Release (1.5.1) of BioPerl has been brought back into the <a href="http://www.freebsd.org/">FreeBSD</a> <a href="http://www.freebsd.org/ports/">Ports Collection</a>. For instructions on how to install it, please take a look into the <a href="https://www.open-bio.org/wiki/Getting_BioPerl">Getting Bioperl</a> section of the <a href="https://www.open-bio.org/wiki/Main_Page">BioPerl Wiki</a>.</p> <p>We encourage people who is taking care of creating packages for other platforms (specific Linux distributions, Mac OS, Windows, etc.) to put in the wiki the necessary documentation about getting and installing BioPerl releases in your favorite OS/distributions.</p>https://www.open-bio.org/2005/12/02/welcome-new-developer/Fri, 02 Dec 2005 22:54:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/12/02/welcome-new-developer/<p>Welcome to new developer Torsten Seemann from <a href="http://www.vicbioinformatics.com/home.shtml">Victorian Bioinformatics Consortium</a>. Torsten has taken on the role of primary maintainer of <a href="https://www.open-bio.org/wiki/Modules:Bio::Tools::Run::StandAloneBlast">Bio::Tools::Run::StandAloneBlast</a>.</p>https://www.open-bio.org/2005/11/21/media-wiki-upgraded/Mon, 21 Nov 2005 20:05:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/21/media-wiki-upgraded/<p>Upgraded to mediawiki 1.5.2 &ndash; all seems to be working, but do notify us if it isn&rsquo;t.</p>https://www.open-bio.org/2005/11/21/no-more-indexphp/Mon, 21 Nov 2005 19:06:17 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/21/no-more-indexphp/<p>index.php is no longer part of the wiki URL. Yah! So</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://bioperl.open-bio.org/wiki/Project_priority_list </span></span></code></pre></div><p>instead of</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://bioperl.open-bio.org/wiki/index.php/Project_priority_list </span></span></code></pre></div><p>I also installed the interwiki table so that inter-wiki linking is much easier. See this page: <a href="http://bioperl.open-bio.org/wiki/Special:Interwiki">http://bioperl.open-bio.org/wiki/Special:Interwiki</a> For example to link to wikipedia you simply need to use the &lsquo;&lsquo;&lsquo;wp&rsquo;&rsquo;&rsquo; prefix. For example [[wp:Bioinformatics]] or else the wikiomics site [[wikiomics:BLAST]].</p>https://www.open-bio.org/2005/11/21/biblio-plugin-for-wiki/Mon, 21 Nov 2005 04:43:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/21/biblio-plugin-for-wiki/<p>I added the <a href="http://martin.jambon.free.fr/biblio_php.html">Biblio plugin</a> for mediawiki so that we could simplify how papers are referenced in our pages. I found this as part of the <a href="http://wikiomics.org">wikiomics</a> project.</p> <p>See the <a href="https://www.open-bio.org/wiki/Help:Editing">help page</a> and the Bioperl wiki <a href="https://www.open-bio.org/wiki/BioPerl_publications">publications page</a> for examples.</p>https://www.open-bio.org/2005/11/20/sort-order-for-each_descendent/Sun, 20 Nov 2005 18:25:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/20/sort-order-for-each_descendent/<p>I&rsquo;ve updated the code for <a href="http://doc.bioperl.org/bioperl-live/Bio/Tree/Node.html">Bio::Tree::Node</a> so that each_Descendent can return the nodes in alphabetical order. This is achieved by pasing in the string &lsquo;alpha&rsquo; (for alphabetical) or &lsquo;revalpha&rsquo; (for reverse alphabetical). For internal nodes, they are sorted in order of the min or max (alphabetically) node in the sub-clade.</p> <p>In addition, you can request the order of writing nodes by <a href="http://doc.bioperl.org/bioperl-live/Bio/TreeIO/newick.html">Bio::TreeIO::newick</a> by passing in the -order_by flag which can be &lsquo;alpha&rsquo;, &lsquo;revalpha&rsquo;, &lsquo;height&rsquo;, or &lsquo;creation&rsquo;.</p> <p>So you can use it like</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>my $treeio = Bio::TreeIO-&gt;new(-format =&gt; &#39;newick&#39;, </span></span><span style="display:flex;"><span> -file =&gt; &#39;file.tre&#39;); </span></span><span style="display:flex;"><span>my $tree = $treeio-&gt;next_tree; </span></span><span style="display:flex;"><span>for my $internal ( grep { ! $internal-&gt;is_Leaf } $tree-&gt;get_nodes ) { </span></span><span style="display:flex;"><span> # this will get the nodes in alphabetical order </span></span><span style="display:flex;"><span> my @subclade = $internal-&gt;each_Descendent(&#39;alpha&#39;); </span></span><span style="display:flex;"><span>} </span></span><span style="display:flex;"><span>my $out = Bio::TreeIO-&gt;new(-format =&gt;&#39;newick&#39;, </span></span><span style="display:flex;"><span> -order_by =&gt; &#39;alpha&#39;, </span></span><span style="display:flex;"><span> -file =&gt; &#39;sorted.tre&#39;); </span></span><span style="display:flex;"><span>$out-&gt;write_tree($tree); </span></span></code></pre></div><p>This code is in <a href="https://www.open-bio.org/wiki/index.php/CVS">CVS</a> now.</p> <p>Also, I fixed the code reference option so that arbitrary functions can be passed in. Here is an example which prints out the nodes from a nexus formated tree file.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>use Bio::TreeIO; </span></span><span style="display:flex;"><span>use strict; </span></span><span style="display:flex;"><span>my $treeio = Bio::TreeIO-&gt;new(-format =&gt; &#39;nexus&#39;, </span></span><span style="display:flex;"><span> -file =&gt; shift); </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>my $tree = $treeio-&gt;next_tree; </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>print join(&#34;,&#34;,map { $_-&gt;id } </span></span><span style="display:flex;"><span> $tree-&gt;get_root_node-&gt;each_Descendent(&amp;my_sort_routine)), &#34;n&#34;; </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>sub my_sort_routine { </span></span><span style="display:flex;"><span> my ($aa,$bb) = @_; </span></span><span style="display:flex;"><span> if( $aa-&gt;is_Leaf &amp;&amp; $bb-&gt;is_Leaf ) { </span></span><span style="display:flex;"><span> return $aa-&gt;id cmp $bb-&gt;id; </span></span><span style="display:flex;"><span> } elsif( $aa-&gt;is_Leaf ) { </span></span><span style="display:flex;"><span> my ($left) = sort { $a-&gt;id cmp $b-&gt;id } </span></span><span style="display:flex;"><span> grep {$_-&gt;is_Leaf } $bb-&gt;get_all_Descendents; </span></span><span style="display:flex;"><span> return $aa-&gt;id cmp $left-&gt;id; </span></span><span style="display:flex;"><span> } elsif( $bb-&gt;is_Leaf ) { </span></span><span style="display:flex;"><span> my ($left) = sort { $a-&gt;id cmp $b-&gt;id } </span></span><span style="display:flex;"><span> grep {$_-&gt;is_Leaf } $aa-&gt;get_all_Descendents; </span></span><span style="display:flex;"><span> return $left-&gt;id cmp $bb-&gt;id; </span></span><span style="display:flex;"><span> } else { </span></span><span style="display:flex;"><span> my ($left) = sort { $a-&gt;id cmp $b-&gt;id } </span></span><span style="display:flex;"><span> grep {$_-&gt;is_Leaf } $aa-&gt;get_all_Descendents; </span></span><span style="display:flex;"><span> my ($right) = sort { $a-&gt;id cmp $b-&gt;id } </span></span><span style="display:flex;"><span> grep {$_-&gt;is_Leaf } $aa-&gt;get_all_Descendents; </span></span><span style="display:flex;"><span> return $left-&gt;id cmp $right-&gt;id; </span></span><span style="display:flex;"><span> } </span></span><span style="display:flex;"><span>} </span></span></code></pre></div>https://www.open-bio.org/2005/11/19/faq-updated/Sat, 19 Nov 2005 14:27:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/19/faq-updated/<p>The Frequently Asked Questions have been entered into the Wiki and is <a href="https://www.open-bio.org/wiki/FAQ">available</a>.</p>https://www.open-bio.org/2005/11/12/seen-on-the-road/Sun, 13 Nov 2005 00:15:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/12/seen-on-the-road/<p>After halloween party at our house from a few years ago there was a little more public direction on who to ask for Bioperl help&hellip;</p> <p><a href="https://www.open-bio.org/wp-content/uploads/2006/01/bioperl_graffiti.jpg"><img src="https://www.open-bio.org/wp-content/uploads/2006/01/bioperl_graffiti.jpg" alt=""></a></p>https://www.open-bio.org/2005/11/06/getting-blastxml-using-remoteblast/Sun, 06 Nov 2005 04:40:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/06/getting-blastxml-using-remoteblast/<p>According to NCBI - BlastXML (and ASN.1) is the only guaranteed <em>always parseable</em> report format that is provided by their web CGI script. Here is some code to specify how the data should be requested (and perhaps this will become the default).</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>my $remote_blastxml = Bio::Tools::Run::RemoteBlast-&gt;new </span></span><span style="display:flex;"><span> (&#39;-verbose&#39; =&gt; $v, </span></span><span style="display:flex;"><span> &#39;-prog&#39; =&gt; $prog, </span></span><span style="display:flex;"><span> &#39;-data&#39; =&gt; $db, </span></span><span style="display:flex;"><span> &#39;-readmethod&#39; =&gt; &#39;xml&#39;, # this tells the parser to use blastxml </span></span><span style="display:flex;"><span> # format for parsing </span></span><span style="display:flex;"><span> &#39;-expect&#39; =&gt; $e_val, </span></span><span style="display:flex;"><span> ); </span></span><span style="display:flex;"><span> # this tells NCBI to send you XML back </span></span><span style="display:flex;"><span>$remote_blastxml-&gt;retrieve_parameter(&#39;FORMAT_TYPE&#39;, &#39;XML&#39;); </span></span></code></pre></div><p>See also <a href="http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast">wiki page</a> and <a href="http://bioperl.org/wiki/NCBI_Blast_email">NCBI email about Remote BLAST</a>.</p> <p>-jason</p>https://www.open-bio.org/2005/11/01/logo-ideas/Wed, 02 Nov 2005 01:20:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/11/01/logo-ideas/<p>I&rsquo;ve started uploading some logo ideas that I&rsquo;ve been playing with. <a href="http://bioperl.open-bio.org/wiki/Potential_Logos">Potential_Logos</a>. These include logos for the blog front page as well as the Wiki site (and generally a BioPerl logo). <a href="http://www.open-bio.org">O|B|F</a> logos are welcome too.</p> <p>-jason</p>https://www.open-bio.org/2005/10/29/new-wiki-content/Sat, 29 Oct 2005 19:24:14 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/10/29/new-wiki-content/<p>I&rsquo;ve started migrating content to the <a href="https://www.open-bio.org/wiki">Wiki Site</a>. I am hoping this will work out well. We need a couple of things.</p> <ol> <li> <p>Decide on a theme for this site, customize it to make it a Bioperl style. Consider having a unifying style across all the <a href="http://www.open-bio.org">O|B|F</a> sites as Chris started doing with the foundation site.</p> </li> <li> <p>Generate a project image (or several that can be rotated) for the header on the site, something with a camel and DNA and images of phylogenetic trees and BLAST searches would be cool.</p> </li> <li> <p>Generate a bioperl logo. I&rsquo;ve started playing with a few things, I&rsquo;ll upload ideas next week.</p> </li> <li> <p>Migrate static content ( <a href="http://bioperl.org/DIST">DIST</a>) and content that is synced from CVS ( <a href="http://bioperl.org/SRC">SRC</a>, <a href="http://bioperl.org/HOWTOs">HOWTOs</a>) over here. Also some of the <a href="http://bioperl.org/Core/Latest/modules.html">Core Documentation</a> pages are pod2html ified and I think we need to figure out how to keep them up to date.</p> </li> </ol> <p>I imagine that <a href="http://bioperl.open-bio.org">this site</a> would be a place to post announcements, blog current code updates, and provide a simple clean interface to Bioperl information. The <a href="wiki">Wiki site</a> will provide more community documentation and a way to keep tutorials and installation help up-to-date.</p> <p>I&rsquo;m going to start a wiki list of these things that need to be done so we can coordinate our efforts and get ideas from the community.</p> <p>There was a request for a forum-like software, something like <a href="http://www.rannala.org/gsf/">Genetic Software Forum</a> that has been setup. But this would duplicate some of the <a href="http://bioperl.org/mailman/listinfo/bioperl-l">email list</a> traffic and I am not sure that we can get developers to both read email and post to the website forum. We are stick in the mud about some things I suspect.</p> <p>-jason</p>https://www.open-bio.org/2005/10/29/biopython-141-released/Sat, 29 Oct 2005 15:37:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/10/29/biopython-141-released/<p>We are pleased to announce the release of Biopython 1.41. Many improvements were made in Biopython during the eight months since the previous release, and the new release contains lots of bugfixes, improvements, new functionalities, and better documentation. To pick a few, there&rsquo;s the new Bio.MEME module by Jason Hackney, updates to the Blast parser using Bertrand Frottier&rsquo;s NCBIXML code, a BLAT parser by Yair Benita, numerous updates in Bio.PDB, CompareACE support in AlignAce, and improved user-friendliness in Bio.Seq.</p> <p>Lots of people of contributed to this release, in particular Frank Kauff (Bio.Nexus), Jason Hackney (Bio.MEME), Thomas Hamelryck (Bio.PDB), Frederic Sohm (Bio.Restriction), James Casbon (Bio.SCOP) for bug fixes and updates, Peter (Bio.Blast.NCBIXML test cases), and of course Jeff Chang, Brad Chapman, Andrew Dalke, and Iddo Friedberg for Biopython and the fool-proof instructions on how to roll a release, which made this a lot easier than I anticipated. My apologies if I forgot to thank somebody.</p> <p>Michiel de Hoon on behalf of the Biopython development team.</p>https://www.open-bio.org/2005/10/13/bioperl-151/Fri, 14 Oct 2005 01:14:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/10/13/bioperl-151/<p>I am pleased to announce the 1.5.1 developer release of Bioperl.</p> <p>Essential links here Core <a href="http://bioperl.org/DIST/bioperl-1.5.1.tar.gz">http://bioperl.org/DIST/bioperl-1.5.1.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-1.5.1.zip">http://bioperl.org/DIST/bioperl-1.5.1.zip</a> <a href="http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2">http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2</a></p> <p>Run <a href="http://bioperl.org/DIST/bioperl-run-1.5.1.tar.gz">http://bioperl.org/DIST/bioperl-run-1.5.1.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-run-1.5.1.zip">http://bioperl.org/DIST/bioperl-run-1.5.1.zip</a> <a href="http://bioperl.org/DIST/bioperl-run-1.5.1.tar.bz2">http://bioperl.org/DIST/bioperl-run-1.5.1.tar.bz2</a></p> <p>Ext <a href="http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.gz">http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-ext-1.5.1.zip">http://bioperl.org/DIST/bioperl-ext-1.5.1.zip</a> <a href="http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.bz2">http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.bz2</a></p> <p>MD5 sum <a href="http://bioperl.org/DIST/SIGNATURES.md5">http://bioperl.org/DIST/SIGNATURES.md5</a></p> <p>Please see <a href="http://portal.open-bio.org/pipermail/bioperl-l/2005-October/019932.html">my mailing list post</a> for more information.</p> <p>I have appended the Change log from Bioperl core compents below 1.5.1 Developer release</p> <p>o Major problem with how Annotations were written out with Bio::Seq is fixed by reverting to old behavior for Bio::Annotation objects.</p> <p>o Bio::SeqIO</p> <p>- genbank.pm \* bug #1871; REFLOOP&rsquo; parsing loop, I changed the pattern to expect at l east 9 spaces at the beginning of a line to indicate line wrapping.</p> <p>\* Treat multi-line SOURCE sections correctly, this defect broke both common_name() and classification()</p> <p>\* parse swissprot fields in genpept file</p> <p>\* parse WGS genbank records</p> <p>- embl.pm \* Changed regexp for ID line. The capturing parentheses are the same, the difference is an optional repeated-not-semi- colon expression following the captured S+. This means the regexp works when the division looks like /PRO;/ or when the division looks like /ANG ;/ - the latter is from EMBL repbase</p> <p>\* fix ID line parsing: the molecule string can have spaces in it. Like: &ldquo;genomic DNA&rdquo;</p> <p>- swiss.pm: bugs #1727, #1734</p> <p>- entrezgene.pm \* Added parser for entrezgene ASN1 (text format) files. Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)</p> <p>o Bio::AlignIO</p> <p>- maf.pm coordinate problem fixed</p> <p>o Bio::Taxonomy and Bio::DB::Taxonomy</p> <p>- Parse NCBI XML now so that nearly all the taxonomy up-and-down can be done via Web without downloading all the sequence. o Bio::Tools::Run::RemoteBlast supports more options and complies to changes to the NCBI interface. It is reccomended that you retrieve the data in XML instead of plain-text BLAST report to insure proper parsing and retrieval of all information as NCBI fully expects to change things in the future. o Bio::Tree and Bio::TreeIO</p> <p>- Fixes so that re-rooting a tree works properly</p> <p>- Writing out nhx format from a newick/nexus file will properly output bootstrap information. The use must move the internal node labels over to bootstraps. for my $node ( grep { ! $_-&gt;is_Leaf } $tree-&gt;get_nodes ) { $node-&gt;bootstrap($node-&gt;id); $node-&gt;id(&rsquo;&rsquo;); } - Nexus parsing is much more flexible now, does not care about LF.</p> <p>- Cladogram drawing module in Bio::Tree::Draw</p> <p>- Node height and depth now properly calculated</p> <p>- fix tree pruning algorithm so that node with 1 child gets merged</p> <p>o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized bugs and improvements were added, see Gbrowse mailing list for most of these.</p> <p>o Bio::DB::GFF partially supports GFF3. See information about gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.</p> <p>o Better location parsing in Bio::Factory::FTLocationFactory - this is part of the engine for parsing EMBL/GenBank feature table locations. Nested join/order-by/complement are allowed now</p> <p>o Bio::PrimarySeqI-&gt;translate now takes named parameters</p> <p>o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence reconstruction) is now supported. Parsing different models and branch specific parametes are now supported.</p> <p>o Bio::Factory::FTLocationFactory - parse hierarchical locations (joins of joins)</p> <p>o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays for getter/setter functions</p> <p>o Bio::SearchIO</p> <p>- blast bug #1739; match scientific notation in score and possible e+ values</p> <p>- blast.pm reads more WU-BLAST parameters and parameters, match a full database pathname,</p> <p>- Handle NCBI WEB and newer BLAST formats specifically (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).</p> <p>- psl off-by-one error fixed</p> <p>- exonerate parsing much improved, CIGAR and VULGAR can be parsed and HSPs can be constructed from them.</p> <p>- HSPs query/hit now have a seqdesc field filled out (this was always available via $hit-&gt;description and $result-&gt;query_description</p> <p>- hmmer.pm can parse -A0 hmmpfam files</p> <p>- Writer::GbrowseGFF more customizeable.</p> <p>o Bio::Tools::Hmmpfam make e-value default score displayed in gff, rather than raw score allow parse of multiple records</p>https://www.open-bio.org/2005/10/08/bioperl-151-rc4/Sun, 09 Oct 2005 00:14:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/10/08/bioperl-151-rc4/<p>Release Candidate 4 for bioperl 1.5.1 (Developer release) core, run, and ext packages is available.</p> <p>Several bug fixes went in last week so I&rsquo;ve made what I hope to be the last release candidate before 1.5.1 goes out.</p> <p>More Info: <a href="http://portal.open-bio.org/pipermail/bioperl-l/2005-October/019904.html">http://portal.open-bio.org/pipermail/bioperl-l/2005-October/019904.html</a></p> <p>Files are here:</p> <p><a href="http://bioperl.org/DIST/bioperl-1.5.1-rc4.tar.gz">http://bioperl.org/DIST/bioperl-1.5.1-rc4.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-1.5.1-rc4.zip">http://bioperl.org/DIST/bioperl-1.5.1-rc4.zip</a> <a href="http://bioperl.org/DIST/bioperl-run-1.5.1-rc4.tar.gz">http://bioperl.org/DIST/bioperl-run-1.5.1-rc4.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-run-1.5.1-rc4.zip">http://bioperl.org/DIST/bioperl-run-1.5.1-rc4.zip</a> <a href="http://bioperl.org/DIST/bioperl-ext-1.5.1-rc4.tar.gz">http://bioperl.org/DIST/bioperl-ext-1.5.1-rc4.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-ext-1.5.1-rc4.zip">http://bioperl.org/DIST/bioperl-ext-1.5.1-rc4.zip</a></p>https://www.open-bio.org/2005/06/24/obf-board-of-directors-meeting/Fri, 24 Jun 2005 17:58:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/06/24/obf-board-of-directors-meeting/<p>The 2005 Board of Directors meeting for the Open Bioinformatics Foundation was held on Thursday, June 24th 2005 in Detroit, MI USA at the site of the BOSC2005 meeting.</p> <p>This was a major meeting and represents the first attempt to build a governance platform for the organization as well as set up the mechanism for building a voting membership. The O|B|F members will be able to direct the operation of the organization and will also be able to join the Board.</p> <p>Other major news from the meeting: - Ewan Birney steps down as president; joins Board as at-large member - Jason Stajich joins board and is elected President - Hilmar Lapp is elected to a new position of &lsquo;Parlimentarian&rsquo; - Determined efforts to build a voting membership body</p> <p>Links to meeting minutes and Election Bylaws follow are below &hellip;</p> <p>The new Election bylaws adopted by the Board can be found here: <a href="https://www.open-bio.org/archives/uploads/OBF-Election-Bylaws-1.pdf">Download file</a></p> <p>Meeting minutes are still being approved; when they are ready this article will be edited and a download link will be inserted here.</p>https://www.open-bio.org/2005/06/24/site-updated-prior-to-server-move/Fri, 24 Jun 2005 14:25:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/06/24/site-updated-prior-to-server-move/<p>The backend MovableType software powering this site was upgraded and the backend storage was switched from berkelyDB to SQL. These preparations are being done to ease the transition of <a href="http://news.open-bio.org">http://news.open-bio.org</a> to a new server. The primary purpose of this news entry is to confirm that the posting system still works after the upgrade!</p>https://www.open-bio.org/2005/06/23/minutes2005-bosc-meeting/Thu, 23 Jun 2005 15:55:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/06/23/minutes2005-bosc-meeting/<p><strong>Venue:</strong> Renaissance Center in Detroit, on the first floor next to the Starbucks.  <strong>Date:</strong> June 23, 2005, 16:15.</p> <h4 id="call-to-order"><strong>Call to order:</strong></h4> <ul> <li>Board members present: Chris, Hilmar, Ewan, Andrew</li> <li>Others: Jason Stajich</li> </ul> <h3 id="chris--treasurers-report">Chris / Treasurer&rsquo;s Report</h3> <ul> <li>Review of the accounts / passing the statements around</li> <li>Summary of response to the fraud attempt</li> <li>Request to activate the debit card. Granted.</li> <li>The account got a $9,000 deposit but we don&rsquo;t know who it comes from. Chris will investigate.</li> <li>We have not yet received our money from the Glasgow BOSC. Chris will follow up on that.</li> <li>Chris will pull the current credit report for Open Bio.</li> <li>Develop a succession / &ldquo;hit by the bus&rdquo; plan for hardware and people. Eg, can we get access to the account if Chris decides to be a beach bum in the S. Pacific?</li> <li>We did not pay Delaware to renew our corporate registration. Chris will look into getting the right person to fix that and pay any penalties.</li> <li>Some discussion about letting Chris make minor (&lt;$1,000) payments without a counter-signature. Hilmar pointed out that&rsquo;s in the new bylaws</li> </ul> <h3 id="new-bylaws-membership">New Bylaws, Membership</h3> <p>Hilmar presentation of the <a href="http://news.open-bio.org/archives/uploads/OBF-Election-Bylaws-1.pdf">new OBF bylaws</a>. We reviewed it and made comments. Some time later he finished.</p> <p>Discussion: how does someone become a member?</p> <ul> <li>Paypal? No, some people don&rsquo;t like Paypal.</li> <li>Apply in person at BOSC or sending contact information to the Parliamentarian?</li> <li>Perhaps have two existing members vouch for a new member?</li> </ul> <p><em>Proposal from Ewan:</em> Move to accept the bylaws as presented with the membership criterion to be developed by the Parliamentarian and adopted in the future. Chris seconded. Motion passsed by unanimous consent.</p> <p>Hilmar proposes to increase the board membership by one. Chris seconded. Motion passsed by unanimous consent.</p> <p>Hilmar nominiates Jason Stajich for a member-at-large seat. Chris seconded. Motion passsed by unanimous consent. Secret ballot carried out and counted as per the new bylaws. Jason elected; 4 yeas - 0 nays</p> <p>Chris nominates Hilmar for Parliamentarian. Jason seconded. Motion passsed by unanimous consent.</p> <p>Ewan presents his written resignation notice for his position as President.</p> <p>Hilmar proposes that the membership requirements for Jason to be a board member to be waived. Chris seconded. Motion passsed by unanimous consent.</p> <p>Hilmar nominates Jason as president. (Allowed under the new bylaws.) Andrew seconded. Motion passsed by unanimous consent. Election took place. Jason elected; 4 yeas - 0 nays</p> <p>Hilmar proposes that the membership requirements for Ewan to be a board member be waived. Seconded by Jason. Motion passsed by unanimous consent.</p> <p>Hilmar nominates Ewan to fill the now empty board-at-large seat. Seconded by Jason. Motion passsed by unanimous consent. Election took place. Ewan is now an at-large board member with 4 yeas - 0 nays</p> <p>Ewan proposes that the people who apply for membership at BOSC will be accepted as members and that the Parliamentarian will incorprate this into the membership requirements. Seconded by Andrew. Motion passsed by unanimous consent.</p> <p><strong>Action item:</strong> Hilmar will prepare forms which will be acceptable for the membership requirements.</p> <p>Discussion of the events leading up to the recent hackathon attempt. The big problems were: lack of funding for room and travel, short lead time for scheduling, and requirement that all people also be at the WWDC, meaning two weeks away. The OBF is willing to help with some of the funding for a hackathon. We will bring this up with Suzi.BOSC 2006</p> <p>Travel to Brazil is expensive and out of the way. Not everyone on the Board is sure they can make it for next year. Should we consider subsidising board travel?</p> <p><strong>Action item:</strong> Does Darin want to organize BOSC for next year? Request for people to volunteer.</p> <h3 id="outreach--diversity">Outreach &amp; Diversity</h3> <p>A general lament on how we&rsquo;re a bunch of white men and we should encourage more diversity. For that matter, we&rsquo;re rather close knit, which is good, but it doesn&rsquo;t help bring in enough new people to lead projects, help with BOSC, be on the Board, etc.</p> <p><em>Chris:</em> Move to adjourn.  <em>Jason:</em> Seconded.  Motion passed by unanimous consent.</p> <p>Closed at 18:15. A two hour meeting.</p>https://www.open-bio.org/2005/06/16/bosc-schedule-posted/Thu, 16 Jun 2005 23:52:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/06/16/bosc-schedule-posted/<p>The <a href="https://www.open-bio.org/bosc2005/">BOSC 2005</a> schedule has been <a href="https://www.open-bio.org/bosc2005/program.pdf">posted</a>. Lightning talks are still being accepted.</p>https://www.open-bio.org/2005/03/17/popgen-howto/Fri, 18 Mar 2005 01:29:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/03/17/popgen-howto/<p>A <a href="http://bioperl.org/HOWTOs/PopGen/">PopGen</a> HOWTO added to the website for using the population genetics modules in Bioperl.</p> <p>The PAML HOWTO is in-process of being updated to describe the new functionalilty.</p>https://www.open-bio.org/2005/02/24/biopython-140-beta-released/Thu, 24 Feb 2005 05:31:23 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/02/24/biopython-140-beta-released/<p>We are pleased to announce the release of Biopython 1.40 beta. It has been nine months since the last official release (1.30), and there are numerous changes, bugfixes, enhancements, goodies and new contributors. Most notable are the addition of the Nexus parser (Frank Kauff w/ Cymon Cox), the CAPS module (Jonathan Taylor), the Restriction enzyme package (Frederic Sohm), hefty improvements to Bio.PDB (Thomas Hamelryck), MutableSeq (Michiel de Hoon), and more. The delay in the release was caused by day jobs creeping into the lives of most core developers. So we are very happy with this release finally out, and we hope to have the non-beta out soon.</p> <p>Too many people to thank, so only a handful are mentioned: Michiel and Thomas, thanks for keeping tabs on things during the release process; Jonathan, Frederic and Frank, thanks for the new modules. Jeff Chang, thanks for all the help and pointers in getting the release out, and for the documentation you meticulously wrote for that purpose. Thanks to all the developers for making this happen, and apologies for not mentioning you all by name and work. There are &gt;170 members on the developers mailing list, 46 people in the CONTRIB file, and if you feel you should be there and you&rsquo;re not, let us know.</p> <p>Iddo Friedberg on behalf of the Biopython development team.</p>https://www.open-bio.org/2005/02/08/beginners-howto/Tue, 08 Feb 2005 14:56:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/02/08/beginners-howto/<p>Brian Osborne and James Thompson have written a Bioperl HOWTO for beginners, for those who are interested in learning about Bioperl but have done very little programmming. Topics include creating a Sequence object, I/O and files, retrieving from Genbank, and using the Sequence object.</p> <p>All HOWTOs are <a href="http://bioperl.org/HOWTOs">published</a> on the <a href="http://bioperl.org">bioperl website</a>.</p>https://www.open-bio.org/2005/01/29/bosc-2005/Sat, 29 Jan 2005 16:48:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/01/29/bosc-2005/<p>BOSC 2005 website <a href="https://www.open-bio.org/bosc/">/bosc/</a></p> <p>The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology.</p> <p>see <a href="http://www.iscb.org/ismb2005">http://www.iscb.org/ismb2005</a> for more information.</p> <p>Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community.</p>https://www.open-bio.org/2005/01/29/bioperl-150-released/Sat, 29 Jan 2005 16:33:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/01/29/bioperl-150-released/<h1 id="bioperl-150-developers-release-is-available-for-download">Bioperl 1.5.0 Developer&rsquo;s release is available for download.</h1> <ul> <li> <p><a href="http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2">http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2</a> 425ac55ecbb4339b7b532ba6d429bb40</p> </li> <li> <p><a href="http://bioperl.org/DIST/bioperl-1.5.0.tar.gz">http://bioperl.org/DIST/bioperl-1.5.0.tar.gz</a> 172472f0675de9a583432e21c9b1b5fc</p> </li> <li> <p><a href="http://bioperl.org/DIST/bioperl-1.5.0.zip">http://bioperl.org/DIST/bioperl-1.5.0.zip</a> 3febcd2445a7393c65981a6f9f13a9ed</p> </li> </ul> <p>We&rsquo;ll update the website to reflect this new release.</p> <p>The odd-numbered releases are called developer releases and are not deposited on CPAN. Please note that the API in 1.5.0 may change before the 1.6.0 release. which will be consider a stable API. We may do another developer release before 1.6.0 goes out.</p> <p>Lots of people have contributed to this release, I apologize for not naming them all. I&rsquo;ll try to cover some: thanks to Aaron Mackey for getting this release started, Brian Osborne for extensive documentation improvements, Nathan Haigh for volunteering to make a PPM of the release and Barry Moore and Nathan answering many of the windows related questions, Allen Day &amp; Scott Cain &amp; Steffen Grossmann for the work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for the work with Unflattener to merge GenBank annotations into GFF3 objects.</p> <p>Please see the AUTHORS file for a complete list of contributors.</p> <p>Jason Stajich on behalf of the Bioperl developers.</p> <p><a href="http://portal.open-bio.org/pipermail/bioperl-l/2005-January/018031.html">http://portal.open-bio.org/pipermail/bioperl-l/2005-January/018031.html</a></p> <p>Here is the info from the Changes file. 1.5 Developer release</p> <ul> <li> <p>Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics provide Jukes-Cantor and Kimura pairwise distance methods, respectively.</p> </li> <li> <p>Bio::AlignIO support for &ldquo;po&rdquo; format of POA, and &ldquo;maf&rdquo;; Bio::AlignIO::largemultifasta is a new alternative to Bio::AlignIO::fasta for temporary file-based manipulation of particularly large multiple sequence alignments.</p> </li> <li> <p>Bio::Assembly::Singlet allows orphan, unassembled sequences to be treated similarly as an assembled contig.</p> </li> <li> <p>Bio::CodonUsage provides new rare_codon() and probable_codons() methods for identifying particular codons that encode a given amino acid.</p> </li> <li> <p>Bio::Coordinate::Utils provides new from_align() method to build a Bio::Coordinate pair directly from a Bio::Align::AlignI-conforming object.</p> </li> <li> <p>Bio::DB::Biblio::eutils is a class for querying NCBI&rsquo;s Eutils. Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI&rsquo;s web service using standard Pubmed query syntax, and retrieve results as XML.</p> </li> <li> <p>Bio::DB::GFF has various sundry bug fixes.</p> </li> <li> <p>Bio::FeatureIO is a new SeqIO-style subsystem for writing/reading genomic features to/from files. I/O classes exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO classes only read/write Bio::SeqFeature::Annotated objects. Notably, the GFF v3 class requires features to be typed into the Sequence Ontology.</p> </li> <li> <p>Bio::Graph namespace contains new modules for manipulation and analysis of protein interaction graphs.</p> </li> <li> <p>Bio::Graphics has many bug fixes and shiny new glyphs.</p> </li> <li> <p>Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file indexing for HMMER reports and FASTA qual files, respectively.</p> </li> <li> <p>Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are new objects that can be placed within a Bio::Map::MapI-compliant genetic/physical map; Bio::Map::Physical provides a new physical map type; Bio::MapIO::fpc provides finger-printed clone mapping import.</p> </li> <li> <p>Bio::Matrix::PSM provide new support for postion-specific (scoring) matrices (e.g. profiles, or &ldquo;possums&rdquo;).</p> </li> <li> <p>Bio::Ontology::Ontology and Bio::Ontology::Term objects can now be instantiated without explicitly using Bio::OntologyIO. This is possible through changes to Bio::Ontology::OntologyStore to download ontology files from the web as necessary. Locations of ontology files are hard-coded into Bio::Ontology::DocumentRegistry.</p> </li> <li> <p>Bio::PopGen includes many new methods and data types for population genetics analyses.</p> </li> <li> <p>New constructor to Bio::Range, unions(). Given a list of ranges, returns another list of &ldquo;flattened&rdquo; ranges &ndash; overlapping ranges are merged into a single range with the mininum and maximum coordinates of the entire overlapping group.</p> </li> <li> <p>Bio::Root::IO now supports -url, in addition to -file and -fh. The new -url argument allows one to specify the network address of a file for input. -url currently only works for GET requests, and thus is read-only.</p> </li> <li> <p>Bio::SearchIO::hmmer now returns individual Hit objects for each domain alignment (thus containing only one HSP); previously separate alignments would be merged into one hit if the domaini nvolved in the alignments was the same, but this only worked when the repeated domain occured without interruption by any other domain, leading to a confusing mixture of Hit and HSP objects.</p> </li> <li> <p>Bio::Search::Result::ResultI-compliant report objects now implement the &ldquo;get_statistics&rdquo; method to access Bio::Search::StatisticsI objects that encapsulate any statistical parameters associated with the search (e.g. Karlin&rsquo;s lambda for BLAST/FASTA).</p> </li> <li> <p>Bio::Seq::LargeLocatableSeq combines the functionality already found in Bio::Seq::LargeSeq and Bio::LocatableSeq.</p> </li> <li> <p>Bio::SeqFeature::Annotated is a replacement for Bio::SeqFeature::Generic. It breaks compliance with the Bio::SeqFeatureI interface because the author was sick of dealing with untyped annotation tags. All Bio::SeqFeature::Annotated annotations are Bio::AnnotationI compliant, and accessible through Bio::Annotation::Collection.</p> </li> <li> <p>Bio::SeqFeature::Primer implements a Tm() method for primer melting point predictions.</p> </li> <li> <p>Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML, InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.</p> </li> <li> <p>Bio::Taxonomy::Node now implements the methods necessary for Bio::Species interoperability.</p> </li> <li> <p>Bio::Tools::CodonTable has new reverse_translate_all() and make_iupac_string() methods.</p> </li> <li> <p>Bio::Tools::dpAlign now provides sequence profile alignments.</p> </li> <li> <p>Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).</p> </li> <li> <p>Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report parsers.</p> </li> <li> <p>Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl) for designing small inhibitory RNA.</p> </li> <li> <p>Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building methods based on a distance matrix.</p> </li> <li> <p>Bio::Tree::Statistics provides an assess_bootstrap() method to calculate bootstrap support values on a guide tree topology, based on provided bootstrap tree topologies.</p> </li> <li> <p>Bio::TreeIO now supports the Pagel (PAG) tree format.</p> </li> </ul>https://www.open-bio.org/2005/01/12/bioperl-15-rc-2/Wed, 12 Jan 2005 19:15:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2005/01/12/bioperl-15-rc-2/<p>Release candidate 2 of Bioperl 1.5.0 is ready for downloading and testing. Please report back to the bioperl list with any problems. We would like to make a developer release by the end of January 2005.</p> <ul> <li><a href="http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.gz">http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.gz</a></li> <li><a href="http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.bz2">http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.bz2</a></li> <li><a href="http://bioperl.org/DIST/bioperl-1.5.0-RC2.zip">http://bioperl.org/DIST/bioperl-1.5.0-RC2.zip</a></li> </ul>https://www.open-bio.org/2004/12/29/bioperl-2005-summary/Wed, 29 Dec 2004 21:54:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/12/29/bioperl-2005-summary/<p>I just wanted to use the end of the year as a chance to reflect on what we&rsquo;ve accomplished in 2004 and think about what 2005 holds for Bioperl. <a href="http://portal.open-bio.org/pipermail/bioperl-l/2004-December/017736.html">List Message</a></p> <p>What happened in 2004? First of all, this year has been really has been productive at a level perhaps only appreciated by the folks who read the bioperl-guts-l list which lists the CVS commits. New modules, bugfixes and code improvements have been steadily making their way into the codebase. Not only has there been lots of traffic, but more people are contributing code and fixes.</p> <p>We have also seen increased contributions to the HOWTOs which we hope will be an effective place to explain how to use sets of modules to complete a particular task. We are continually working to improve the documentation. This is a balance between a developer trying to get something accomplished for their own research and wanting other people to use their code (and not wanting to field lots of emails about a particular module). Open source software written solely by volunteers suffers from a reward system which values code over documentation and writing tutorials. We welcome ideas on changes which would help this and are currently thinking about ways to reward the productive documenters as well as coders.</p> <p>We had a chance to have a 5 day Bootcamp in June thanks to Sylvain Foisy, the University of Montreal and the Quebec Bioinformatics Network (BioneQ). We hope to do another one of these in 2006. If there is a general interest in more widespread Bioperl tutorials please forward them to myself or the bioperl list and we can consider how something like this could be organized in conjunction with a conference or meeting.</p> <p>How popular is Bioperl? The 2002 paper has 60+ citations according to Web of Science and we&rsquo;re seeing use in a broader context than just sequence analysis. At least one published paper about modules which were already part of the codebase has appeared suggesting software availability and collaboration can happen prior to publication. The website has been consistently gets around 300,000 hits per month which isn&rsquo;t bad considering that the content doesn&rsquo;t change very much and this is just a site for one toolkit for specific aspect of science. The bioperl-l mailing list has seen an average 341 mails per month (not correcting for spam) which has seen a lot of questions answered and ideas hashed out.</p> <p>How can you help out? I want to use this chance to also appeal to those who use Bioperl and have been sitting on your hands waiting to jump in. It is a collaborative project that only works if new people jump in an contribute ideas and manpower. We&rsquo;ve had many examples of people who have just jumped on board the project, fixed some bugs, contributed a module and went on their merry way. We&rsquo;ve also had other people who have jumped in, contributed code, and found themselves fully engaged in the project and its internal workings almost immediately. Not to wax poetic, but it was about 5 years ago that fresh out of college, I started reading the mailing list, read Steve Chervitz&rsquo;s email plea for people to <a href="http://bioperl.org/pipermail/bioperl-l/1999-December/003354.html">&ldquo;ask not what Bioperl can do for you, ask what you can do for Bioperl&rdquo;</a> and just jumped right in. I can only hope to influence some more folks who might have wanted to contribute but were waiting for the invitation. Well come on over, we&rsquo;d love to have you taking part.</p> <p>As for some specifics. - Parsing of Species information out from the ORGANISM lines in SwissProt, GenBank, and EMBL is pretty spotty and could take some work. - Some more parsers for formats that people have asked for - a Spidey parser (NCBI&rsquo;s mRNA -&gt; genomic alignment tool) - Work on the Structure modules for dealing with protein structure data - Integrate new applications into bioperl-run and further cleanup the existing modules so they are more consistent - Volunteer to be the next release master.</p> <p>What does the future hold for Bioperl? We expect to have a 1.5 release of bioperl in 1st quarter of 2005 - this is the domain of Aaron Mackey who agreed to be the release master (who has his hands full right now, but I&rsquo;m sure will ask for help when he needs it). This should incorporate many new modules and bug fixes but be compatible with the 1.4 API as well. Details on the schedule for 1.5 sometime after the holidays.</p> <p>The future depends entirely on who steps up to work on the project next year. In 2005, I am resolving to limit myself from the front guard of mailing list question answering. This is in part finish my PhD research and focus on building more specific tools to support my research questions, but also it is time for other people to contribute and share the spotlight and be a know-it-all. Bioperl is very much a labor of love and it is an integral part of the tools I use in my own work so I expect to focus more directly on those things I need in the coming year and help out where I can.</p> <p>My hope is that some of the new folks who have stepped up to contribute will help by continuing the course we have set to have high quality releases, a full test suite, POD documentation for every module, and overall documentation for using modules in HOWTOs and tutorials. If there are new or unexplored areas the project should consider I hope that you will speak up and suggest them.</p> <p>There is discussion underfoot that a new Bioperl object model may be born. This has been called Bioperl2 and Bioperl-NG. The idea is it would try and create a leaner and cleaner code base which is does things like event-based parsing, autogenerated code for things like getters/setters, and could do things faster and easier than we are currently. Generally there is a lot of legacy code and legacy design in Bioperl and it would be beneficial to have a project that was free of these constraints. At the same time there is an expectation that a project like this would also need to achieve something more than what the current bioperl API cannot do so it incumbent on the new project to have goals that are higher than what Bioperl can do.</p> <p>Thank you I&rsquo;d like to finally thank some people who have done a lot this year. Of course I&rsquo;m not going to remember to name everyone, but I just wanted to highlight some folks who have endeavored not only get the toolkit to do what they want, but also to help out other people get started with it.</p> <p>The people who have kept the project going. These are usual suspects how have labored to do the dirty grunt work cleaning up boring bugs, adding documentation, preparing a release, keeping the servers going, etc. They also code too, but wanted to highlight that they have really been critical to keeping the project going by doing the things that most people don&rsquo;t want to bother with. Brian Osborne Aaron Mackey Chris Dagdigian Kyle Jenson (mailing list and site searching at <a href="http://search.open-bio.org">http://search.open-bio.org</a>)</p> <p>Some usual suspects who have been helping maintain their modules and generally being Bioperl knowledgeable on the list: Scott Cain Steve Chervitz Allen Day Donald Jackson Stefan Kirov Hilmar Lapp Josh Lauricha Heikki Lehvaslaiho Chris Mungall Jurgen Plentinckx Lincon Stein</p> <p>There are new several people who have taken up the slack as those before them have drifted onto other commitments. (metaphoric slack of course, not trying to accuse anyone of being a &lsquo;slacker&rsquo;). Thanks for jumping in, fixing bugs, running tests, giving feedback, and just getting involved. It is really encouraging when the project can be a 2-way street and not just a one way flow information going out from a few people who post answers to the list. Richard Adams Sean Davis Rob Edwards Nathan Haigh Marc Logghe Barry Moore Remo Sanges James Thompson Koen van der Drift (Bioperl available via fink on OS X)</p> <p>Thanks also to Peter van Heusden and Electric Genetics which are undertaking a code audit of Bioperl and should have many helpful feedback points for us.</p> <p>I&rsquo;ve probably forgotten some people, please post a followup if I have neglected someone as I would like you to be recognized for your work since we don&rsquo;t give out a whole lot else right now.</p> <p>A safe and prosperous New Year to you all.</p> <p>Jason Stajich on behalf of the Bioperl core developers.</p>https://www.open-bio.org/2004/11/14/bioperl-preparing-15-release/Sun, 14 Nov 2004 17:37:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/11/14/bioperl-preparing-15-release/<p>Bioperl developers are preparing a 1.5 release, you can grab the pre-release for testing at <a href="http://bioperl.org/DIST">http://bioperl.org/DIST</a>. We would greatly appreciate you downloading and testing this code before it is released by running &lsquo;make test&rsquo;.</p> <p>See <a href="http://portal.open-bio.org/pipermail/bioperl-l/2004-November/017351.html">Aaron&rsquo;s post</a> announcing the RC1 candidate.</p>https://www.open-bio.org/2004/05/14/biopython-130-release/Fri, 14 May 2004 14:59:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/05/14/biopython-130-release/<p>I&rsquo;m happy to announce a new release of Biopython 1.30, available today from <a href="http://biopython.org">http://biopython.org</a>. This release contains a number of new modules and substantial changes to older modules. As a result of the changes, we&rsquo;ve bumped up to a brand new major number. Please do download, test with your code, and report any bugs or problems to the normal lists (biopython at biopython.org or biopython-dev at biopython.org). For the full details about changes, please see: <a href="http://portal.open-bio.org/pipermail/biopython/2004-May/002078.html">http://portal.open-bio.org/pipermail/biopython/2004-May/002078.html</a></p>https://www.open-bio.org/2004/04/06/bioperl-bootcamp-june-21-25/Tue, 06 Apr 2004 06:06:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/04/06/bioperl-bootcamp-june-21-25/<p><a href="http://bioperl.org/pipermail/bioperl-l/2004-April/015481.html">The Mailing list post</a></p> <p>Continuing on the BioJava Bootcamp of 2003, The Quebec Bioinformatics Network (BioneQ) is organizing its first BioPerl Bootcamp, to be held at the Universite de Montreal from June 21-25 2004.</p> <p>The invited speakers are leaders in the use of Perl in bioinformatics and development of BioPerl:</p> <p>Aaron Mackey (U. of Pennsylvania) Jason Stajich (Duke University) Lincoln Stein (Cold Spring Harbor Labs)</p> <p>Seminars and exercise sessions will be in a Linux computer lab for a total hands-on experience.</p> <p>++ A demonstrated knowledge of programming is a pre-requisite ++</p> <p>++ Registration fee is US $200 ++</p> <p>++ Places are limited !! ++</p> <p>If you or someone in your group is interested by this workshop, e-mail a letter of intent and a file with your cv to bioperl-bootcamp at bioneq.qc.ca.</p> <p>Best regards</p> <p>Sylvain Foisy</p>https://www.open-bio.org/2004/02/20/bioperl-14-for-windows/Fri, 20 Feb 2004 17:08:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/02/20/bioperl-14-for-windows/<p><strong>Bioperl version 1.4 for Windows</strong> is available. Thanks once again to Nigam Shah for creating and testing the PPM and PPD files.</p>https://www.open-bio.org/2004/02/18/bioknoppix/Thu, 19 Feb 2004 02:33:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/02/18/bioknoppix/<p><a href="http://bioknoppix.hpcf.upr.edu/">BioKnoppix</a> is a new live CD linux, based on <a href="http://www.knopper.net/knoppix/index-en.html">KNOPPIX</a>, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!</p>https://www.open-bio.org/2004/02/17/biopython-124-release/Tue, 17 Feb 2004 04:37:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2004/02/17/biopython-124-release/<p>I&rsquo;m happy to announce the 1.24 release of Biopython. As normal Biopython is available from <a href="http://biopython.org">http://biopython.org</a>.</p> <p>The major changes in this release, in addition to the usual bug fixes, are:</p> <p>New parsers for Phred and Ace format files &ndash; thanks to Frank Kauff New Code for dealing with NMR data &ndash; thanks to Bob Bussell New SeqUtils modules for codon usage, isoelectric points and other protein properties &ndash; thanks to Yair Benita New code for dealing with Wise contributed by Michael EZ-Retrieve sequence retrieval now supported thanks to Jeff Bio.Cluster updated along with documentation by Michiel BioSQL fixed so it now works with the current SQL schema &ndash; thanks to Yves Bastide for patches</p>https://www.open-bio.org/2003/12/23/bioperl-release-14/Tue, 23 Dec 2003 13:36:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/12/23/bioperl-release-14/<p>The stable Bioperl release 1.4 is available for immediate use at: <a href="http://bioperl.org/DIST">http://bioperl.org/DIST</a>.</p> <p>We are releasing simultaneously three modules:</p> <ul> <li> <p>bioperl-core - core bioperl modules ( <a href="http://bioperl.org/DIST/current_core_stable.tar.gz">gz</a> <a href="http://bioperl.org/DIST/current_core_stable.tar.bz2">b2z</a>)</p> </li> <li> <p>bioperl-ext - C compiled extensions ( <a href="http://bioperl.org/DIST/current_ext_stable.tar.gz">gz</a> <a href="http://bioperl.org/DIST/current_ext_stable.tar.bz2">b2z</a>)</p> </li> <li> <p>bioperl-run - wrappers for external programs ( <a href="http://bioperl.org/DIST/current_run_stable.tar.gz">gz</a> <a href="http://bioperl.org/DIST/current_run_stable.tar.bz2">b2z</a>)</p> </li> </ul> <p>They will also appear shortly at <a href="http://iubio.bio.indiana.edu/soft/molbio/perl/bioperl/">the IUBIO mirror</a> (later today) and in <a href="http://search.cpan.org/dist/bioperl/">CPAN</a>.</p> <p>Remember, all the external modules needed by bioperl-core can be installed from CPAN under name <a href="http://search.cpan.org/dist/Bundle-BioPerl/">Bundle-BioPerl</a>.</p> <h3 id="changes">Changes</h3> <p>Over 3000 file changes have gone into this release since the 1.2 development tree was branched off from the main. These are the main feature enhancements:</p> <ul> <li> <p>installable scripts</p> </li> <li> <p>global module version from Bio::Root:Version</p> </li> <li> <p>Bio::Graphics - major improvements; added SVG support</p> </li> <li> <p>Bio::Popgen - population genetics</p> </li> <li> <p>Bio::Restriction - new restrion analysis modulues</p> </li> <li> <p>Bio::Tools::Analysis - web based DNA and Protein analysis framework and several implementaions</p> </li> <li> <p>Bio::Seq::Meta - per residue annotable sequences</p> </li> <li> <p>Bio::Matrix- including Bio::Matrix::PSM - Position Scoring Matrix</p> </li> <li> <p>Bio::Ontology - major contributions</p> </li> <li> <p>Bio:Tree</p> </li> <li> <p>Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA</p> </li> <li> <p>Bio::SeqFeature::Tools - seqFeature mapping tools, e.g. Bio::SeqFeature::Tools::Unflattener.pm</p> </li> <li> <p>Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment (needs Bioperl-ext)</p> </li> <li> <p>new Bio::SearchIO formats</p> </li> <li> <p>new Bio::SeqIO formats: tab, kegg, tigr, game; important fixes for old modulues</p> </li> <li> <p>Bio::AlignIO: maf</p> </li> <li> <p>improved Bio::Tools::Genewise</p> </li> <li> <p>Bio::SeqIO now can recognize sequence formats automatically from stream</p> </li> <li> <p>new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,</p> </li> <li> <p>several new HOWTOs: SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat Databases</p> </li> <li> <p>hundreds of new and improved files</p> </li> </ul> <p>For detailed documentation, see individual module documentation in the distribution or in <a href="http://doc.bioperl.org/">http://doc.bioperl.org/</a>. The tutorials are available at <a href="http://bioperl.org/HOWTOs/">http://bioperl.org/HOWTOs/</a>.</p> <p>This release is a result of hard work by the bioperl core team, nearly hundred developers and countless suggestions and bug reports at the bioperl mailing list (<a href="mailto:bioperl-l@bioperl.org">bioperl-l@bioperl.org</a>) or the the bioperl bug tracking system ( <a href="http://bugzilla.bioperl.org/">http://bugzilla.bioperl.org/</a>).</p> <p>Wishing you all Peaceful Christmas,</p> <p>-Heikki and the bioperl core developers</p>https://www.open-bio.org/2003/11/26/svg-support-for-biographics/Wed, 26 Nov 2003 15:53:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/11/26/svg-support-for-biographics/<p>Todd Harris has released <a href="http://toddot.net/projects/GD-SVG/index.shtml">GD::SVG</a> in <a href="http://search.cpan.org/author/TWH/GD-SVG-0.19/">CPAN</a>. This module implements support for most features of GD that are used by Bio::Graphics (together with the <a href="http://search.cpan.org/author/RONAN/SVG-2.27/">SVG</a> module).</p> <p>Try out the publication publication quality graphics directly from <a href="http://cvs.bioperl.org/">CVS</a> and help to squash the last bugs before stable bioperl release. See <code>all_glyphs.pl</code> and <code>dynamic_glyphs.pl</code> in <code>examples/biographics</code> directory.</p>https://www.open-bio.org/2003/11/24/howto-simplewebanalysis/Mon, 24 Nov 2003 15:10:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/11/24/howto-simplewebanalysis/<p>Need to write a wrapper around sequence analysis service in a web form? Richard Adams has written <a href="http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioperl-live/doc/howto/html/SimpleWebAnalysis.html?rev=1.1&amp;cvsroot=bioperl">a HOWTO document about his<br> Bio::Tools::Analysis modules</a>. Available in CVS or in the latest developer release. See into BIOPERL/doc/howto/{sgml|html|pdf|txt} for the SimpleWebAnalysis document in your favourite format.</p> <p>Summary:</p> <p>Richard has written a superclass Bio::Tools::Analysis::SimpleAnalysisBase, which implements Bio::SimpleAnalysisI and inherits from Bio::WebAgent. Adding a new form-based sequence service is easily done by sub-classing, specifying a some parameters and overriding just three methods. Nine different services have been added to date, with more to come.</p>https://www.open-bio.org/2003/10/19/biopython-123-release/Mon, 20 Oct 2003 00:28:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/10/19/biopython-123-release/<p>Jeff announces a new release of Biopython:</p> <p>Biopython 1.23 is now available from the website at: <a href="http://www.biopython.org/">http://www.biopython.org/</a></p> <p>This is mostly a maintenance release, which fixes some problems in the installation. You do not need to update from 1.22 unless you are using the Bio.Cluster, Bio.KDTree, or Bio.PDB.mmCIF packages. The changes made in this release are: Fixed distribution of files in Bio/Cluster Now distributing Bio/KDTree/_KDTree.swig.C minor updates in installation code added mmCIF support for PDB files</p> <p>As usual, please report bugs to <a href="mailto:biopython-dev@biopython.org">biopython-dev@biopython.org</a>, or the bug database also available from the website.</p>https://www.open-bio.org/2003/09/21/slides-of-bioperl-db-biosql-talk-at-bosc03/Sun, 21 Sep 2003 09:36:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/09/21/slides-of-bioperl-db-biosql-talk-at-bosc03/<p>I posted the <a href="https://www.open-bio.org/bosc2003/slides/Persistent_Bioperl_BOSC03.pdf">slides</a> for the Bioperl-db/BioSQL talk I gave at BOSC03.</p> <p>-hilmar</p>https://www.open-bio.org/2003/09/19/release-announcement-bioperl-microarray-01/Fri, 19 Sep 2003 06:09:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/09/19/release-announcement-bioperl-microarray-01/<p>The Bioperl developers are pleased to announce a 0.1 release of bioperl-microarray, a Bioperl extension package dedicated to manipulation of microarray data.</p> <p>The package is implemented using IO conventions Bioperl developers should already be familiar with. Data types currently supported are:</p> <p>Affymetrix GeneChip CEL files (read and write) Affymetrix GeneChip CDF files (read) Affymetrix GeneChip Microarray Suite 5.0 normalized files (read) Affymetrix GeneChip dChip normalized files (read)</p> <p>Data types for which support is planned in a 0.2 release include:</p> <p>Bio::MAGE objects and MAGE-ML (read and write) Affymetrix SNPChip genotype files (read) GenePix GPR files (read)</p> <p>Release packages are available from: <a href="http://www.bioperl.org/DIST/">http://www.bioperl.org/DIST/</a> <a href="http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.bz2">http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.bz2</a> <a href="http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.gz">http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.gz</a> <a href="http://www.bioperl.org/DIST/bioperl-microarray-0.1.zip">http://www.bioperl.org/DIST/bioperl-microarray-0.1.zip</a></p> <p>Documentation available from: <a href="http://doc.bioperl.org/bioperl-microarray/">http://doc.bioperl.org/bioperl-microarray/</a></p> <p>Subscribe to the bioperl-microarray mailing list at: <a href="http://bioperl.org/mailman/listinfo/bioperl-microarray/">http://bioperl.org/mailman/listinfo/bioperl-microarray/</a></p> <p>Report bugs at: <a href="http://bugzilla.bioperl.org/">http://bugzilla.bioperl.org/</a></p>https://www.open-bio.org/2003/09/18/bioperl-123-released/Thu, 18 Sep 2003 23:12:19 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/09/18/bioperl-123-released/<p>Bioperl 1.2.3</p> <p>On behalf of the Bioperl developers, we are pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile web-based sequence databases, Alignment parsing and manipulation, parsing of and data representation of output from a majority of standard bioinformatics tools, and many more features.</p> <p>This release constitutes several major bugfixes from the 1.2.2 release earlier this summer and provides some new minor functionality improvements. This release is intended to be compatible with code which has been programmed using the API in the 1.2.x series of releases.</p> <p>The release is available as always from <a href="http://bioperl.org/DIST/">http://bioperl.org/DIST/</a>.</p> <p>Bioperl 1.2.3</p> <p>On behalf of the Bioperl developers, I am pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile and webbased sequence databases, Alignment parsing and manipulation, parsing of and data representation of output from a majority of standard bioinformatics tools, and many more features.</p> <p>This release constitutes several major bugfixes from the 1.2.2 release earlier this summer and provides some new minor functionality improvements. This release is intended to be compatible with code which has been programmed using the API in the 1.2.x series of releases.</p> <p>The release is available as always from <a href="http://bioperl.org/DIST/">http://bioperl.org/DIST/</a> <a href="http://bioperl.org/DIST/bioperl-1.2.3.tar.bz2">http://bioperl.org/DIST/bioperl-1.2.3.tar.bz2</a> <a href="http://bioperl.org/DIST/bioperl-1.2.3.tar.gz">http://bioperl.org/DIST/bioperl-1.2.3.tar.gz</a> <a href="http://bioperl.org/DIST/bioperl-1.2.3.zip">http://bioperl.org/DIST/bioperl-1.2.3.zip</a></p> <p>As well as from mirrors generously provided by Don Gilbert at Indiana University <a href="http://iubio.bio.indiana.edu/">http://iubio.bio.indiana.edu/</a></p> <p>MD5 signatures for the release files c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 72b4a23f7372e820a7a7d9a72e7a0e76 bioperl-1.2.3.tar.gz e3bef5ca6ec6692bc253b75046100b64 bioperl-1.2.3.zip</p> <p>HTML-ized documentation for the release is available from the documentation website <a href="http://doc.bioperl.org/">http://doc.bioperl.org/</a> <a href="http://doc.bioperl.org/releases/bioperl-1.2.3/">http://doc.bioperl.org/releases/bioperl-1.2.3/</a></p> <p>Related Projects ---&mdash;&mdash;&mdash;&mdash;-</p> <p>The Generic Genome Browser which depends on bioperl will likely release a new version which will utilize features in bioperl 1.2.3. This is coordinated by Lincoln Stein and Scott Cain. Code is available from the project site at <a href="http://www.gmod.org">www.gmod.org</a>.</p> <p>We plan to release a new version of bioperl-run in the coming week. bioperl-run is a package of perl module wrappers around many applications common to bioinformatics analyses. Shawn Hoon is responsible for overseeing this release. Previous and future releases are available at <a href="http://bioperl.org/DIST/">http://bioperl.org/DIST/</a> and in CPAN and as always from our CVS repository <a href="http://cvs.open-bio.org">http://cvs.open-bio.org</a>.</p> <p>A brand new package bioperl-microarray will be released this week as well, version 0.1. This is a project headed by Allen Day and he will be announcing a code release shortly. The code will be available from CPAN, <a href="http://bioperl.org/DIST">http://bioperl.org/DIST</a>, and <a href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a>.</p> <p>Another recent project which has not been released yet, but should be out this fall is bioperl-pedigree. This will include codes for parsing and representing pedigree data and will interface with genotype parsing and representations already part of the Bioperl Core. This package is overseen by Jason Stajich. Code is available from our CVS repository and will be available at <a href="http://bioperl.org/DIST">http://bioperl.org/DIST</a>.</p> <p>Contributors ---&mdash;&mdash;&mdash;</p> <p>The hard work of many people has gone into this release, please see <a href="http://bioperl.org/Core/Latest/AUTHORS.html">AUTHORS</a> file included in the release for a complete list of individuals who have contributed to the project.</p> <p>We would especially like to thank those who have provided bug reports and feedback about the modules to help us improve them. We would like to welcome several new developers who have joined us recently to provide code improvements and implementations of new areas for Bioperl.</p> <p>Future plans ---&mdash;&mdash;&mdash; We intend to focus our energy on the next set of developer&rsquo;s releases in the Fall of 2003 which will be numbered 1.3.x and will lead to the next stable release 1.4 in 2004.</p> <p>We encourage new and old developers to be part of the development cycle as well as users to provide feedback and bug reports.</p> <p>Bugs ---- Bugs should be reported at our bug tracking site. Information about bugs in the Changes are also available from this site. <a href="http://bugzilla.bioperl.org/">http://bugzilla.bioperl.org</a></p> <p>A synopsis of changes from the Changes file</p> <hr> <h2 id="123-stable-release-update">1.2.3 Stable release update</h2> <ul> <li> <p>Bug #1475 - Fix and add speedup to spliced_seq for remote location handling.</p> </li> <li> <p>Bug #1477 - Sel &ndash;&gt; Sec abbreviation fixed</p> </li> <li> <p>Fix bug #1487 where paring in-between locations when end &lt; start caused the FTLocationFactory logic to fail.</p> </li> <li> <p>Fix bug #1489 which was not dealing with keywords as an arrayref properly (this is fixed on the main trunk because keywords returns a string and the array is accessible via get_keywords).</p> </li> <li> <p>Bio::Tree::Tree memory leak (bug #1480) fixed Added a new initialization option -nodelete which won&rsquo;t try and cleanup the containing nodes if this is true.</p> </li> <li> <p>Bug with parsing labeled nodes with Bio::TreeIO::newick fixed this was only present on the branch for the 1.2.1 and 1.2.2 series</p> <ul> <li>Also merged main trunk changes to the branch which make newick -&gt; nhx round tripping more effective (storing branch length and bootstrap values in same locate for NodeNHX and Node implementations.) Fixes to TreeIO parsing for labeled internal also required small changes to TreeIO::nhx. Improved tests for this module as well.</li> </ul> </li> <li> <p>Bio::SearchIO</p> <ul> <li> <p>Fixed bugs in BLAST parsing which couldn&rsquo;t parse NCBI gapped blast properly (was losing hit significance values due to the extra unexpeted column).</p> </li> <li> <p>Parsing of blastcl3 (netblast from NCBI) now can handle case of integer overflow (# of letters in nt seq dbs is &gt; MAX_INT) although doesn&rsquo;t try to correct it - will get the negative number for you. Added a test for this as well.</p> </li> <li> <p>Fixed HMMER parsing bug which prevented parsing when a hmmpfam report has no top-level family classification scores but does have scores and alignments for individual domains.</p> </li> <li> <p>Parsing FASTA reports where ungapped percent ID is &lt; 10 and the regular expression to match the line was missing the possibility of an extra space. This is rare, which is why we probably did not catch it before.</p> </li> <li> <p>BLAST parsing picks up more of the statistics/parameter fields at the bottom of reports. Still not fully complete.</p> </li> <li> <p>SearchIO::Writer::HTMLResultWriter and TextResultWriter were fixed to include many improvements and added flexiblity in outputting the files. Bug #1495 was also fixed in the process.</p> </li> </ul> </li> <li> <p>Bio::DB::GFF</p> <ul> <li> <p>Update for GFF3 compatibility.</p> </li> <li> <p>Added scripts for importing from UCSC and GenBank.</p> </li> <li> <p>Added a 1.2003 version number.</p> </li> </ul> </li> <li> <p>Bio::Graphics</p> <ul> <li> <p>Updated tutorial.</p> </li> <li> <p>Added a 1.2003 version number.</p> </li> </ul> </li> <li> <p>SeqIO::swiss Bug #1504 fixed with swiss writing which was not properly writing keywords out.</p> </li> <li> <p>Bio::SeqIO::genbank</p> <ul> <li> <p>Fixed bug/enhancement #1513 where dates of the form D-MMM-YYYY were not parsed. Even though this is invalid format we can handle it - and also cleanup the date string so it is properly formatted.</p> </li> <li> <p>Bug/enhancement #1517 fixed so that SEGMENT line can be parsed and written with Genbank format. Similarly bug #1515 is fixed to parse in the ORIGIN text.</p> </li> </ul> </li> <li> <p>Bio::SeqIO::fasta, a new method called preferred_id_type allows you to specify the ID type, one of (accession accession.version display primary). See Bio::SeqIO::preferred_id_type method documentation for more information.</p> </li> <li> <p>Unigene parsing updated to handle file format changes by NCBI</p> </li> </ul> <h2 id="jason-stajich-on-behalf-of-the-bioperl-developers">Jason Stajich on behalf of the Bioperl developers.</h2> <p>Jason Stajich Duke University jason at cgt.mc.duke.edu</p>https://www.open-bio.org/2003/08/30/server-downtime-announcement/Sat, 30 Aug 2003 21:07:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/08/30/server-downtime-announcement/<p>Hi Everyone,</p> <p>Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.</p> <p>Simply put &ndash; Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone.</p> <p>Technically the changeover will be swift as the circuit and new routers/firewalls are already in place. Should be a matter of bringing down the old gear and lighting up the new stuff.</p> <p>The backbone change will have a significant affect on us though &ndash; all of our server IP addresses will change.</p> <p>The change is scheduled for the evening (EST/EDT timezone) of September 2nd 2003. I&rsquo;ll be onsite at Wyeth in the datacenter as the change occurs so that I can bring down our servers and plug in the new IP addresses.</p> <p>The really nice thing is that all of our primary and secondary DNS nameservers are hosted at places other than Wyeth. This means that we can almost instantly be pushing out the new correct IP addresses for all of our open-bio.org, biojava.org etc. domain names.</p> <p>If I can get my act together during the day on Tuesday I&rsquo;ll start seeding our DNS servers with shorter TTL values which will speed up the spread of the new information.</p> <p>For people with &lsquo;fresh&rsquo; DNS data our servers will appear back on the internet within 30 minutes or so. For people behind nameserver caches that do not refresh all that often please expect our servers to &ldquo;vanish&rdquo; from the internet for a period of about 8-24 hours while the new information propagates out through the internet.</p> <p>Regards, Chris open-bio.org</p>https://www.open-bio.org/2003/08/14/recent-bioperl-additions-and-bug-fixes/Fri, 15 Aug 2003 02:49:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/08/14/recent-bioperl-additions-and-bug-fixes/<p>Jason has summarized a significant amount of work he has done on the CVS tree. Major work done on Bio::PopGen, Bio::Matrix and bug fixes to Bio::Tree and Bio::SeqIO.</p> <p>All the juicy details can be read in his bioperl posting archived here: <a href="http://bioperl.org/pipermail/bioperl-l/2003-August/013168.html">http://bioperl.org/pipermail/bioperl-l/2003-August/013168.html</a></p>https://www.open-bio.org/2003/07/27/biopython-120-released/Mon, 28 Jul 2003 02:33:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/07/27/biopython-120-released/<p>Available now at <a href="http://biopython.org/download/">http://biopython.org/download/</a></p> <p>Changes include: added Andrew Dalke&rsquo;s EUtils library added Michiel de Hoon&rsquo;s gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman&rsquo;s fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler&rsquo;s NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman&rsquo;s fixes to Genbank code &ndash; now parses whole database Kayte Lindner&rsquo;s LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich&rsquo;s patch to read T_Coffee files Larry Heisler&rsquo;s fix for primer3 output Bio.Medline now uses proper iterator objects copen now handles SIGTERM correctly small bugfixes and updates in Thomas Hamelryck&rsquo;s PDB package bugfixes and updates to SeqIO.FASTA reader updates to Registry system, conforms to 2003 hackathon OBDA spec Yu Huang patch to support tblastn in wublast expression</p>https://www.open-bio.org/2003/07/27/biojava-in-anger-translated-to-french-and-japanese/Mon, 28 Jul 2003 02:30:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/07/27/biojava-in-anger-translated-to-french-and-japanese/<p>The &ldquo;Biojava in Anger: A Tutorial and Recipe Book for Those in a Hurry&rdquo; posted online at <a href="http://www.biojava.org/docs/bj_in_anger/index.htm">http://www.biojava.org/docs/bj_in_anger/index.htm</a> has been translated into <a href="http://www3.sympatico.ca/foisys/bj_in_anger">French</a> and <a href="http://www.biojava.org/docs/bj_in_anger/ja/index.htm">Japanese</a></p>https://www.open-bio.org/2003/07/15/new-restriction-analysis-classes/Wed, 16 Jul 2003 02:31:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/07/15/new-restriction-analysis-classes/<p>Rob Edwards and Heikki Lehvaslaiho have been writing new restriction analysis classes. These will eventually replace the long serving Bio::Tools::RestrictionEnzyme by Steve Chervitz. The first working versions are in CVS.</p> <p><a href="http://bio.perl.org/images/bio_restriction.png">A UML graph</a> shows the class relationships. A more verbose overview is below.</p> <p><strong>Bio::Restriction::Enzyme</strong> class knows (almost) everything there to know about restriction enzymes.</p> <p>There are two subclasses of Enzyme: 1) Bio::Restriction::Enzyme::MultiSite and 2) Bio::Restriction::Enzyme::MultiCut that handle relatively rare cases when recognition sites of the enzyme is more complex than can be expressed using IUPAC code or there are four cut sites per site.</p> <p><strong>Bio::Restriction::EnzymeCollection</strong> object is a set of Enzymes. It is created by Bio::Restriction::IO. This class works like Bio::SeqIO class, but if you call it without parameters, you get a default selection of 530 bare-boned Enzymes.</p> <p>If you want select your own set, you can read in data from REBASE database flat files. Two formats, <em>itype2</em> and <em>withrefm</em>, are now supported.</p> <p>Any attribute of an Enzyme can easily be used to filter them out of one collection into an other.</p> <p><strong>Bio::Restriction::Analysis</strong> uses an EnzymeCollection to cut any Bio::PrimarySeqI implementing sequence into fragments. There are methods to find enzymes that cut the sequence to a given number of time, or do not cut at all, and retrieve the fragments.</p>https://www.open-bio.org/2003/07/08/bioperl-122-released/Tue, 08 Jul 2003 20:27:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/07/08/bioperl-122-released/<p>This is a bug fix release from the stable branch.</p> <p>The Bioperl release 1.2.2 is available at <a href="http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz">http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz</a> and is propagating around CPAN now.</p> <p>Bioperl-run is a collection of modules that wrap bioinformatics applications to allow running them from bioperl. The release cycle of bioperl-run follows the core. The latest bioperl-run release is therefore at: <a href="http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz">http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz</a></p> <p>The main bug fixes in this release are:</p> <p>bioperl</p> <ul> <li> <p>OBDA Registry code is up to latest specs and fuly functional</p> </li> <li> <p>Sequence retrieval from NCBI works again after URL change (Bio::DB::GenBank)</p> </li> <li> <p>The BLAST output parsed now works on megablast and parses even the last hit</p> </li> <li> <p>Result writers now correctly report alignment start/end info for translated BLAST/FASTA searches (Bio::SearchIO::Writer::(HTML|Text)ResultWriter)</p> </li> <li> <p>Improvements in closing and keeping open file handles</p> </li> <li> <p>Robustness of Bio::Graphics modules have been improved</p> </li> <li> <p>Other improved modules:</p> <ul> <li> <p>Bio::OntologyIO::dagflat</p> </li> <li> <p>Bio::Annotation::OntologyTerm</p> </li> <li> <p>Bio::TreeIO::newick</p> </li> <li> <p>Bio::Tools::BPbl2seq</p> </li> <li> <p>Bio::Tools::Genemark</p> </li> <li> <p>Bio::SeqIO::genbank</p> </li> </ul> </li> </ul> <p>bioperl-run</p> <ul> <li> <p>SoapLab and PISE improvements</p> </li> <li> <p>New wrapper for Vista: <a href="http://www-gsd.lbl.gov/vista/">http://www-gsd.lbl.gov/vista/</a> (Bio::Tools::Run::Vista)</p> </li> <li> <p>Other improved modules:</p> <ul> <li> <p>Bio::Tools::Run::Eponine</p> </li> <li> <p>Bio::Tools::Run::FootPrinter</p> </li> <li> <p>Bio::Tools::Run::Genewise</p> </li> <li> <p>Bio::Tools::Run::Genscan</p> </li> <li> <p>Bio::Tools::Run::Hmmpfam</p> </li> <li> <p>Bio::Tools::Run::Mdust</p> </li> <li> <p>Bio::Tools::Run::Signalp</p> </li> <li> <p>Bio::Tools::Run::Phylo::Phylip::SeqBoot</p> </li> <li> <p>Bio::Tools::Run::Phylo::Phylip::Neighbor</p> </li> <li> <p>Bio::Tools::Run::Alignment::Blat</p> </li> <li> <p>Bio::Tools::Run::Alignment::Lagan</p> </li> </ul> </li> </ul> <p>More details are in distribution file &lsquo;Changes&rsquo;.</p> <p>Thank you for all who reported bugs and made this release possible.</p>https://www.open-bio.org/2003/07/02/bosc2003-pictures-are-online/Wed, 02 Jul 2003 04:59:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/07/02/bosc2003-pictures-are-online/<p>Our &ldquo;Bioinformatics Open Source Conference&rdquo; was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful &mdash; 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.</p> <p>Pictures are online here: <a href="http://gallery.open-bio.org/">http://gallery.open-bio.org/</a></p>https://www.open-bio.org/2003/07/02/release-candidate-122-available/Wed, 02 Jul 2003 04:45:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/07/02/release-candidate-122-available/<p>A possible release candidate for BioPerl 1.2.2 is now available for download: <a href="http://bioperl.org/DIST/bioperl-1.2.2rc1.tar.gz">http://bioperl.org/DIST/bioperl-1.2.2rc1.tar.gz</a></p> <p>Please download and give it a test. New aditions, features and fixes are in the &ldquo;Changes&rdquo; file.</p>https://www.open-bio.org/2003/06/28/bosc-finishes-and-i-weep-as-i-miss-it-already/Sat, 28 Jun 2003 11:08:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/28/bosc-finishes-and-i-weep-as-i-miss-it-already/<p>BOSC always comes and goes so fast. I am a melancholy kind of guy so whenever things finish up I get a little misty eyed with regrets at the things I could have done and the people I could have met. But it was all so great it makes me smile with the understanding of the entire world. Plus weeping really gets you the women &ndash; makes you look quite sensitive. And I am all about sensitivity. But before I got into this mindset, I tried to write down what happened. Read and feel my joy.</p> <p>You may be wondering what Australia is like. So am I. So far I have been entirely in the service of you, the faithful reader of BOSC news, and have been basically a good boy attending conferences and generally getting my money&rsquo;s worth. All this science. All in Australia.</p> <p>But yes, in case you are wondering if I suddenly turned into an all-contributing hard-core science type who works day and night thinking only of how I can further increase the general scientific knowledge of the world, this is not at all true. So last night it was time to explore the wonderful world of Australian bars. And I&rsquo;m happy to report on that; if I could remember any of it.</p> <p>Okay, I can remember. I&rsquo;m not all that bad, dontchaknow. My first impressions of this region of Australia basically center around two points &ndash; there are not a lot of bars around here, and damn these streets are complicated. Sadly, the first impression is likely due to the second &ndash; I am the kind of person that get readily lost. But no one cares &ndash; the point is that we ended up at the apparently only bar on this side of the river separating our conference site from the downtown casino part of Brisbane; South Brisbane versus the rest of Brisbane.</p> <p>As an amateur sociologist, amongst other things, I am very interested in the people of Australia. Specifically, I was watching the flight information on the plane ride from Melbourne to Brisbane and noticed something very interesting and peculiar. The flight info basically said the same things &ndash; fasten your seatbelt, put on your oxygen mask before helping small children and invalids around you, blah blah blah. The interesting thing is that even though it was the exact same information, it was presented in an entirely different sort of fashion. The language and intonations of the talk was all in English, but it was Australian English, a factor of living in Australia and speaking with Australian people. Its more than just different phrases, but a completely different way of thinking about saying a sentence.</p> <p>The search for understanding these differences of course proceeded directly to the bar. Understand the Australian animal in its native environment. Study the behavior and write it all down in the notebook. I forgot my notebook. Or if I had one it sunk to the bottom of the Brisbane river when I fell in. But I can remember what I learned and the key to it all is this &ndash; Australians love karaoke. We ended up in bar featuring karaoke that was so massive that we actually confused it as being two bars. I talked with several Australian women, on a purely professional basis of course, and asked extensively about my in-flight language realizations. I came to the conclusion that an Australian can&rsquo;t say what it means to be Australian any more than I can say what it is like to be an American. You suck up the culture and people and just become what you become without thinking about it and then you are that region. In one day, or one week, or one month, I am never going to learn what it&rsquo;s like to be Australian. So we all gave up on that quest, drank a lot of beer (mmm, good beer) and I sang karaoke for no apparent reason. And it sucked.</p> <p>That last bit of philosophy and thinking was incredibly boring, but of course it is my mindset for the next few days in Australia. Experience it all, understand it all, wake up with no memories of the previous night next to eighteen Australian women on the roof of the conference center wondering what substance inspired you to get a tattoo of a kangaroo on your forehead. I like wallabies much better.</p> <p>And there are talks going on. I am diligent. This is what I heard. It may not necessarily be what was actually said, but all one can report on is their perception of reality. Before I degenerate into cheesy Matrix-philosophy pretending that I actually know something about philosophical thinking further then watching Kevin Spacey play a philosophy professor in a movie on the plane, here&rsquo;s how the talks have been going:</p> <p><strong>You&rsquo;re my PAL. Heh. Heh. &ndash; Matthew Goode</strong></p> <p>Let&rsquo;s say you have to do phylogenies. Lots of us do. I can faithfully say as a current study of phylogenetic techniques that these analyses might be the single most complicated thing on this planet. One consequence of all this is that with all the assumptions and differences in the variety of techniques you normally want to try multiple analyses on your data. My normal thinking is &ndash; do a lot of trees in various ways. If you can get yourself the same basic tree using a variety of acceptable methods, then you can probably get yourself to trust it. So the thing you would like to be able to do is write code that will run all of these various trees using different methods and assumptions, let it go all night, wake up in the morning and then evaluate it. If you program in Java, you are lucky enough to have this fine project to help you with this goal. This code looks incredible &ndash; it has all your favorite algorithms and substitution models and all those good things. Beautiful. My highest recommendation. Four stars. I recommend the oyster platter with sea clams in mint garlic sauce. Tasty.</p> <p><strong>Generic Model Organisms and their Database &ndash; Suzanna Lewis</strong></p> <p>Continuing on a food theme (damn, when is lunch?), let&rsquo;s say you take a dash of collaboration, a pinch of model organisms (geez, these cheesy recipe metaphors are really painfully bad. I will stop now), and you mix it all up (oh yeah, I was supposed to stop that. I promise now. Promise.) with some folks who know how to code and you get out a model organism database. The history of these types of databases is that each organism had a central type of database that a research organization worked on. Each organism had it&rsquo;s own schemas and tools and people working on it. The more organisms that came about, the more this development philosophy led into duplication of tools. Additionally, some databases had nicer tools for certain things, depending on the expertise of the people in that group, and other organism databases wanted to use it. Well thanks to the genius of many great people in the open-source biology world, it was decided to build a generic model organism database with shared tools. Every lab donated certain tools, they all began to work together, and the <a href="http://thaisoul.ru">beauty and elegance</a> and greatness (man, I am feeling really happy-happy this early morning; everyone is beautiful and happy and time to go frolic in the grass with bunnies and sunflowers and, stay on task, stay on task) became GMOD. This set of tools has great things for literature curation, gene expression data, genome organization, laboratory notebooks, genome analysis &ndash; basically everything you&rsquo;d like to have for your organism. So, yeah, I&rsquo;ve got this whole plan for job searching &ndash; find a job working on an organism that needs a database and get the job setting up the database. Use GMOD, forget to mention that you just used all this free open source, code, and then take six months off traveling around the world on a sailboat you built yourself when you are &ldquo;working&rdquo; on developing this database. I think I&rsquo;m gonna sail my boat to Puerto Rico.</p> <p><strong>Biopython &ndash; me</strong></p> <p>This was the worst talk I&rsquo;ve ever seen. This speaker is complete bollocks. I would have walked out if I wasn&rsquo;t up there giving the talk.</p> <p><strong>Lightning Talks &ndash; lots of people</strong></p> <p>Come on these go every five minutes. The only good way to describe them is with stream of consciousness. Plus I&rsquo;ve been reading lots of Joyce, so what are you gonna do. Spreadsheets. Those are all about biologists. We love spreadsheets. Well not me, but let me tell you that the folks who write Excel should hire several people in my lab as stress testers for new version of Excel. They wouldn&rsquo;t even have to pay them. But the point is that getting your data and programs to be easily integrable with spreadsheets is incredibly smart.</p> <p>Java beans. Web Services. These are very good things and putting them together is even better. This is the kind of thing that could make you famously famous. Like the famous Amos. That is my favorite episode of Taxi ever, if you haven&rsquo;t seen it. If you believe, they put a man on the moon.</p> <p>Lightning talks are flying by and where am I where is the pointer not in my pocket maybe up on the stage I couldn&rsquo;t have lost it could I have that would be terrible. Three lightning talks in a row. That is serious. I get lost with a single talk to give. Of course, my brain is small. Buzzwords are really in the house right now. After the beans, after the java. Now XML. UML. JML, HML, RNA, DNA, WWW, WWF, RDF. Networks. All those terms and good words about Biopython. Associate in your mind &ndash; Biopython, buzzword, Biopython, buzzword, Biopython, buzzword. You know you want to. Hold on a second, I am writing a blog. I am writing a story, and the talk is about weblogs. Cosmic occurrence. Integrated with this kind of ridiculous rambling (well, he might have better rambling then I can manage) are PubMed entries. So you are actually bringing in science with your rambling and potentially contributing to a quality discussion about research articles. The only bad thing is that words like BioPHP pop up. What happened to Biopython. Dueling it out PHP versus Python. Whoah, this is really degenerating. I need a better filter on my brain.</p> <p>Microarray data from all over. Philosphically, all these organisms must fit together somehow, especially in the wonderful land of Louisiana where they&rsquo;re eating cajun food. Somehow all of the microarrays come together in my head. Normalization. C++. BASE. Microarray databases. Work-flow for open source microarray analysis. Honestly, I wish I was getting into the world of microarrays at the current time &ndash; exploring these types of open-source projects and all the active development in the area really makes me incredibly excited and interested. Which shows you exactly the kind of dork I am.</p> <p>Population genetics. Wow. Not seen very often in the ol&rsquo; bioinformatics circles. Very nice to see, I know several people in my lab who would be salivating right now. I am also salivating along with them as it&rsquo;s written in Python. PyPop. Nice. It uses dataflows and goes back and forth with Excel. Once again, we know what it&rsquo;s like to work with laboratory biologists completely in love with Excel. Here&rsquo;s the URL for those of you who would be searching just like me: <a href="http://allele5.biol.berkeley.edu/pypop/">http://allele5.biol.berkeley.edu/pypop/</a></p> <p>The really nice thing about BOSC this year is that there is lots of room for people to make contributions &ldquo;on-the-fly.&rdquo; A really nice example of this type of interactive talk is from Andrew, who is talking about his experiences contributing to BioPerl right now. Honestly, this is really one of the great things about BOSC in my mind &ndash; getting people interested in and contributing to projects. I am back into my the world is beautiful and lets frolic with bunnies and bikini babes mindset.</p> <p>The other great thing about BOSC is exemplified in this next talk (and for me in the PyPop talk) &ndash; learning about software that might do something you need to know. Right now we are looking at pretty pictures of sequences and picking out problems with sequences; very nice visualization tools for looking at tons of sequences that come off a sequencer (quality values, sequence features). This is incredibly useful for finding problems with the sequencer, with the assembly, with the quality of sequences.</p> <p>Two messages for five minutes. I have to disagree with Richard, who doesn&rsquo;t feel that crops are sexy. I find Sorghum incredibly sexy, but purely in a platonic sort of way. Again &ndash; learning about useful tools. Do you need to track genealogies and matings for your crosses in the field? Talk with Richard, he has got your software.</p> <p>Social policy bonds is what we are hearing about right now. The basic question is whether companies or governments (closed versus open, basically) are better at producing useful things for society. This is economics, and honestly I don&rsquo;t know anything about economics other than a single (but enlightening) agricultural economics class I took back in my senior year to fulfill some graduation requirements (but also &lsquo;cause I was interested, of course). However, stretching your mind is extremely important to continue to keep yourself an intelligent contributing member of society (or in my case, to pretend). The idea is to fund open-source by putting a &ldquo;reward&rdquo; on getting something done, and then paying the reward to the first group or person who accomplishes it. This gets at the question of who is most efficient at producing a useful software product, and the benefit is in supporting software &ldquo;freelancers&rdquo; as opposed to building research institutes or the like to produce the things you would like. My immediate concerns would be &ndash; who determines what makes a &ldquo;good&rdquo; software product that does something. This could build a niche for software junk-bond type traders who could churn out patched together code that did something but wasn&rsquo;t extensible or potentially good for everyone. Interesting ideas, all the way.</p> <p>Sadly, the evil that is computer battery time is now eating away at my ability to record further events. Surely this will bring cheers and tears of happiness from those folks who were wondering exactly when I would stop all this damn rambling. Well now is the time as the battery dies and the lack of appropriate power converters leaves me with no other choices but declare myself finished for the day. Plus my fingers hurt.</p>https://www.open-bio.org/2003/06/28/they-let-me-into-australia-and-this-is-what-i-saw/Sat, 28 Jun 2003 09:26:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/28/they-let-me-into-australia-and-this-is-what-i-saw/<p>If you are not lucky enough to be here in wonderfully beautiful Brisbane with beaches next to the river and where every man and woman is a perfect physical specimen, then you can read all about BOSC colored through my mind. Enjoy.</p> <p>Where the hell am I? I distinctly heard someone refer to me as mate and I was supposed to be heading to Australia, so I&rsquo;m thinking that&rsquo;s where I might be. After three thousand straight hours of airports and planes and ticket counters where bored <a href="http://samolets.com/aviakompanii/">airline workers</a> are informing you that you won&rsquo;t reach your destination until three days after your expected date and offer you a 10 dollar food and beverage coupons for your trouble, it&rsquo;s hard to grasp reality. And yes, of course I spent that 10 dollars on beer. What the hell else would I want to buy in the airport? Okay, Bloody Mary&rsquo;s, but I only had 10 dollars so you gotta make it stretch at those airline prices.</p> <p>But it&rsquo;s okay. Now it&rsquo;s another morning, another day. Well, maybe it&rsquo;s a new day. Or maybe it&rsquo;s the last day. Or damn, it could be two days ahead or three days behind or Christmas or next year&rsquo;s New Year&rsquo;s Eve wooo everyone let&rsquo;s celebrate the beginning of a new millennium. Woo! Man, I am totally messed up.</p> <p>So let me tell you something you should not do. You should not travel across the United States and then across the world (up and down) in a mad marathon trip that takes approximately 48 hours of flight delays and being left over in airports and sitting on plains with old ladies next to you telling you their life stories and, man, you would have thought she&rsquo;d have noticed I fell asleep a half hour ago. Another Fosters please, kind flight attendant. But, yes, you should not make this kind of trip, then go straight to a conference, try and run a little meeting of Biopython, take a quick shower, eat a Kabob, start drinking tasty Australia brews named VB interspersed with Tequila shots, sing a karaoke song in the worst possible drunken manner at the best Friday night Karaoke in all of Brisbane according to native Brisbaneans I chatted with, then wander home completely lost throughout half of Brisbane without a map or any idea where you are going being assaulted by random threatening Brisbaneans who happen to up in the middle of the night and then stumbling across people smoking hookah&rsquo;s right in the middle of the sidewalk whoah where was that bar I gotta get back there. Do not do this. I did this. It was a mistake. I am in Australia. And I am completely mad.</p> <p>It is with this state of mind that I bring you a report for Australia on BOSC. Good god, this is not an official report sponsored by any reasonable person. What is it then? It&rsquo;s the kind of rambling I can manage and it&rsquo;s how BOSC looks through my eyes and do not look too carefully or scrutinize too closely lest you feel it is your civic duty to have me locked up immediately as a threat to myself and others. Come on, friends, I am completely harmless. And this is what I&rsquo;ve seen so far in the land down under at the number one meeting in the entire world of open-source biology folks.</p> <p><strong>Python and Systems Biology &ndash; Michiel de Hoon</strong></p> <p>Cool graphics with python. So let&rsquo;s say we&rsquo;ve got one hundred million expression data and we want to make a gene regulatory network from them. To put it simply, you have information about how genes express and would like to tie them together in an understandable way. This is the wide and wonderful world of Systems Biology. And that&rsquo;s where we are today. This involves delving into the head-splitting mania that is differential equations, and I&rsquo;m taking it for granted that there are some pretty smart mathematically inclined folks are doing things correctly. You can too, as they are all implemented for your use in Python. As always, open-source is helping you not think; more beer time. I can steal that phrase this year since Jason isn&rsquo;t here this year. Ha. Back to the talk &ndash; another thing you might want to do with your gene expression data is try and predict the regulatory transcription factors causing the expression patterns. I&rsquo;m certainly fond of the belief that cis and trans factors affecting genes are nearly as important as the gene and protein sequences; so it fills the dorky scientific part of me with delight to think about understanding and combining these types of factors into analyses. And all in Python. Always Python. Sweet. Of course, also sweet open-source since you can get the code and documentation and tutorials about how to get started programming with Python. We want to help you help yourself.</p> <p><strong>Eukaryotic Linear Motifs and Disorder &ndash; Rune Linding</strong></p> <p>This one day I&rsquo;m walking along, minding my own business, whistling gently the tune to my favorite Frank Sinatra song, and I run into this protein. Bam, right outta nowhere. Some of the time you meet a new protein and it&rsquo;s wearing a Hello My Name Is (my name is, my name is) tag and you are all set and you can give it a heide-ho and be on your way. But most of the time you meet this protein and have zero idea what exactly it is called, or what it does. There are lots of ways to learn how exactly to meet this protein, but what we are talking about here is learning about the protein by learning it&rsquo;s peptide motifs. So yeah, peptide motifs are these short linear stretches of protein sequence which are conserved. They often serve as binding sites for other proteins. So, an alternative method to learn about proteins is to discover these regions within your unknown protein, and use these regions to make predictions about the function of your protein. That&rsquo;s the idea, as my fuzzy brain can understand it. In addition to this approach, you can also use a more standard approach to look for functional sites in the proteins. But I dig the disordered small linear motifs so I rambled on about that the most. Sue me. There is a nice database to search and classify proteins using these methods, which is what this talk is all about. As with all good things it&rsquo;s developed in Python using Biopython. Bonus.</p> <p><strong>Sort of like close to Lectin Domains &ndash; Alex Zelensky</strong></p> <p>This domain completely rules. It has more then 2000 references in GenPept and tons of ligands and groups and types all over vertebrates. So, we have got to sort this thing out. I completely sympathize with this type of analysis as a common question a nice laboratory scientist might come up with it &ndash; hey, this domain seems really cool, can I look at how it works over the world of all the sequences. You think &ndash; no worries, I&rsquo;ll download a couple of these bad boys from NCBI, do a little phylogenetic tree (using of course the most appropriate method for my question (scientific-type insertion sponsored by the Foundation to Impress Brad&rsquo;s PhD committee and let him graduate and pass all his exams)) and then go to lunch and slug back a couple of martinis. Of course, when you actually get into it you find that this family you just happened to be interested in spans every single organism ever sequenced and you realize that your martini plans with famous supermodels might have to be put on hold for a year and a half. So this is exactly the problem we are getting into here and the solution in this case, which makes me really hope that next time I am interested in a family of proteins I will be interested in this domain, was to develop an on-line database of these motifs completely sorted out. Beautiful, MySQL, BioPerl. Life is good and I&rsquo;m gonna make that lunch date; give Claudia a call to let her know.</p> <p><strong>Nice popular terms like Web Services &ndash; Martin Senger</strong></p> <p>If you ever accidentally forget to uncheck one of those &ldquo;send me as many mails as possible&rdquo; boxes while filling out a form to download Java from the good folks at Sun, then you will be like me and find your work mailbox completely filled every day with magazines of complete rubbish called things like &ldquo;System Administrator&rsquo;s Weekly.&rdquo; These magazines suck hard. They are killing so many trees. To the person out there that is sending me these magazines &ndash; please stop, I never read them. I don&rsquo;t even look at them. I just let them pile up until they reach a level so high that it is declared a national hazard and I have to throw them away. My point, however, is that if you glance at the cover of any of these millions of magazines you will see the words Web Services. You will see these words over and over and over and over again. We love Web Services. It will save the world. So what exactly is it. XML, SOAP, web protocols. Sending data between distributed places using standard interoperable protocols and specifications. This will likely not go away anytime soon, so it&rsquo;s a good thing to read at least a page about it so if someone mentions it &ndash; say, between body shots on a stripper at a local sleazy dive bar &ndash; you will be able to make a reasonable comment about it. Either &ldquo;web services&rsquo; rulz&rdquo; or &ldquo;web services&rsquo; suck&rdquo; normally works. Choose your side. But, I&rsquo;m distracted. The point is that if you need to get data in the future, you will likely find that more and more of it will be available through web services. This is the case in bioinformatics, and the EBI and EMBL folks are jumping on the bandwagon. An excellent example is OpenBQS &ndash; in short terms you can get all of MEDLINE through web services. Sweet. I just want to end this with one point &ndash; Web Services are like high school sex. I had trouble concentrating on the rest of the talk once I got that thought in my head. I blame it all on the cheerleaders packing out my Memphis to LAX flight of hell.</p>https://www.open-bio.org/2003/06/27/montreal-biojava-bootcamp-announced/Fri, 27 Jun 2003 06:24:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/27/montreal-biojava-bootcamp-announced/<p>BioneQ, the Quebec Bioinformatics Network, is organizing the first North American BioJava Bootcamp from August 18th to 22nd. We have invited Matthew Pocock to come to Montreal to present the material that has been presented to the European Bootcamps for quite some time now. On the agenda (preliminary):</p> <p>-Sequence I/O and manipulations; -BLAST and FASTA parsing; -Using databases with BioJava; -Intro to Sequence GUI.</p> <p>The bootcamp will be at the Universite de Montreal and the registration fee is $250US. If you are interested, use the following link to register:</p> <p><a href="http://132.204.90.239/bioneq/biojava_workshop.jsp">http://132.204.90.239/bioneq/biojava_workshop.jsp</a></p> <p>Please paste in your CV for evaluation of programming experience/knowledge. Places are quite limited (20) so register soon.</p>https://www.open-bio.org/2003/06/27/bioperl-workshop-materials-online/Fri, 27 Jun 2003 06:22:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/27/bioperl-workshop-materials-online/<p>Heikki has converted some Bioperl workshop materials to a web slide show that is available here:</p> <p><a href="http://www.ebi.ac.uk/~lehvasla/bioperl/">http://www.ebi.ac.uk/~lehvasla/bioperl/</a></p>https://www.open-bio.org/2003/06/18/biojava-13-released/Wed, 18 Jun 2003 06:09:12 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/18/biojava-13-released/<p>Thomas Down writes:</p> <p>After a long series of pre-releases (and many bug fixes), I&rsquo;ve just finished building BioJava 1.30. Source, binaries, and javadocs can all be found at:</p> <p><a href="http://www.biojava.org/download/">http://www.biojava.org/download/</a></p> <p>As with the pre-releases, separate binaries are available for java platform releases 1.3 and 1.4. The 1.4 releases include some extra features which depend on jdk1.4 extensions such as the java.nio package.</p> <p>Highlights of this release include:</p> <p>- Packed storage of sequence data in memory</p> <p>- Better support for the OBDA database access standards</p> <p>- Improvements to the parsers for output from tools like blast and fasta.</p> <p>- Many enhancements to the FeatureFilter system.</p> <p>Please check out the javadocs for information on these and other new features.</p> <p>I&rsquo;d also like to take this opportunity to recomment the excellent BioJava in Anger website, which is now hosted on biojava.org:</p> <p><a href="http://www.biojava.org/docs/bj">http://www.biojava.org/docs/bj</a>_in_anger/index.htm</p> <p>Thanks to everyone who has made this release possible:</p> <p>Aroul Ramadass Brian Gilman Brian King Cambridge Antibody Technology (CAT) David Allen David H. Klatte, Ph.D. David Huen David Waring Ewan Birney Francois Pepin Gerald Loeffler Greg Cox Hanning Ni Jason Stajich Kalle Naslund Keith James Kim Rutherford Lachlan Coin Laurent Jourdren Leen Ammeraal Lei Lai Mark Schreiber Martin Senger Matthew Pocock Mayo Foundation Michael Heuer Michael Jones Moses Hohman Nimesh Singh Paul Seed Rhett Sutphin Robin Emig Ron Kuhn Russell Smithies Samiul Hasan Thad Welch Thomas Down</p> <p>I hope you all find it useful,</p> <p>Thomas.</p>https://www.open-bio.org/2003/06/17/chromatogram-viewing-with-java/Tue, 17 Jun 2003 06:18:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/17/chromatogram-viewing-with-java/<p>Rhett Sutphin provides a mini-primer and some example code that shows how to view Chromatogram files with java.</p> <p>His full posting can be read here: <a href="http://biojava.org/pipermail/biojava-l/2003-June/003896.html">http://pw600a.bioperl.org/pipermail/biojava-l/2003-June/003896.html</a></p>https://www.open-bio.org/2003/06/12/the-open-biological-database-access-obda-introduction-for-bioperl/Thu, 12 Jun 2003 15:11:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/12/the-open-biological-database-access-obda-introduction-for-bioperl/<p>Do you need to access sequences from multiple places? Would you like to easily retrieve your own local sequences from indexed flat files, all other sequences on species X from department wide raletional database and the rest from global internet servers?</p> <p>The Open Biological Database Access (OBDA) System was designed so that one could use the same application code to access data from all three of the database types by simply changing a few lines in a &ldquo;configuration file&rdquo;. This makes application code more portable and easier to maintain.</p> <p>This document gives an overview and shows how to use it in BioPerl: <a href="http://www.bioperl.org/HOWTOs/html/OBDA_Access.html">http://www.bioperl.org/HOWTOs/html/OBDA_Access.html</a> <a href="http://www.bioperl.org/HOWTOs/pdf/OBDA">http://www.bioperl.org/HOWTOs/pdf/OBDA</a>_Access.pdf</p> <p>OBDA System is also implemented in BioJava, BioPython and BioRuby.</p>https://www.open-bio.org/2003/06/05/biojava-tutorial-updated/Thu, 05 Jun 2003 21:46:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/06/05/biojava-tutorial-updated/<p>Mark writes:</p> <p>The tutorial site BioJava in Anger has been updated so the code examples reflect the new APIs in the upcomming BioJava 1.3 release. Take a peek at <a href="http://bioconf.otago.ac.nz/biojava">http://bioconf.otago.ac.nz/biojava</a></p>https://www.open-bio.org/2003/05/29/bioperl-run-120-released/Thu, 29 May 2003 23:52:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/05/29/bioperl-run-120-released/<p>Shawn Hoon announces the release of bioperl-run-1.2.0 which is an extention to the bioperl framework that contains modules that act as wrappers for common informatics applications.</p> <p>The full release announcement can be read here: <a href="http://bioperl.org/pipermail/bioperl-l/2003-May/012308.html">http://bioperl.org/pipermail/bioperl-l/2003-May/012308.html</a></p>https://www.open-bio.org/2003/05/28/avantgo-friendly-channel-for-bioperl-list/Wed, 28 May 2003 08:29:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/05/28/avantgo-friendly-channel-for-bioperl-list/<p>Jonathan Epstein has a simple script and directions for browsing bioperl list traffic offline via a mobile device.</p> <p>The full post can be read online at: <a href="http://bioperl.org/pipermail/bioperl-l/2003-May/012287.html">http://bioperl.org/pipermail/bioperl-l/2003-May/012287.html</a></p>https://www.open-bio.org/2003/05/23/agp-bases-das-reference-server-available/Sat, 24 May 2003 00:04:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/05/23/agp-bases-das-reference-server-available/<p>Tony writes:</p> <p>I have just checked in to the Bio::Das perl beta CVS repository (&ldquo;Bio-Das2&rdquo;) a collection of modules that creates a minimal DAS reference server from a single AGP file (or a directory of one or more files). There is also a sample server script in the &ldquo;eg&rdquo; directory.</p> <p>Briefly, the server is started using something like:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>cd ./eg </span></span><span style="display:flex;"><span>./agpserver --dsn ncbi31 --port 3000 --agpfile ./AGP/chr1.agp </span></span></code></pre></div><p>It can then be used by a DAS client in the normal way. It is simple (no frills!) and capable of serving assembly information, entry_points, DSN info, features across a segment and features by ID. No other DAS commands are supported yet.</p> <p>I wrote it because our chromosome finishers needed to be able to view assemblies as they updated their AGPs. We have a little web-based ensembl-ish graphical viewer that displays the assembly.</p> <p>The server uses either DBD::CSV (default) or Mysql for backend SQL storage. The former so that anybody can run a server anywhere without having to be DB savvy, the latter for better performance. It simply goes:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>./agpserver </span></span><span style="display:flex;"><span>--dsn Name for this DAS datasource </span></span><span style="display:flex;"><span>--agpdir &lt;./dirname&gt; Directory holding AGP file(s) </span></span><span style="display:flex;"><span>or </span></span><span style="display:flex;"><span>--agpfile Single AGP file </span></span><span style="display:flex;"><span>--port DAS server port (default = 9999) </span></span><span style="display:flex;"><span>--tmpdir CSV temp. directory (default = /tmp) </span></span><span style="display:flex;"><span>[ --backend mysql Use a mysql backend (default = csv) </span></span><span style="display:flex;"><span>--dbhost Mysql server hostname </span></span><span style="display:flex;"><span>--dbname Mysql database name </span></span><span style="display:flex;"><span>--username Mysql username (needs write access) </span></span><span style="display:flex;"><span>--password Mysql password </span></span><span style="display:flex;"><span>--dbport Mysql server port (default =3306) </span></span><span style="display:flex;"><span>] </span></span></code></pre></div><p>eg:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>./agpserver --dsn ncbi31 --agpdir ./TEST --port 3000 </span></span><span style="display:flex;"><span>Loading AGP file: chrX.agp </span></span><span style="display:flex;"><span>Loading AGP file: chrY.agp </span></span><span style="display:flex;"><span>Please contact me at this URL: http://hostname:3000/das/dsn/{command} </span></span></code></pre></div>https://www.open-bio.org/2003/05/23/parser-for-ab-initio-gene-predictor-glimmerm-in-cvs/Fri, 23 May 2003 23:55:21 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/05/23/parser-for-ab-initio-gene-predictor-glimmerm-in-cvs/<p>Jason writes:</p> <p>I&rsquo;ve added a parser for the ab initio gene predictor GlimmerM in Bio::Tools::Glimmer. Tests are added to t/Genpred.t now.</p> <p>It follows the Bio::Tools::AnalysisParser interface which support the next_prediction call and returns a Bio::Tools::Prediction::Gene object in the same way as Genscan.</p> <p>I also have some scripts for building the training set file so you can run Glimmer on other species. There is also a similar script for building custom splice sites file for Genewise which I&rsquo;ll commit soon. Basically it takes as input a GFF file which has exons annotated (typically from Sim4/Exonerate alignments of cDNA to DNA) and a reference to the genomic DNA db (typically just a flatfile which we index with Bio::DB::Flat).</p> <p>Not sure where to put these - scripts/gene_prediction ?</p>https://www.open-bio.org/2003/05/23/biosql-and-bioperl-db-inching-towards-release/Fri, 23 May 2003 23:51:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/05/23/biosql-and-bioperl-db-inching-towards-release/<p>Hilmar writes:</p> <p>I got the Oracle version of the biosql schema fully migrated, at least as far as I can tell from here. I&rsquo;m going to commit the new version some time today. There will also be a sql*plus migration script from pre-Singapore to the current version that supposedly keeps your data intact (be sure to read the disclaimer though).</p> <p>This means we&rsquo;re getting ready to release Biosql 1.0, possibly as early as next week. If anyone sees any problems with the current schema that he/she thinks should be corrected before this release, please speak up now. I guess I should make an effort and generate an updated ERD before release; the dated ones are confusing wrt the current schema. If there is consensus I&rsquo;ll put out a release candidate early next week.</p> <p>Bioperl-db should be working against the mysql, PostgreSQL, and Oracle versions (once I&rsquo;ve committed that one). The major deficiency here is POD documentation of the modules, specifically updating old modules, and adding/updating the SYNOPSIS sections. I guess a programmer&rsquo;s guide would also be helpful. For the next weeks to come I&rsquo;m unfortunately not in a position to be able to spend the time it would require to bring the POD documentation up to speed. Would anyone else care to help out? What is generally people&rsquo;s take on how good the documentation should be before we release this? Maybe not care too much and just go ahead to have something officially blessed that can be downloaded?</p> <p>Jason, with respect to the marker database in bioperl-db, what is your vote on keeping it in the distribution? The problem is that the schema is MySQL-specific, so if someone wants biosql on Pg or Oracle you still have to set up Mysql in order to make all tests pass. An option could be to check the driver in the markerdb-related tests and skip everything if it&rsquo;s not mysql.</p> <p>The next feature I&rsquo;m going to add to biosql is a table for expression data that basically resembles the data cube with various dimensions (roughly, bioentry, term [quantitation type], term [sample annotation]). No LIMS info (yet) other than sample annotation as far as it fits the term table. In my view, this would be a post-1.0 thing. Do people agree?</p>https://www.open-bio.org/2003/05/11/new-biopythonorg-website/Mon, 12 May 2003 01:02:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/05/11/new-biopythonorg-website/<p>The day you&rsquo;ve been waiting for is finally here. That&rsquo;s right, it&rsquo;s time for a brand new biopython.org website! Woo. Thanks to the hard work of Chris Dagdigian and your Biopython team, we&rsquo;ve got our new website set up on a new up to date Linux server. Come check out all the excitement at <a href="http://biopython.org">biopython.org</a>.</p> <p>Read the enthralling announcement in it&rsquo;s entirety at:</p> <p><a href="http://www.biopython.org/pipermail/biopython/2003-May/001287.html">http://www.biopython.org/pipermail/biopython/2003-May/001287.html</a></p>https://www.open-bio.org/2003/04/17/new-tab-sequence-format/Thu, 17 Apr 2003 20:09:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/04/17/new-tab-sequence-format/<p>Heikki writes:</p> <p>Philip Lijnzaad has written a new sequence format module called &rsquo;tab&rsquo;. It is in CVS. Here is the blurb he wrote:</p> <p>It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine that you have a format converter &lsquo;seqconvert&rsquo; along the following lines:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>my $in = Bio::SeqIO-&gt;newFh(-fh =&gt; *STDIN , &#39;-format&#39; =&gt; $from); </span></span><span style="display:flex;"><span>my $out = Bio::SeqIO-&gt;newFh(-fh=&gt; *STDOUT, &#39;-format&#39; =&gt; $to); </span></span><span style="display:flex;"><span>print $out $_ while &lt;$in&gt;; </span></span></code></pre></div><p>then you can very easily filter sequence files for duplicates as:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ seqconvert &lt; foo.fa -from fasta -to tab | sort -u | </span></span><span style="display:flex;"><span>seqconvert -from tab -to fasta &gt; foo-unique.fa </span></span></code></pre></div><p>Or grep [-v] for certain sequences with:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ seqconvert &lt; foo.fa -from fasta -to tab | grep -v &#39;^S[a-z]*control&#39;| </span></span><span style="display:flex;"><span>seqconvert -from tab -to fasta &gt; foo-without-controls.fa </span></span></code></pre></div><p>Or chop up a huge file with sequences into smaller chunks with:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ seqconvert &lt; all.fa -from fasta -to tab | split -l 10 - chunk- </span></span><span style="display:flex;"><span>$ for i in chunk-*; do seqconvert -from tab -to fasta &lt;$i&gt; $i.fa; done </span></span><span style="display:flex;"><span># (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing </span></span><span style="display:flex;"><span># 10 sequences) </span></span></code></pre></div>https://www.open-bio.org/2003/04/08/windows-ppm-for-bioperl-121-available/Wed, 09 Apr 2003 00:50:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/04/08/windows-ppm-for-bioperl-121-available/<p>Nigam Shah has created the necessary PPM/PPD distribution files for bioperl-1.2 .1 that will allow ActiveState perl users on Windows machines to easily install the bioperl suite and the most common bioperl external module dependencies. The PPD file is online at <a href="http://bioperl.org/ftp/DIST/Bioperl-1.2.1.ppd">http://bioperl.org/ftp/DIST/Bioperl-1.2.1.ppd</a>. The actual PPD file is at <a href="http://bioperl.org/DIST/bioperl-1.2.1-ppm.tar.gz">http://bioperl.org/DIST/bioperl-1.2.1-ppm.tar.gz</a></p> <p>More information on bioperl Windows installations can be read online at <a href="http://www.bioperl.org/Core/Latest/INSTALL.WIN">http://www.bioperl.org/Core/Latest/INSTALL.WIN</a></p>https://www.open-bio.org/2003/04/08/moby-dic-iii-pictures-meeting-minutes-online/Wed, 09 Apr 2003 00:37:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/04/08/moby-dic-iii-pictures-meeting-minutes-online/<p>March 15-16, 2003 &ndash; About a dozen Moby developers gathered recently. Minutes from the meeting are online at <a href="http://www.biomoby.org/twiki/bin/view/TWiki/CarnegieTAIR">http://www.biomoby.org/twiki/bin/view/TWiki/CarnegieTAIR</a> and pictures are online at <a href="http://biomoby.org/MOBY-DIC-III/MOBYDICIII.html">http://biomoby.org/MOBY-DIC-III/MOBYDICIII.html</a></p>https://www.open-bio.org/2003/03/31/bioperl-121-released/Tue, 01 Apr 2003 02:56:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/31/bioperl-121-released/<p>The release is available at <a href="http://www.bioperl.org/ftp/DIST/bioperl-1.2.1.tar.gz">http://www.bioperl.org/ftp/DIST/bioperl-1.2.1.tar.gz</a> and is propagating around CPAN now.</p> <p>The main bug fixes in this release are:</p> <p>- inclusion of WrapperBase, making StandAloneBlast work from the release</p> <p>- fixes and cleanup of Bio::Coordinate</p> <p>- fixes to Bio::Index::EMBL and bpindex</p> <p>The 1.2.1 release does see some major additions in the Ontology area. These were not present in the 1.2 release, so nothing should break. The inclusion of these modules into the stable branch (something which normally should not happen) was specifically so that the bioperl-db project, the bioperl bindings of the cross-language BioSQL project can be targetted to work with the 1.2 stable series, rather than the development releases. We (the core) believe that this was the best solution, encouraging a stable release of bioperl-db (due out I suspect in a month or so - Hilmar Lapp is the driver for this).</p> <p>As always, the release was herded out by the Bioperl developers. Special mention goes to both Jason Stajich and Heikki Lehvaslaiho for their bug fixing and tweaking, and to Hilmar Lapp for the ontology modules.</p> <p>Enjoy!</p>https://www.open-bio.org/2003/03/30/prerelease-bioperl-121-available-for-testing/Sun, 30 Mar 2003 20:52:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/30/prerelease-bioperl-121-available-for-testing/<p>We need you!</p> <p>Please download and help test a potential 1.2.1 release candidate that is available at <a href="http://bioperl.org/ftp/birney/bioperl-1.2.1-rc2.tar.gz">http://bioperl.org/ftp/birney/bioperl-1.2.1-rc2.tar.gz</a></p> <p>If all goes well the official bioperl-1.2.1 will be released early next week.</p>https://www.open-bio.org/2003/03/25/stanford-releases-gotermfinder-modules/Tue, 25 Mar 2003 06:02:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/25/stanford-releases-gotermfinder-modules/<p>GO::TermFinder will take a list of genes (any name that appears in an annotation file will do, though there are caveats for ambiguous names), an ontology file, and an annotation file, and determine the P_values for the observed frequency of annotation to those genes for each GO node. There are currently some differences between how the P-values are</p> <p>The full announcement can be read here: <a href="http://bio.perl.org/pipermail/bioperl-l/2003-March/011707.html">http://bio.perl.org/pipermail/bioperl-l/2003-March/011707.html</a></p>https://www.open-bio.org/2003/03/25/foundation-views-wrongly-characterized-in-genome-technology/Tue, 25 Mar 2003 05:56:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/25/foundation-views-wrongly-characterized-in-genome-technology/<p>In the March 2003 issue of Genome Technology, &ldquo;Opposite Strand&rdquo; contributor Gerald Barnett&rsquo;s insightful article on &ldquo;free choice for open source&rdquo; is blighted by a gross misattribution. He writes that Open Bioinformatics Foundation has proposed that <strong>&ldquo;all federally funded bioinformatics software should be released as open source.&rdquo;</strong> In fact, the O|B|F has explicitly rejected this extreme and inflexible view, as specified in our January 2002 statement on public funding &amp; open source, which states:</p> <h2></h2> <p>&ldquo;The Open Bioinformatics Foundation believes that scientific software developed with public support should be distributed under terms analogous to those applied to biological materials. In common with treatment of reagents under the UBMTA and good practice, we believe that the essential source code necessary for reproducing published results should be made readily available for non-commercial research use.</p> <p>&ldquo;While acknowledging that open source licenses may not be optimal in every instance, we believe that development and release of software under open source licenses is often beneficial and efficient in creating valuable scientific software, and in encouraging its widespread use and most successful exploitation.</p> <p>&ldquo;We view researchers as the individuals most capable of determining if their software will be developed and exploited in an optimal manner under an open source license, and we therefore encourage institutions to delegate to their scientists the opportunity to select non-restrictive and open source licenses for their software.&rdquo;</p> <h2></h2> <p>We believe that Gerald has confused the Open Bioinformatics Foundation (<a href="http://open-bio.org">http://open-bio.org</a>) with the efforts of a similar sounding group located at <a href="http://www.openinformatics.org/">http://www.openinformatics.org/</a></p> <p>The O|B|F Board is preparing a response that will be sent to the magazine.</p>https://www.open-bio.org/2003/03/17/new-mailing-list-bioped-l/Mon, 17 Mar 2003 16:26:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/17/new-mailing-list-bioped-l/<p>A new mailing list has been created for discussion of software system for genotypes, pedigrees, and linkage data at <a href="https://www.open-bio.org/mailman/listinfo/bioped-l">/mailman/listinfo/bioped-l</a></p> <p>This is intended to build off the initial work done in Perl for bioperl-pedigree but is applicable to all who want to contribute to the design or implementation in any language. Database persistence and pedigree rendering are initial areas that will be addressed.</p>https://www.open-bio.org/2003/03/16/bioperl-v121-rc1-available-for-testing/Mon, 17 Mar 2003 03:05:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/16/bioperl-v121-rc1-available-for-testing/<p>A release candidate for an eventual Bioperl 1.2.1 release is online at: <a href="http://bioperl.org/ftp/birney/bioperl-1.2.1-rc1.tar.gz">http://bioperl.org/ftp/birney/bioperl-1.2.1-rc1.tar.gz</a></p> <p>We need people to install and test this package on as many systems and architectures as possible.</p>https://www.open-bio.org/2003/03/16/ncicb-reviews-two-lsid-resolution-proposals/Sun, 16 Mar 2003 07:47:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/16/ncicb-reviews-two-lsid-resolution-proposals/<p>Members of the caCORE team at the NCICB have been discussing if and how best to use LSIDs. Attached is an analysis of the two LSID Resolution proposals. The document also includes brief descriptions of two use cases that seem appropriate to us. We would be very interested in any responses to this analysis.</p> <p>The document is also available at: <a href="ftp://ftp1.nci.nih.gov/pub/cacore/caBIO/lsid/lsid_memo.doc">ftp://ftp1.nci.nih.gov/pub/cacore/caBIO/lsid/lsid_memo.doc</a></p> <p>Joshua Phillips SAIC Advanced Information Technology Center, Annapolis, MD NCI Center for Bioinformatics, Gaithersburg, MD Phone: (301) 402-7087</p>https://www.open-bio.org/2003/03/12/technical-report-on-semantic-standards/Wed, 12 Mar 2003 07:43:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/12/technical-report-on-semantic-standards/<p>Andrew Farmer writes:</p> <p>Here&rsquo;s the current revision of my writeup on semantic standards; the only major difference between this and the version I sent out earlier is the addition of a section covering DAML-S, the extension of DAML to develop an upper ontology for describing services (complementary to WSDL).</p> <p>MOBY PROJECT: TECHNICAL REPORT ON SEMANTIC STANDARDS</p> <p>Date: 3/12/03 Author: Andrew Farmer Version: 1.1</p> <p>This is intended to give a high-level overview of the work that others are doing in the area of &ldquo;semantic&rdquo; representation standards for the web.</p> <p>The full report can be read online at: <a href="http://biomoby.org/pipermail/moby-l/2003-March/000434.html">http://biomoby.org/pipermail/moby-l/2003-March/000434.html</a></p>https://www.open-bio.org/2003/03/10/moby-messaging-layer-technical-report-updated/Tue, 11 Mar 2003 01:03:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/10/moby-messaging-layer-technical-report-updated/<p>MOBY PROJECT: TECHNICAL REPORT ON WEB MESSAGING LAYER</p> <p>Date: March 9, 2003 Author: Lincoln Stein Version: 1.0</p> <p>This report concerns the messaging layer of the Moby project, that point at which semantic information is exchanged between the data consumer (the biologist or client process) and the data provider (the model organism system database).</p> <p>Full report can be read at: <a href="http://open-bio.org/pipermail/moby-l/2003-March/000433.html">http://open-bio.org/pipermail/moby-l/2003-March/000433.html</a></p>https://www.open-bio.org/2003/03/10/ontology-overhaul-migration-to-12-branch-imminent/Mon, 10 Mar 2003 20:27:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/10/ontology-overhaul-migration-to-12-branch-imminent/<p>This is the last call for people to test drive and/or criticize the Bio::Ontology &amp; Bio::OntologyIO re-design and implementation.</p> <p>The interfaces and modules to look at comprise of Bio::Ontology::OntologyI, Bio::Ontology::TermI, and Bio::OntologyIO. If you care about implementations (as Aaron says most people do rather than bothering with interfaces), check out Bio::Ontology::Ontology, Bio::Ontology::Term, and Bio::OntologyIO.</p> <p>This is the last call for people to test drive and/or criticize the Bio::Ontology &amp; Bio::OntologyIO re-design and implementation.</p> <p>The interfaces and modules to look at comprise of Bio::Ontology::OntologyI, Bio::Ontology::TermI, and Bio::OntologyIO. If you care about implementations (as Aaron says most people do rather than bothering with interfaces), check out Bio::Ontology::Ontology, Bio::Ontology::Term, and Bio::OntologyIO. If you are curious about OntologyEngineI implementations (which basically are the ones powering queries on terms and all their relationships), check out Bio::Ontology::OntologyEngineI for the interface definition and Bio::Ontology::SimpleGOEngine and Bio::Ontology::SimpleOntologyEngine for the currently existing implementations.</p> <p>Make yourself heard if you think something needs to be amended or changed or whatever; after the release of 1.2.1 you will meet reluctance to change the branch API.</p> <p>Unless there are objections or ensuing debates what should be changed before release, I&rsquo;ll start migrating to the branch tomorrow, aiming for a release by the end of the week (Friday).</p>https://www.open-bio.org/2003/03/08/prototype-of-a-new-biopythonorg-website/Sat, 08 Mar 2003 22:10:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/08/prototype-of-a-new-biopythonorg-website/<p>Brad has been working hard on trying to put together a new biopython.org page that incorporates the open-bio news server and the look and feel of the upcoming open-bio page.</p> <p>More details about how you can check out the new site and how it is implemented are on the biopython-dev mailing list:</p> <p><a href="http://www.biopython.org/pipermail/biopython-dev/2003-March/001214.html">http://www.biopython.org/pipermail/biopython-dev/2003-March/001214.html</a></p>https://www.open-bio.org/2003/03/07/working-on-the-biopython-website/Fri, 07 Mar 2003 17:18:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/07/working-on-the-biopython-website/<p>Brad is working on an update of the Biopython website and is so obsessed with it that he is working on it during his minimal lunch time in which he should be enjoying the nice friendly sunshine of a Georgia friday.</p> <p>This is really not exciting news, but I need some Biopython news to test the news gathering capabilities of the main Biopython page. More info once I actually get something accomplished.</p>https://www.open-bio.org/2003/03/04/bioperl-list-summary-january-2003/Tue, 04 Mar 2003 19:51:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/03/04/bioperl-list-summary-january-2003/<p>As I seem to be volunteering for more and more BioPerl documentation jobs recently, I thought I&rsquo;d pool my resources and recycle some of my tuits to write a list summary. Expect these to be sporadic and incomplete; my goal is to highlight important questions, changes, fixes, and proposals, not recapitulate all list traffic.</p> <ul> <li><a href="#introduction">Introduction</a></li> <li><a href="#questions">Questions</a></li> <li><a href="#changes/additions">Changes/Additions</a></li> <li><a href="#fixes">Fixes</a></li> <li><a href="#proposals">Proposals</a></li> <li><a href="#conclusion">Conclusion</a></li> </ul> <hr> <h1 id="introduction">Introduction</h1> <p>As I seem to be volunteering for more and more BioPerl documentation jobs recently, I thought I&rsquo;d pool my resources and recycle some of my tuits to write a list summary. Expect these to be sporadic and incomplete; my goal is to highlight important questions, changes, fixes, and proposals, not recapitulate all list traffic. I&rsquo;ll try to include appropriate links to specific messages, or at least to the parent message. It&rsquo;ll probably take me awhile to get good at this, so please bear with me (and do send any suggestions).</p> <p>To play a bit of catch up, I&rsquo;m now going to loosely summarize the entire month of January (leaving a few topics untouched that are better addressed in February). February&rsquo;s summary will be ready soon, after which you&rsquo;ll see more easily digestable weekly (or perhaps bi-weekly) summaries. I&rsquo;ll also be posting the HTML-ized summaries on my O&rsquo;Reilly weblog with active hyperlinks.</p> <p>One item from December 31 of 2002 bears mentioning: Ewan Birney released stable version 1.2, with significant new functionality, and important updates to code that makes use of NCBI web services; upgrading is highly recommended, although some of the January list activity reflects small trials and tribulations with this release.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?S17521DA3 </span></span></code></pre></div><hr> <h1 id="questions">Questions</h1> <ul> <li> <p><strong>Searching the mailing list archives</strong></p> <p>This seemed like an appropriate topic to put at the top of my list. The Bioperl-l mailing list isn&rsquo;t exactly as high-traffic as perl5-porters or the linux kernel mailing list, but it is a mixture of both deeply technical development issues and novice user questions. While the BioPerl tutorial and documentation are the first places one should look for answers, the second place must be the archives of the mailing list. Brain Osborne pointed out that &ldquo;the Search box is hidden below the Thanks link at <a href="https://www.bioperl.org">www.bioperl.org</a>&rdquo;.</p> <p>It wasn&rsquo;t mentioned, but the &ldquo;htdig&rdquo; link Hilmar Lapp pointed out (which is also below the search box) does not actually index the bioperl mailing list, but seems to search all other OBF-affiliated lists (biojava, biopython, etc) &hellip;</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://users.bioperl.org/htdig/ </span></span></code></pre></div><p>Michal Kurowski pointed out that &ldquo;the quickest way of accessing old postings seems to be a group archive from the mailman pages&rdquo; and that &ldquo;you can even download the whole thing and use it as a local mailbox&rdquo;, which happens to be very useful if you want to write list summaries. Mailman archives are at:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://bioperl.org/pipermail/bioperl-l/ </span></span></code></pre></div></li> <li> <p><strong>Bioperl 1.2 builds under cygwin</strong></p> <p>John Nash reports that he was able to build the 1.2 distribution under cygwin once MakeMaker issues were overcome (in his case by upgrading to perl 5.8.0). Other tips are provided:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?S23631DA3 </span></span><span style="display:flex;"><span>http://makeashorterlink.com/?M27643DA3 </span></span></code></pre></div></li> <li> <p><strong>Getting/untarring the 1.2 distribution</strong></p> <p>Some people had trouble either FTPing the 1.2 distribution, or with successfully untarring the tarball. These problems seemed to have resolved by themselves, and may have been related to router issues at the server. For the record, bioperl-1.2 can be found at:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://www.bioperl.org/ftp/DIST/bioperl-1.2.tar.gz </span></span></code></pre></div></li> <li> <p><strong>man pages with bioperl-1.2</strong></p> <p>People may have noticed that the &ldquo;make&rdquo; process for bioperl-1.2 does not generate nor install man pages. Ewan Birney explains, &ldquo;In 1.2 we had to drop the manifyfication stage of the makefile because it was triggering a line-too-long error on some OSs due to shell constraints&rdquo;. If you wish to get them back, comment (or delete) out the MY::manifypods sub in Makefile.PL</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?F10761DA3 </span></span></code></pre></div></li> <li> <p><strong>Converting ABI trace to Phred format</strong></p> <p>When asked why an ABI trace file read via SeqIO::abi didn&rsquo;t generate a Bio::Seq::SeqWithQuality (a sequence with associated quality values), Aaron Mackey replied, &ldquo;I&rsquo;m not sure why abi.pm in the bioperl distribution doesn&rsquo;t set it&rsquo;s sequence factory to SeqWithQuality&rdquo;; I&rsquo;m still not sure why. See the fix at:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?H2C954DA3 </span></span></code></pre></div></li> <li> <p><strong>biocorba status</strong></p> <p>When asked about the status of the biocorba project, Jason Stajich replied, &ldquo;We have working bindings in java,perl,python and bridges to the respective Bio* toolkits from these bindings for servers and clients based on a slightly modified BSANE IDL spec from OMG&rdquo;. He qualified that statement with &ldquo;none of the original developers are using it in any of their work so development and final rounds of testing have not really happened&rdquo;</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?G57A42DA3 </span></span></code></pre></div></li> <li> <p><strong>DNA Smith-Waterman</strong></p> <p>Yee Man has reimplemented the classic Smith-Waterman algorithm, with algorithmic improvements as suggested by Gotoh (affine gaps) and Myers &amp; Miller (linear space), and wondered whether it would be a good addition to the BioPerl C-coded extension library (which currently contains a protein-only Smith-Waterman implementation by Ewan Birney, pSW.pm). Some discussion about classic (and novel) dynamic programming algorithms ensued, which eventually boiled down to a desire to have the generic (but extremely fast) Smith-Waterman code (written by Webb Miller) used by Bill Pearson&rsquo;s SSEARCH implementation made more widely available as a linkable C library (which BioPerl could then subsume). Interested parties should contact me. Relatedly, to answer one of our FAQ&rsquo;s yet again, if you currently want to do Smith-Waterman on DNA sequences, you should use BioPerl&rsquo;s bindings to the EMBOSS suite of sequence utilities.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?Y20B21DA3 </span></span><span style="display:flex;"><span>http://makeashorterlink.com/?M12B23DA3 </span></span></code></pre></div></li> <li> <p><strong>using AUTOLOAD for get/set accessors</strong></p> <p>The BioPerl code is full of explicitly coded accessor methods; often we are asked why we don&rsquo;t use more code-efficient methods of autogenerating these identical functions (via AUTOLOAD or Class::MakeMethod). The discussion is long-ranging, but it boils down to wanting every accessor to have the same functionality with respect to undef values and return value behavior, as dictated by our accessor &ldquo;boilerplate&rdquo; (which we kindly ask everyone to use). Yes, we know we can achieve that via sophisticated Class::MakeMethod usage, but we have bigger fish to fry at the moment. There&rsquo;s another, subtler issue about interfaces and implementation method introspection, but I&rsquo;ll leave that to a later discussion.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?Z22C32DA3 </span></span></code></pre></div></li> <li> <p><strong>Bio:Seq no longer a RangeI (bug in Bio::Graphics::Panel)</strong></p> <p>Much to the consternation of Lincoln Stein (and his legions of Bio::Graphics users), BioPerl 1.2 introduced a change to Bio::Seq in that it no longer complies with the Bio::RangeI interface; see Heikki Lehvaslaiho&rsquo;s &ldquo;This has to be cruft!&rdquo; message from November:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?Q53C41DA3 </span></span></code></pre></div><p>Unfortunately, Bio::Graphics::Panel relied on Bio::Seq having a &ldquo;start&rdquo; method, so lots of existing code broke. A number of fixes were recommended, including a) using a Bio::Seq::SeqFactory to generate Bio::LocatableSeq&rsquo;s (which do implement RangeI methods), b) patching your Bio::Graphics::Panel and c) upgrading BioPerl 1.2 to the live CVS development version. A BioPerl 1.2.1 is forthcoming for this, and other reasons.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?R17C61DA3 </span></span><span style="display:flex;"><span>http://makeashorterlink.com/?S3AC21DA3 </span></span></code></pre></div></li> <li> <p><strong>complement(join(e1, e2)) vs. join(complement(e1), <code>complement(e2))</code></strong></p> <p>Periodically, people ask &ldquo;Is it possible to have bioperl output features in Genbank format of the form &ldquo;complement(join(1..50,60..100))&rdquo; rather than &ldquo;join(complement(1..50),complement(60..100))?&rdquo; This time it degenerated a little into a discussion about whether these two representations were semantically equivalent (short answer: yes). The answer to the original question is that BioPerl parses either representation into the same structure, which can only be &ldquo;dumped&rdquo; in one representation (presently, the latter).</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?H2CC16DA3 </span></span></code></pre></div></li> <li> <p><strong>GenBank <code>bond()</code> FT operator</strong></p> <p>Recent GenBank files have begun to exhibit a new feature location operator, &ldquo;bond&rdquo;, to identify dicysteine bonds in proteins and mRNA splice sites in RefSeq sequences. BioPerl has no concept of this location operator (which is really more of a feature, and would be better represented as a /bond feature table entry), and so currently dies when parsing a record containing it. A brute force fix is provided, but a better answer is yet to appear:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?L24D12DA3 </span></span></code></pre></div></li> </ul> <hr> <h1 id="changesadditions">Changes/Additions</h1> <ul> <li> <p><strong>SearchIO now has megablast parser</strong></p> <p>Jason Stajich writes, &ldquo;The oft requested megablast parser has now been implemented in SearchIO&rdquo;. This should be available in the upcoming bioperl 1.2.1 bug-fix release, as well as CVS.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?O29D62DA3 </span></span></code></pre></div></li> <li> <p><strong>bl2seq parser needs to know report type to get strand right</strong></p> <p>No matter how hard he tried, Dave Arenillas couldn&rsquo;t retrieve HSP strand information from a bl2seq (BLAST two sequences against each other) report. After &ldquo;a little bit of detective work&rdquo;, Jason Stajich found that the Bio::Tools::BPbl2seq report object needs to be told the program type (e.g. &ldquo;blastn&rdquo;) since it&rsquo;s not smart enough to guess it by context alone. The patch to BPbl2seq.pm is available via CVS.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?M2ED52DA3 </span></span></code></pre></div></li> <li> <p><strong>bioperl.rpm in biolinux.org distribution</strong></p> <p>Marc Logghe reports that &ldquo;A couple of friends of mine have started up <a href="https://www.biolinux.org">www.biolinux.org</a> [ &hellip; and] are offering a number of rpm packages for free download like e.g. emboss, sim4, phylip, ncbiblast, &hellip;&rdquo;. After some discussion about what a bugbear packaging BioPerl can be (most dependencies are not critical for the entire package, only certain subparts that may or may not be useful for a given person), Hunter Matthews chimed in that he&rsquo;d likely be able to make a bioperl 1.2 rpm (he had previously made a 1.0 rpm); Hunter adds &ldquo;7.3 would be the most likely target platform&rdquo;. Marc Logghe later reported that &ldquo;the bioperl rpm&rsquo;s for RedHat and Suse are on line at <a href="http://biolinux.org/bioperl.html">http://biolinux.org/bioperl.html&rdquo;</a></p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?S16E22DA3 </span></span></code></pre></div></li> <li> <p><strong>example scripts reorganization for installation as &ldquo;production&rdquo; code</strong></p> <p>Spurred on by an earlier conversation regarding the perl scripts scattered between examples/ and scripts/, Brian Osborne has taken up the challenge to reorganize and reshape these so that those functional scripts with adequate POD and a .PLS suffix all live in scripts/ and get installed for &ldquo;production&rdquo; use. Scripts should remain in examples/ if they are simply &ldquo;proof-of-concept&rdquo; code, or just poorly documented. Everyone liked this, and from the CVS activity, it looks like the work is progressing.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?R29E32DA3 </span></span></code></pre></div></li> <li> <p><strong>Bio::Seq::SequenceTrace</strong></p> <p>Chad Matsalla has added a Bio::Seq::SequenceTrace object, to &ldquo;mimic the information available in a scf &lsquo;Sequence Chromatogram File&rdquo;&rsquo;. It slices and dices. In the process, Chad ended up rewriting his Bio::SeqIO::scf code, &ldquo;because the old module was somewhat &hellip; clunky&rdquo;.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?R3AE25DA3 </span></span></code></pre></div></li> <li> <p><strong>MLAGAN/LAGAN support</strong></p> <p>Stephen Montgomery has supplied both MLAGAN and LAGAN wrappers and parsers (the Lagan Tookit is a set of alignment programs for comparative genomics).</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?N11F24DA3 </span></span></code></pre></div></li> </ul> <hr> <h1 id="fixes">Fixes</h1> <ul> <li> <p><strong>SeqIO/scf.pm bug</strong></p> <p>Tony Cox &ldquo;finally got around to checking in a fix for the SeqIO/scf module when it has to deal with 8-bit encoded trace data&rdquo;. It&rsquo;s not yet clear where this fix stands with Chad Matsalla&rsquo;s rewrite of Bio/SeqIO/scf.pm</p> </li> <li> <p><strong>Bio::Tools::Run::WrapperBase.pm missing from 1.2</strong></p> <p>Because of some code migration between bioperl subprojects, Bio/Tools/Run/WrapperBase.pm went missing in the 1.2 release, causing a wide variety of failures. The 1.2.1 release will address this, or you can retrieve the missing file and install it manually from here:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?B20015EA3 </span></span></code></pre></div></li> <li> <p><strong>bug fixes in Blast HSP tiling code</strong></p> <p>After finding that for certain BLAST reports the &ldquo;blast&rdquo; and &ldquo;psiblast&rdquo; SearchIO parsers gave mildly differing values for &ldquo;frac_identical&rdquo; and &ldquo;frac_conserved&rdquo;, Jason Stajich did some auditing of the HSP tiling code and found a few inconsistencies which have since been fixed. End result: frac_identical and frac_conserved should be better behaved and actually correct.</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?V26053EA3 </span></span></code></pre></div></li> </ul> <hr> <h1 id="proposals">Proposals</h1> <ul> <li> <p><strong>Project ideas for the aspiring biohacker</strong></p> <p>Periodically, we&rsquo;re asked &ldquo;I&rsquo;d like to get involved, do you have any project ideas a newbie could work on?&rdquo;. Jason Stajich shot out a few choice ideas including &ldquo;blastz&rdquo; SearchIO parsing, which was briefly discussed. Get involved!</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?D28022EA3 </span></span></code></pre></div></li> <li> <p><strong>Bio::Perl namespace export groups</strong></p> <p>The Bio::Perl module is a top-level, &ldquo;novice&rdquo; interface to a few small tidbits of BioPerl functionality. Many first-time users appreciate the simplicity of the Bio::Perl interface, and so we&rsquo;d like to extend it&rsquo;s reach into other &ldquo;meaty&rdquo; areas of BioPerl functionality. Here we talk about how we might achieve this using custom export tags (a la CGI.pm and others). Another area where someone could make a dramatic impact without writing any new modules!</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>http://makeashorterlink.com/?D4A025EA3 </span></span></code></pre></div></li> </ul> <hr> <h1 id="conclusion">Conclusion</h1> <p>Well, that&rsquo;s it for this installment. Stay tuned for February (a much busier month!).</p>https://www.open-bio.org/2003/02/28/bioperl-reality-vs-myth-presentation-is-online/Fri, 28 Feb 2003 17:18:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/28/bioperl-reality-vs-myth-presentation-is-online/<p>Nat Goodman gave a talk on his impressions with BioPerl at a recent OReilly Bioinformatics Technology Conference.</p> <p>The powerpoint slides can be downloaded here: <a href="http://conferences.oreillynet.com/presentations/bio2003/goodman_nat.ppt">http://conferences.oreillynet.com/presentations/bio2003/goodman_nat.ppt</a></p> <p>All of the conference talks can be downloaded here (worth checking out): <a href="http://conferences.oreillynet.com/pub/w/21/presentations.html">http://conferences.oreillynet.com/pub/w/21/presentations.html</a></p> <p>From the session info:</p> <p>Goodman</p>https://www.open-bio.org/2003/02/28/postgresql-issues-with-bioperl-db/Fri, 28 Feb 2003 16:59:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/28/postgresql-issues-with-bioperl-db/<p>Hilmar writes:</p> <p>Here&rsquo;s the background.</p> <p>The current code in the bioperl-db adaptors to biosql run the connection with AutoCommit off, which means the client determines the transaction. Load_seqdatabase.pl (the main script for loading databases into biosql) treats one sequence entry as one transaction. If any sql statement required for loading the sequence fails unexpectedly, the whole transaction is rolled back, otherwise it is committed once the entry and all its annotation went in successfully. The emphasis rests on &lsquo;unexpectedly&rsquo;: INSERTs may fail due to unique key violations, which is caught and triggers a look-up of the affected entry by unique key. E.g. a dbxref may already exist; if so, it needs to be looked up in order to establish the association with the bioentry.</p> <p>Here&rsquo;s the problem.</p> <p>If within a transaction a particular statement fails, in Oracle and MySQL/InnoDB only that particular statement fails, not the previous ones in the same transaction, nor the subsequent ones. If you commit the transaction, all the succeeded statements&rsquo; results get committed. In PostgreSQL, however, the entire transaction fails and is invalidated, making all previous and all subsequent statements fail until you call rollback (you cannot call commit on a failed transaction).</p> <p>The fulll message and email discussion thread can be read at: <a href="http://bioperl.org/pipermail/bioperl-l/2003-February/011343.html">http://bioperl.org/pipermail/bioperl-l/2003-February/011343.html</a></p>https://www.open-bio.org/2003/02/28/major-bioontology-overhaul/Fri, 28 Feb 2003 16:54:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/28/major-bioontology-overhaul/<p>Hilmar writes:</p> <p>Triggered by what happened during the hackathon in Singapore, the Bioperl Ontology object model needs to undergo a number of changes that I&rsquo;m going to describe below, along with a proposal how to resolve the issues. I have largely implemented the proposal and barring major objections I&rsquo;m ready to commit tonight or tomorrow morning. Even though some of these things significantly change the API, we (I, backed by the core people) propose to migrate these changes over to the &lsquo;stable&rsquo; 1.2 branch, to be able to release bioperl-db (bridges to the biosql schema) in dependency on a stable bioperl branch.</p> <p>The full post can be read at: <a href="http://bioperl.org/pipermail/bioperl-l/2003-February/011337.html">http://bioperl.org/pipermail/bioperl-l/2003-February/011337.html</a></p>https://www.open-bio.org/2003/02/26/technical-report-on-moby-web-messaging-layer/Wed, 26 Feb 2003 21:10:31 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/26/technical-report-on-moby-web-messaging-layer/<p>Date: February 24, 2003 Author: Lincoln Stein Version: early</p> <p>This report concerns the messaging layer of the Moby project, that point at which semantic information is exchanged between the data consumer (i.e. the biologist) and the data provider (i.e. the model organism system administrator).</p> <p>There are a wide variety of possible messaging systems. Here are a number of prominent ones listed in rough chronological order.</p> <ol> <li>Custom messaging system using raw TCP/IP</li> <li>Custom messaging system using BEEP (an IEEE applications protocol framework)</li> <li>ASN.1 exchange</li> <li>Microsoft DCOM</li> <li>REST</li> <li>CORBA</li> <li>XML-RPC</li> <li>SOAP</li> <li>.NET</li> </ol> <p>For the purposes of this assessment, I ignored 1, 2, 3 and 4. I rejected custom messaging because it is a fallback position. We should only reinvent the wheel if we are absolutely certain that none of the other will meet our requirements. Exchange of messages via ASN.1 streams and Microsoft DCOM can rightly be treated as legacy solutions that have found important places in niche applications but are not accepted as solutions for enabling the exchange of semantic information across administrative domains. SOAP arises from, and supersedes, XML-RPC, and so are folded together. I will not consider NET because its marketing literature gives me a headache. This leaves REST, CORBA, and SOAP.</p> <p>I will now consider these in chronological order.</p> <p>---&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&mdash;&ndash;</p> <p>REST ----</p> <p>REST stands for REpresentation State Transfer, and is a term coined by Roy Fielding in his graduate thesis to describe a style of information architecture that had already become the de facto standard for the World Wide Web. According to Fielding, REST is suited for scaleable applications in which relatively large hypermedia representations of information resources are exchanged within the &ldquo;anarchic network.&rdquo;</p> <p>Key Features:</p> <p>a) Resources are identified using stable addresses, the URI.</p> <p>b) Resources are never exchanged themselves. Instead representations of resources are exchanged. A particular resource, such as a database entry, may be represented in multiple ways, e.g. as an HTML file or a postscript file. Resources are viewed as changing with time.</p> <p>c) REST has many nouns, but very few verbs. Its verbs follow the CRUD paradigm, and consist of PUT, GET, POST and DELETE. Its nouns are an extensible set of hypermedia representations.</p> <p>d) REST is stateless, and places the burden of maintaining session information squarely on the client.</p> <p>e) REST is close to the transport layer, and allows but does not require applications to be concerned with performance issues such as caching, parsing, and rendering latency.</p> <p>Discussion:</p> <p>Probably the most unique aspect of REST is its use of URIs to address each resource. For example, in a DAS application, a URI can be used to identify a particular segment of a genome:</p> <p><a href="http://my.site/das/d-melanogaster/r3.1/2R">http://my.site/das/d-melanogaster/r3.1/2R</a></p> <p>This identifies the genome of drosophila melanogaster, assembly release version 3.1, chromosome arm 2R. To fetch the list of features from this region, one would issue a GET request on the following URL:</p> <p>GET <a href="http://my.site/das/d-melanogaster/r3.1/2R/features">http://my.site/das/d-melanogaster/r3.1/2R/features</a></p> <p>To address an individual feature named &ldquo;exon00001&rdquo;, one refers to this</p> <p>GET <a href="http://my.site/das/d-melanogaster/r3.1/2R/features/exon00001">http://my.site/das/d-melanogaster/r3.1/2R/features/exon00001</a></p> <p>To add a new feature to the chromosome, one issues a PUT:</p> <p>PUT <a href="http://my.site/das/d-melanogaster/r3.1/2R/features/exon00002">http://my.site/das/d-melanogaster/r3.1/2R/features/exon00002</a></p> <p>Updates and deletes are handled similarly.</p> <p>REST is elegant because it allows very generic software to be written. For example, caching code does not have to know anything about the contents of the data it caches, and fetching code can simply hand off the data it receives to the appropriate helper application. However, it is unclear to me how REST can be used to handle transformative tasks. For example, do we transform genes into GO_terms this way?</p> <p>GET <a href="http://my.site/das/d-melanogaster/genes/notch/GO">http://my.site/das/d-melanogaster/genes/notch/GO</a>_terms</p> <p>If we want to pass parameters to the request, do we do it with a query string?</p> <p>GET <a href="http://my.site/das/d-melanogaster/genes/notch/GO">http://my.site/das/d-melanogaster/genes/notch/GO</a>_terms?descendents=true</p> <p>Who is using REST:</p> <p>In one sense, everyone is. In another sense, no one. Aside from WebDAV, there are very few &ldquo;pure REST&rdquo; applications out there. There are many almost-REST services, but a variety of common practices, such as the use of cookies, interferes with REST by confusing the semantics of stateless information transfer operations.</p> <p>DAS/1 is fairly close to a REST application, but it does some things that are discouraged by the REST design, such as using POST to mean GET.</p> <p>Software support:</p> <p>There is significant infrastructural support for REST services. It&rsquo;s the web!</p> <p>==================================================================</p> <p>CORBA</p>https://www.open-bio.org/2003/02/26/3-new-biojava-tutorial-entries/Wed, 26 Feb 2003 20:57:37 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/26/3-new-biojava-tutorial-entries/<p>Mark has updated his &ldquo;Biojava in Anger&rdquo; website to add three more tutorials. One on <strong>OrderNDistributions</strong> another on <strong>WeightMatrices</strong> and one on <strong>Profile HMMs</strong>.</p> <p>The website URL is <a href="http://bioconf.otago.ac.nz/biojava/">http://bioconf.otago.ac.nz/biojava/</a></p>https://www.open-bio.org/2003/02/21/biocoordinate-modules-ready-for-use/Fri, 21 Feb 2003 10:20:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/21/biocoordinate-modules-ready-for-use/<p>Generic and gene-specific coordinate system mappers are ready for use. These modules can ease the pain of mapping sequence features from one sequence coordinate to other ones, e.g. from cds to genomic and chromosomal.</p> <p>See the announcement at <a href="http://bioperl.org/pipermail/bioperl-l/2003-February/011110.html">http://bioperl.org/pipermail/bioperl-l/2003-February/011110.html</a></p> <p>Code and documentation updates were finished at the Singapore BioHackathon. The fixes will be part of the upcoming 1.2.1 bioperl release.</p>https://www.open-bio.org/2003/02/20/how-to-become-a-bioperl-hacker/Thu, 20 Feb 2003 09:24:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/20/how-to-become-a-bioperl-hacker/<p>Ewan talks about how one becomes a bioperl developer and how those invitations to hackathons get sorted out&hellip;</p> <p><a href="http://bioperl.org/pipermail/bioperl-l/2003-February/011226.html">http://bioperl.org/pipermail/bioperl-l/2003-February/011226.html</a></p>https://www.open-bio.org/2003/02/20/next-generation-sequence-features/Thu, 20 Feb 2003 09:02:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/20/next-generation-sequence-features/<p>[Excerpt] &hellip;Bioperl hackers who have been at Singapore have been discussing the next generation of sequence feature handling. As any developer - and indeed user - who has used bioperl might have noticed, our sequence feature model is quite complex - this is because we have a number of drivers, in particular&hellip;</p> <p>The full message was posted to the bioperl-l mailing list and can be read online at <a href="http://bioperl.org/pipermail/bioperl-l/2003-February/011225.html">http://bioperl.org/pipermail/bioperl-l/2003-February/011225.html</a></p>https://www.open-bio.org/2003/02/20/2003-singapore-hackathon/Thu, 20 Feb 2003 04:36:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/20/2003-singapore-hackathon/<p>About 30 open source informatics developers are hacking away in Singapore now working on various efforts. The main website is at <a href="http://hackathon.open-bio.org">http://hackathon.open-bio.org</a> and contains links to the Blog site and the picture gallery.</p>https://www.open-bio.org/2003/02/17/chris-breaks-devopen-bioorg/Mon, 17 Feb 2003 07:02:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/02/17/chris-breaks-devopen-bioorg/<p>Urgent notice &ndash;&gt; Primary CVS server has been relocated to pub.open-bio.org</p> <p>&ldquo;dev.open-bio.org&rdquo; &ndash; our primary developer server is down in Boston with a corrupt password file. Chris blames the Solaris audit subsystem for not liking root commands issued via SSH connections :)</p> <p>We have moved the CVS repositories to a Linux box called &ldquo;pub.open-bio.org&rdquo;. Developer accounts have been created <strong>but with different passwords</strong>. Email the OBF Sysadmin team at <a href="mailto:root-l@open-bio.org">root-l@open-bio.org</a> to get your new password.</p> <p>Note: This news affects developers only (ie people who have write/commit access to one or more codebase repositories). Our Anonymous CVS server ( <a href="http://cvs.open-bio.org">cvs.open-bio.org</a>) is unaffected.</p>https://www.open-bio.org/2003/01/27/biojava-in-the-news/Mon, 27 Jan 2003 06:54:34 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/01/27/biojava-in-the-news/<p>Mark reports:</p> <p>Just noticed a little snippit about biojava in the latest issue of the scientist <a href="http://www.the-scientist.com/yr2003/jan/labcon_030127.html">http://www.the-scientist.com/yr2003/jan/labcon_030127.html</a> (free registration required to view the article)</p>https://www.open-bio.org/2003/01/13/bioperl-in-the-news/Mon, 13 Jan 2003 08:01:21 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/01/13/bioperl-in-the-news/<p>Jason reports:</p> <p>Bioperl 1.2 was mentioned in &lsquo;The Scientist&rsquo; (free registration required to read this link) <a href="http://www.the-scientist.com/yr2003/jan/labcon_030113.html">http://www.the-scientist.com/yr2003/jan/labcon_030113.html</a></p>https://www.open-bio.org/2003/01/13/biojava-snapshot-13pre1-available/Mon, 13 Jan 2003 06:48:14 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/01/13/biojava-snapshot-13pre1-available/<p>Thomas Down reports:</p> <p>We&rsquo;ve had a number of requests recently for a more recent snapshot of the biojava-live code, so I&rsquo;ve just put together a biojava-1.3pre1 release. Get source, binaries, and javadocs from: <a href="http://www.biojava.org/download/">http://www.biojava.org/download/</a></p> <p>This isn&rsquo;t absolutely set in stone yet, but should give a reasonable indication of what the forthcoming 1.3 series is going to look like. All testing and comments welcome!</p> <p>One thing to note about the *binary* release: I&rsquo;ve compiled this using Sun JDK 1.4.1. There may be compatibility problems with Java 1.3 runtime envionments in some cases, so if you&rsquo;re using Java 1.3 and think you&rsquo;ve found a bug, please try downloading the source and recompiling. I&rsquo;ve released jdk1.4 binaries this time as an experiment. If there are violent objections, we can always do back to jdk1.3.1 for compiling binary releases, or perhaps provide both. Please let me know if you have any thoughts on this, or if it causes you trouble.</p>https://www.open-bio.org/2003/01/08/40-biojava-tutorials-available/Wed, 08 Jan 2003 06:43:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2003/01/08/40-biojava-tutorials-available/<p>Mark Schreiber has posted more than 40 tutorials on using &ldquo;biojava in anger&rdquo; at <a href="http://bioconf.otago.ac.nz/biojava/">http://bioconf.otago.ac.nz/biojava/</a></p>https://www.open-bio.org/2002/12/31/bioperl-12-released/Tue, 31 Dec 2002 06:34:26 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2002/12/31/bioperl-12-released/<p>The 1.2 Bioperl release <a href="http://bioperl.org/pipermail/bioperl-announce-l/2002-December/000197.html">is now available</a> from the <a href="http://bioperl.org/Core/Latest/">usual location</a>.</p>https://www.open-bio.org/2002/08/15/2002-bioinformatics-open-source-conference/Thu, 15 Aug 2002 22:23:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2002/08/15/2002-bioinformatics-open-source-conference/<p>Site URL is: <a href="http://open-bio.org/bosc2002/">http://open-bio.org/bosc2002</a> and the pictures from the event are available at <a href="http://gallery.open-bio.org/gallery/bosc2002">http://gallery.open-bio.org/gallery/bosc2001</a></p>https://www.open-bio.org/2002/08/02/minutes2002-bosc-meeting/Fri, 02 Aug 2002 15:42:17 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2002/08/02/minutes2002-bosc-meeting/<h3 id="august-2-2002">August 2, 2002</h3> <p>Edmonton, Alberta, Canada</p> <h3 id="call-to-order">Call to order</h3> <p>Board members present: Hilmar, Chris, Ewan, Steven, Andrew</p> <h3 id="recognition-of-observers-about-21">Recognition of observers (about 21)</h3> <p>This meeting was open to the the public. I don&rsquo;t know all of the people who commented, hence the question marks.</p> <h3 id="review-of-schedule-by-ewan">Review of schedule by Ewan</h3> <p>Steven - asked about money owed us from Hidelberg meeting Chris - says it&rsquo;s about 20-30 commercial people Decided to follow up on that money - assigned to Chris (AI) Steven - asked about audit Chris, financials Jan. to Jan. year; report out next year Action item: Chris to find an accountant to audit</p> <h3 id="bosc-2003-lead-by-ewan">BOSC 2003, lead by Ewan</h3> <ul> <li>do we want BOSC next year? if yes: <ul> <li>part of ISMB?</li> <li>affiliated with other projects</li> </ul> </li> </ul> <p>straw vote showed enthusiastic support for BOSC 2003</p> <p>Lincoln suggested survey of attendees tomorrow ?? suggested too small for standalone conference Martin - price to Oz not bad Chris - but subjective impression of distance ??? - will be better Asia/Pacific input Janet - A/P can help grow the community Ewan - build a travel fund? ??? - give concrete examples of other conference sites when doing the survey ORA would be too expensive and submerged RECOMB in April in Berlin Thomas - reemphasized the international / worldwide aspect of the conference Lincoln - web meetings cut in half when moved to OZ Chris - worried about losing people for next year, re costs, esp. if using professional organization</p> <h3 id="organizing-bosc-2003-lead-by-ewan">Organizing BOSC 2003, lead by Ewan</h3> <p>Request for volunteers - all declined Request for suggestions of volunteers Ewan volunteered Elia Stupka Elia tentatively agreed this morning Doreen said she would help, but not organize Motion: Ewan nominated Elia as organizer. Andrew seconded Motion passsed by unanimous consent Motion: Ewan nominated Doreen as &ldquo;BOSC 2004 organizer in waiting&rdquo; Chris seconded Motion passsed by unanimous consent</p> <h3 id="2003-hackathon-lead-by-ewan">2003 Hackathon, lead by Ewan</h3> <p>Belief that hackathon helped in intergroup cohesiveness and should be repeated Andrew: What about funding? Chris: I3C, through Brian Gilman, may fund the hackathon Cost between 30 to 50 grand Jason: What influence will I3C have on the funding / what will they get out of it? Ewan: Sponser should not have influence on the scedule. May pick some attendees, write press. Hilmar: What about government funding? Ewan: Overhead is prohibitive compared to corporate sponsership. Steven: Could redirect gov&rsquo;t funding through a university (as was done for ISMB, using San Diego) Matthew: hackathon a great idea Lincoln: we should be able to get corporate sponsership pretty easily - great press ??? - didn&rsquo;t get much output / documentation / etc Ewan: we should invite documenters Hilmar: What about a &lsquo;doc-athon&rsquo;? Ewan: doc people may find the social interactions of a hackathon more useful Motion: Create a hackathon committee with Ewan as chair. Main goals are to identify funding sources and site for hackathon. Chris seconded. Motion passsed by unanimous consent Misc., lead by Ewan Chris: Interest earned by idle cash Motion: Chris Investigate ways to make interest in no-risk way to make interest. Ewan seconded. Motion passsed by unanimous consent</p> <h3 id="obf-branding">OBF Branding</h3> <p>Should we work on a logo? Tentative yes. Idea is to get community input for logo and get a professional organization to cleaned up. Also work on unifying web pages, etc. Hilmar: Why? Chris: Help present a more professional image Ewan: Likes O|B|F Andrew agrees. Motion by Steven that Chris can spend up to $2,000 on the branding project, with further discussion to occur. Ewan seconded. Motion passsed by unanimous consent</p> <h3 id="digital-certificates">Digital certificates</h3> <p>BioJava wants to sign jar files. May want secure web connections May want multiple certificates, eg, one for the different projects. Lincoln: certificates for web different than for jar and has its own costs. Agreed that we can ignore secure web connections. Chris: jar signing costs a few $100 a year Matthew: who has signing authority?</p> <h4 id="virus-scanning-of-inbound-and-outbound-mail">Virus scanning of inbound and outbound mail.</h4> <p>Ewan: Authorize Chris to look into virus scanning and digital certificates, report costs and benefits, and allow a vote on expenses over email. Andrew seconds. Motion passed by unanimous consent Steven:relevant NIH grants, like conference grants we are a &ldquo;rounding error&rdquo; compared to most conferences but grant administration has overhead. Another grant: PAs, as for software development should we investigate that? Probably no, but proposing the idea Andrew: what is a PA? Program announcement, interested in area, expect to spend money, doesn&rsquo;t guarantee funding, but encourages. Lincoln: some can be recurring Doreen: funds for technical writer or other non-developer Chris: OBF lacks in administration; what&rsquo;s the overhead? Lincoln (and Steven): would need to admin through a site (like CSHL) with experience in admin&rsquo;ing these sorts of grants. Ewan: We direct and support groups which get the PA funding, rather than go through us. Is that feasible? Lincoln: Study sections are mostly concerned about the likelihood of success, so shouldn&rsquo;t be a problem Decided that Steven would encourage others to work with the OBF, but not really look for it outselves, unless it was really adventagous No need for a motion. More enthusiastic about the NIH grant Steven: we should provide more funding to speakers Ewan suggested that Doreen look into funding, esp. long term (5 year funding) from NIH Chris offered to help Steven:Do we need a response to the ISCB open source statement found in &hellip;. ? Some statements are quite wrong, in the view of many open source people. Ewan: OBF stay away from policy influence as an organization Andrew: why bother? Steven: what about a simple statement in the minutes? Johann: Win (and others) pointed out corrections before it was published, and it still went through. Janet: would it interfere with our associations with ICMB? Lincoln: we should be a more vocal source Ewan: but we are a support organization, not leading the direction. Uncomfortable with setting the direction. Lincoln: this is a clarification of our policy Lincoln: should there be a response? No, theirs is a reponse to ours. First, check our statement to see if we agree with it. Ewan: reads statement aloud. Ewan and Andrew are still comfortable. Some questions about wording. Steven clarified. Chris: we should mention this to people tomorrow, esp. those who are members, to reponse individually Lincoln: document will be used as leverage to funding agencies to justify research proposal. Eg, &ldquo;this isthe ISCB approved level 3 development model&rdquo;. Used for policy decisions. Jason: as members we should be offended, but OBF? not sure. Andrew: I haven&rsquo;t read this document yet. Ewan: Stay away from &ldquo;journalistic ping-pong&rdquo; Steven: vote was close. Be polite, but make our point(as ISCB members) known. ???: could argument from a technical level be used for leverage. Ewan and Lincoln: no Matthew: statement should say what open source means Motion by Ewan to modify statement to point to the opensource.org definition of &ldquo;open source&rdquo; and to confer later to clarify our position. Steven seconded. Motion passsed by unanimous consent</p> <p>Vote to accept minutes of last meeting. Unanimous consent. Make meeting minutes available. Question about making comments from people publically available. No one objected nor wanted to be anonymous.</p> <p>Mark Wilkinson wanted to assign BioMOBY copyright to OBF Consensus is that we see no problems with that ??? what about moving services to collab.net / sourceforge-style installation Ewan: suggest talking with Chris about that; don&rsquo;t yet need board involvement Lincoln: keep our own hardware. Yep. Steven: want to make publications at least as available as the software. Ewan: declined to accept that topic &ndash; getting late Hilmar: How do we handle nominations for new board members? Expanding the board? Chris: we have some templates already which we could use Chris: call for suggestions (eg, from church groups and other non-profits organization Action item: Hilmar will look into this Chris proposed we adjurn. Ewan seconded. Motion passed by unanimous consent.</p>https://www.open-bio.org/2002/07/01/july-2002-obf-newsletter/Mon, 01 Jul 2002 22:13:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2002/07/01/july-2002-obf-newsletter/<p>Available online at <a href="http://open-bio.org/newsletters/2002-08-newsletter.html">http://open-bio.org/newsletters/2002-08-newsletter.html</a></p>https://www.open-bio.org/2002/01/01/obf-statement-on-public-funding-open-source/Tue, 01 Jan 2002 23:41:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2002/01/01/obf-statement-on-public-funding-open-source/<p>Preliminary Policy Statement on Public Funding and Open Source</p> <p>The Open Bioinformatics Foundation believes that scientific software developed with public support should be distributed under terms analogous to those applied to biological materials. In common with treatment of reagents under the UBMTA and good practice, we believe that the essential source code necessary for reproducing published results should be made readily available for non-commercial research use.</p> <p>While acknowledging that open source licenses may not be optimal in every instance, we believe that development and release of software under open source licenses is often beneficial and efficient in creating valuable scientific software, and in encouraging its widespread use and most successful exploitation.</p> <p>We view researchers as the individuals most capable of determining if their software will be developed and exploited in an optimal manner under an open source license, and we therefore encourage institutions to delegate to their scientists the opportunity to select non-restrictive and open source licenses for their software.</p> <h3></h3> <p>The Open Bioinformatics Foundation is a 501(c)(3) non-profit (pending) organization dedicated to supporting the development, distribution, and understanding of collaborative software in computational biology and bioinformatics. Dating from 1994 and incorporated in 2001, the Foundation sponsors the annual Biological Open Source Conference, software development workshops, and provides umbrella support to the Bioperl, Biopython, BioJava, and other open source bioinformatics development efforts. More than 1000 individuals have signed on to Foundation lists or attended its conferences. Also referred to as open-bio and O|B|F, the Open Bioinformatics Foundation has no affiliation with the similarly named groups at openinformatics.org or bioinformatics.org. The Foundation&rsquo;s website is at <a href="http://open-bio.org/">http://open-bio.org/</a></p>https://www.open-bio.org/2001/10/01/october-2001-obf-newsletter/Mon, 01 Oct 2001 22:11:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2001/10/01/october-2001-obf-newsletter/<p>Available online at <a href="http://open-bio.org/pipermail/open-bioinformatics-foundation/2001-October/000001.html">http://open-bio.org/pipermail/open-bioinformatics-foundation/2001-October/000001.html</a></p>https://www.open-bio.org/2001/06/15/2001-bioinformatics-open-source-converence/Fri, 15 Jun 2001 22:22:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2001/06/15/2001-bioinformatics-open-source-converence/<p>Site URL is: <a href="http://open-bio.org/bosc2001/">http://open-bio.org/bosc2001</a> and the pictures from the event are available at <a href="http://gallery.open-bio.org/gallery/bosc2001">http://gallery.open-bio.org/gallery/bosc2001</a></p>https://www.open-bio.org/all/Mon, 01 Jan 0001 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/all/https://www.open-bio.org/search/Mon, 01 Jan 0001 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/search/