https://www.open-bio.org/category/community/Recent content in Community on Open Bioinformatics FoundationHugoen-USboard@open-bio.org (Open Bioinformatics Foundation)board@open-bio.org (Open Bioinformatics Foundation)Fri, 26 Jun 2026 00:00:00 +0000https://www.open-bio.org/2026/06/17/2026-06-17-francesco-micocci-bits2026/Fri, 26 Jun 2026 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2026/06/17/2026-06-17-francesco-micocci-bits2026/<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. <a href="https://github.com/Vehx35">Francesco Maria Antonio Micocci</a>,</em></strong> <em><strong>a Undergraduate Student at</strong></em> <em><strong>University Of Turin</strong></em>, <strong><em>was awarded an OBF Event Fellowship to attend</em></strong> <em><strong>the</strong></em> <strong><em><a href="https://bioinformatics.it/bits2026">BITS2026 Conference</a></em></strong> <em><strong>and</strong></em> <strong><em><a href="https://younginfolife.github.io/events/2026-biohackathon">BioHackathon2026</a></em></strong>.</p> <p>Attending a conference for the first time and as an undergraduate student can be really intimidating. Finding yourself in rooms filled with affirmed researchers and topics you’ve not studied before. That was exactly the situation I found myself in at the recent Biohackathon and BITS2026 in the beautiful city of Padova.</p> <p>I want to thank the Open Bioinformatics Foundation (OBF) for giving me the opportunity to participate in these events, without their support I wouldn&rsquo;t have been able to embark on this experience.</p> <h2 id="the-biohackathon">The BioHackathon</h2> <p>As soon as I arrived in the city and after a rapid lunch, I found myself catapulted right into the action. After the groups were formed by the organizers, we got access to the GitHub repository. As an undergraduate, looking at the assigned tasks was a mix of excitement and panic. Quickly I came to realize that most of what we had to do I had only little knowledge of. While I felt like I couldn&rsquo;t be of much help to the rest of the group, I got to learn a lot from the other members that didn’t leave me out even when I was clearly having difficulties. <img src="https://www.open-bio.org/img/2026/2026-06-17-Micocci-Francesco-hackathon.jpg" alt="A group photo of all the Biohackathon participants"></p> <h2 id="the-conference">The Conference</h2> <p>After the Hackathon, on the second day the conference finally started. To be really honest, the various talk sessions were packed with advanced topics that were lightyears ahead of my actual knowledge. But while the technical details went mostly over my head, listening to the speakers gave me an idea of where the field of bioinformatics is heading. Instead of feeling discouraged, it was actually motivating. Seeing how some of the knowledge I already possess is used in real life applications gave me a boost. <img src="https://www.open-bio.org/img/2026/2026-06-17-Micocci-Francesco-conference.jpg" alt="A group photo of all the BITS2026 participants"></p> <h2 id="the-poster-session-the-turning-point">The Poster Session: The turning point</h2> <p>While I felt a bit out of place during the oral sessions, now it was time for the poster session. That was my chance to share our work and get feedback from the community. At first, I was quite nervous, but soon people came to read our poster and had a chat about it, then all the nervousness faded away. It was amazing to explain our project and to receive feedback from experienced researchers. This fantastic experience ended then with wonderful news. We won the best poster award! Getting this recognition completed this experience in the best possible way. I couldn’t really believe it! For an undergraduate like me getting an award like this and seeing people actually appreciating my work felt unreal. <em>You can view and download the full award-winning poster on <a href="https://zenodo.org/records/20763335">Zenodo</a>.</em> <img src="https://www.open-bio.org/img/2026/2026-06-17-Micocci-Francesco-poster.jpg" alt="Presenting the JupyDo Poster"></p> <h2 id="not-only-science">Not only Science</h2> <p>This experience was not only about science. The social moments have been one of the best sides of this conference. Whether it was discussing projects over a coffee during breaks, having a laugh during dinners, or enjoying a drink with people, I always felt welcomed in the community. <img src="https://www.open-bio.org/img/2026/2026-06-17-Micocci-Francesco-social.jpg" alt="A Social Aperitif with all the Biohackathon participants"></p> <h2 id="conclusion-a-message-to-other-undergraduate-students">Conclusion: A message to other Undergraduate students</h2> <p>Looking back at this whole experience, I think it taught me that you don’t need to know everything to be part of the bioinformatics and open source world. All you need is curiosity and the willingness to learn.</p> <p>Once again, I want to express my gratitude to OBF for making all of this possible. If you are an undergraduate student thinking about applying for an OBF travel grant to attend these events: don’t hesitate, do it. You could get an opportunity to learn, meet incredible people that you wouldn&rsquo;t experience otherwise, and you might also walk away with a win you didn’t expect coming!</p>https://www.open-bio.org/2026/06/24/event-fellowship-2026-2/Wed, 24 Jun 2026 00:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2026/06/24/event-fellowship-2026-2/<hr> <p>The call for applications for round 2 of the<a href="https://www.open-bio.org/event-awards/"> OBF Event Fellowship</a> for 2026 is now open. The deadline for this round is 1 August 2026. 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 &ndash;<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 between September 2026 to August 2027. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. 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/img/2026-02-02-image-kiragu.jpg.png" alt="David Kiragu at the 2025 AIBBC conference"></p> <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 had three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.</p> <p>Looking back at the first round of 2026, we received 40 applications, and six applicants were selected to support their participation in various events.</p> <ol> <li> <p>Francesco Maria Antonio Micocci: BITS 2026 &amp; BioHackathon 2026, 26-29 May 2026</p> </li> <li> <p>Aditya Karna: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026</p> </li> <li> <p>Lee Jia Wei: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026</p> </li> <li> <p>Anastasia Bratulin: 34th Conference on Intelligent Systems for Molecular Biology, July 12-16, 2026</p> </li> <li> <p>Jeremy Fan: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026</p> </li> <li> <p>Neha Arora: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026</p> </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://www.open-bio.org/event-awards/">apply for the fellowship</a> before 1 August 2026.</strong></p>https://www.open-bio.org/posts/CollaborationFest-2026/Wed, 13 May 2026 02:30:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/posts/CollaborationFest-2026/<img src="https://www.open-bio.org/img/2026/CoFest2025-people-working-at-table-horiz.jpeg" alt ="People working at a table at CoFest 2025"/> <br/> The OBF/BOSC CollaborationFest (aka CoFest) is a collaborative event where participants get to work together on code, documentation, training materials, challenging analysis problems, use cases, and more. Participants can bring their own project ideas or pitch in on others’ projects. <p>BOSC has organized CoFests every year before or after ISMB since 2010. This year, CoFest will take place after ISMB 2026 on <strong>Friday, July 17 and Saturday, July 18</strong> (9am-5pm each day). The location is in central Washington, D.C. (not far from the ISMB location); the exact address will be shared with those who register. There will be limited opportunities for virtual participation; videoconferencing is not guaranteed but participants will be able to interact on Slack.</p> <p>CoFest is free, but registration is mandatory, and space is limited. To sign up:</p> <ol> <li>Add yourself to <a href="https://docs.google.com/spreadsheets/d/1HvB9nHCBiCrSLWR9BNG5ypMecEbn7MOOnWIZxagQwRo/edit">this spreadsheet</a> to help us gauge interest, coordinate topic groups and logistics</li> <li>Add your project ideas to <a href="https://docs.google.com/document/d/1x7h4Tx3Y8IrcDSkSs_LylVFzQhjNKmQpwAbizQnyxYQ/edit?tab=t.0">this 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> for discussion before/during/after CoFest!</li> </ol> <p>We&rsquo;re excited to see you in July at BOSC@ISMB and hope you’ll stick around for CoFest right after.</p> <p>For more information on CoFest (including updates about planned projects and activities), please visit our <a href="https://www.open-bio.org/events/bosc-2026/collaborationfest/">CoFest page</a>.</p> <p>Big thanks to <a href="https://computercraft-usa.com/">Computercraft</a> for providing the meeting space, and to <a href="https://seqera.io/">Seqera</a>, whose sponsorship is helping cover the cost of lunches!</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/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/2025/10/07/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/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/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/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/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/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/2024/06/18/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/2024/02/23/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/2024/01/19/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/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/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/2023/08/14/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/2023/07/10/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/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/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/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/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/2022/07/25/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/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/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/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/2022/01/27/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/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/2021/09/30/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/2021/07/28/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/2021/06/11/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/2021/05/28/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/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/2021/01/28/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/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/2020/08/22/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/2020/08/13/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/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/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/2020/02/17/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/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/2019/11/14/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/2019/11/12/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/2019/09/30/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/2019/08/07/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/2019/07/16/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/2019/05/31/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/2019/04/08/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/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/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/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/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 biopython-1.73-cp27-cp27m-win32.whl 178be72d7b294a2a15c92630bbee2a81 biopython-1.73-cp27-cp27m-win_amd64.whl 32fc6184cbf21faca0776251570b2c58 biopython-1.73-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 5c78b8210de0b511c208facf7325c7e6 biopython-1.73-cp34-cp34m-manylinux1_i686.whl ae414b4666900567579cc92df4223521 biopython-1.73-cp34-cp34m-manylinux1_x86_64.whl 1b0d7ba1b4c097b318213431d9b6b99e biopython-1.73-cp34-cp34m-win32.whl 04a91b6ea826596b0c8b643b743d176f biopython-1.73-cp34-cp34m-win_amd64.whl a8ecaa7bf30fd912536881228e754664 biopython-1.73-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 0676a634a73e049903a4bc36e3b60fc3 biopython-1.73-cp35-cp35m-manylinux1_i686.whl 6d4ebb6131a611a71816b0208747de55 biopython-1.73-cp35-cp35m-manylinux1_x86_64.whl 65165d6551e43bdc18e0912935f9c7fd biopython-1.73-cp35-cp35m-win32.whl 24c6352a143ea28c47bff5da754f0af9 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biopython-1.73.tar.gz 478d71daf63e9b57775fbd5aaa8f48f1 biopython-1.73.zip</code> <code>$ sha256sum biopython-1.73* c43a47ad3397336aa7af5a0bb5ebec91aa2ae328b71421e550cf7e7f80d00f69 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 0302d5be80850fbaa93789ab516d189c9400755901cfe566a324e8fea10ed39b biopython-1.73-cp27-cp27m-manylinux1_i686.whl e5b5666724cab7983aebeb593e52dd276ff9fdabb3669d57db8b5ea303a097a5 biopython-1.73-cp27-cp27m-manylinux1_x86_64.whl 21723d79a1d15e99c823b440dd37176259dffa686e2a015919ad255d89238491 biopython-1.73-cp27-cp27mu-manylinux1_i686.whl 85d53b91406aacfef673fb3cf24873d978654fa49d52b5ab4d9c3b0d06b003d6 biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl c5beb53e2d5a5a573baaaa449a32d3adfb3d03bd7752adbcb20a62d6e8041e03 biopython-1.73-cp27-cp27m-win32.whl add575d5b81eec95381a53ca8c042e9de9e506b24734ec773690247d997eaa69 biopython-1.73-cp27-cp27m-win_amd64.whl 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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/2018/06/14/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 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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/2018/03/05/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/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/2017/09/05/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/2017/04/05/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/2016/07/21/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/2016/05/27/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/2015/06/05/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/2015/05/01/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/2015/03/26/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/2014/09/18/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/2014/05/29/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/2014/03/04/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/2013/12/06/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/2013/11/12/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/2013/08/28/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/2013/02/05/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/2012/11/06/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/2012/10/12/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/2012/07/30/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/2012/04/24/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/2012/03/16/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/2011/10/28/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/2011/08/18/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/2011/03/18/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/2010/11/18/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/2010/08/26/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/2010/05/20/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/2010/04/07/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/2010/03/21/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/2010/01/18/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/2009/12/18/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/2009/12/14/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/2009/11/22/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/2009/09/29/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/2009/09/02/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/2009/06/23/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/2009/06/01/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/2009/04/03/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/2009/03/22/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/2009/02/24/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/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/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/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>