https://www.open-bio.org/category/obf/Recent content in Obf on Open Bioinformatics FoundationHugoen-USboard@open-bio.org (Open Bioinformatics Foundation)board@open-bio.org (Open Bioinformatics Foundation)Wed, 02 Apr 2025 14:49:50 +0000https://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/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/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/2023/03/29/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/2022/09/29/obf-public-board-meeting-2022-10-21/Thu, 29 Sep 2022 17:33:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/09/29/obf-public-board-meeting-2022-10-21/<h2 id="date-time-and-how-to-join"><strong>Date, Time, and How to Join</strong></h2> <ul> <li>Date and time: 2022-10-21, 15:00 UTC (8am PT / 11am ET / 4pm UK)</li> </ul> <h2 id="agenda">Agenda</h2> <h3 id="board-officer-elections">Board Officer Elections</h3> <ul> <li>Chris Fields wishes to step down as Secretary, and Nomi Harris is standing for election to this role</li> <li>This will be an electronic ballot of the current board members</li> </ul> <h3 id="elections-to-the-board">Elections to the Board</h3> <ul> <li>Iddo Friedberg, running for Board member at-large ( <a href="https://www.open-bio.org/wp-content/uploads/2022/10/OBF-Statement-Iddo-Friedberg.pdf">statement of interest</a>)</li> <li>This will be an electronic ballot of the current board members</li> </ul> <h3 id="bylaw-changes">Bylaw Changes</h3> <ul> <li>We periodically review our bylaws</li> <li>Changes must formally approved by the Board at a public board meeting</li> <li>We plan minor changes to avoid gendered language, including subsuming the Secretary role (with historical gendered associations) into a Vice President role.</li> <li>Proposed changes expressed as a <a href="https://github.com/OBF/obf-docs/pull/102">Pull Request</a></li> </ul> <h3 id="minutes">Minutes</h3> <p>After the meeting, the meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs/tree/master/minutes">obf-docs GitHub repository</a>.</p>https://www.open-bio.org/2022/08/18/bhki-sponsorship/Thu, 18 Aug 2022 14:30:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2022/08/18/bhki-sponsorship/<p>The OBF Community Support Sponsorship scheme aims to sponsor small open-source-focused events like a scientific meeting, small conference, training workshop, hackathon, or time-limited series like monthly seminars. See <a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">details in this post</a>. One application was funded under this program to prototype the workflow, with OBF offering financial support for a <a href="https://bhki.org/2022/08/17/empowering-our-community-with-bioinformatics-data-management-and-soft-skills/">seminar series hosted by the Bioinformatics Hub Kenya</a>. Congratulations to Michael Kofia Landi for leading this application and working collaboratively with the BHKi team – Pauline Karega, David Kiragu, Margaret Wanjiku and Festus Nyasimi – and OBF Board including Treasurer Heather Wiencko, to help establish a process for this new type of OBF funding.</p> <p><a href="https://bhki.org/2022/08/17/empowering-our-community-with-bioinformatics-data-management-and-soft-skills/"><img src="https://www.open-bio.org/wp-content/uploads/2022/08/Bioinformatica_Hub_Logo-918x1024.png" alt=""></a></p>https://www.open-bio.org/2022/07/25/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/2022/05/17/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/2022/01/27/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/2022/01/04/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/2021/10/06/two-new-members-elected-to-obf-board/Wed, 06 Oct 2021 10:20:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/10/06/two-new-members-elected-to-obf-board/<p>The OBF held a public Board meeting on September 21, 2021, via Zoom. During the meeting, one Board member, Bastian Greshake Tzovaras, whose term expired, was elected to another term as Board member-at-large, and two new Board members were elected: Hilyatuz Zahroh and Caleb Kibet. Additionally, two proposals were presented (see below). The meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs">obf-docs GitHub repository</a>.</p> <p><a href="https://twitter.com/hilyatuz_zahroh">Hilyatuz (&ldquo;Hilya&rdquo;) Zahroh</a> is a bioinformatician at the Genetics Research Centre, Universitas YARSI, in Indonesia. She also works with Asia Pacific Bioinformatics Network ( <a href="https://www.apbionet.org/">APBioNet</a>) to facilitate the sharing of bioinformatics knowledge and skills through education and trainings in the Asia-Pacific region, and is involved with RINarxiv, a preprint server for Indonesia. She was a vice-chair of the 18th International Conference on Bioinformatics (InCoB) 2019, and the treasurer of the Bioinformatics and Biodiversity Conference (BBC) 2020. Hilya is committed to fast-forwarding science by promoting open access in bioinformatics and facilitating the learning of bioinformatics skills within communities.</p> <p><a href="https://twitter.com/Calkibet">Caleb Kipkurui Kibet</a> is a bioinformatics researcher at ICIPE, the International Centre of Insect Physiology and Ecology in Kenya, as well as an adjunct lecturer at Pwani University. He is the founder and project lead of <a href="https://github.com/BioinfoNet">OpenScienceKE</a>, which seeks to promote open science practices in bioinformatics. In 2019-2020, Caleb was a Mozilla Open Science Fellow; his work involved developing FAIR Genomics Data Management policy, frameworks, and infrastructure; building a community of Open Science enthusiasts; and promoting the adoption of machine learning tools in biomedical research.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/10/obf-board-meeting-Sep2021-composite.png" alt=""></p> <p>Above: Board candidates Caleb Kibet (bottom left) and Hilyatuz Zahroh (bottom right) with current Board members during the public OBF Board meeting on 21-Sept-2021.</p> <p>Two proposals were announced as pending submission to the OBF membership for a vote of approval:</p> <ol> <li> <p>The OBF is proposing a Community Support Sponsorship grant programme (see <a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">/2021/05/11/obf-community-support-sponsorship/</a>), which would give funds to grassroots communities in return for our logo appearing on their event webpages and materials, acknowledging our support. We seek community input; please add your comments to <a href="https://github.com/OBF/obf-docs/issues/86">https://github.com/OBF/obf-docs/issues/86</a>.</p> </li> <li> <p>The OBF would like to adopt a code of conduct (COC) for its activities including meetings and member projects. See pull request <a href="https://github.com/OBF/obf-docs/pull/78">https://github.com/OBF/obf-docs/pull/78</a> for the proposal, and please share your thoughts.</p> </li> </ol> <p>A membership vote on these will be held within the next 6 weeks, and the Board resolved to accept the result as binding for whether to formally implement them.</p>https://www.open-bio.org/2021/09/30/event-fellowship-deadline-extended-to-october-4-2021/Thu, 30 Sep 2021 18:37:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/30/event-fellowship-deadline-extended-to-october-4-2021/<p>The deadline for applying for an OBF Event Fellowship has just been extended to <strong>October 4, 2021</strong>! The OBF Event Fellowship program is aimed at increasing diverse participation at events relating to open source bioinformatics. You can <a href="https://www.open-bio.org/blog/">read blog posts</a> by previous Event Fellowship recipients.</p> <p>See more details on <a href="https://www.open-bio.org/event-awards/">our webpage</a>, and submit your application at <strong><a href="https://forms.gle/7ocmgvypiFHeFNfy7">https://forms.gle/7ocmgvypiFHeFNfy7</a></strong>!</p>https://www.open-bio.org/2021/09/11/obf-public-board-meeting-2021-09-21/Sat, 11 Sep 2021 16:59:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/09/11/obf-public-board-meeting-2021-09-21/<h2 id="date-time-and-how-to-join"><strong>Date, Time, and How to Join</strong></h2> <p>Date and time: 2021-09-21, 17:00 UTC (10am PT / 1pm ET / 18:00 UK) Participation link: <a href="https://lbnl.zoom.us/j/97312757115">https://lbnl.zoom.us/j/97312757115</a> Password: OBF2021 Meeting ID: 973 1275 7115</p> <h2 id="agenda">Agenda</h2> <p><strong>Approve minutes from the previous Public Board Meeting:</strong> <a href="https://github.com/OBF/obf-docs/pull/87">https://github.com/OBF/obf-docs/pull/87</a></p> <h3 id="term-expirations-and-elections-to-the-board-electronic-ballot">Term expirations and Elections to the Board (electronic ballot)</h3> <ul> <li>Hilyatuz Zahroh and Caleb Kibet, running for Board member at-large</li> <li>Board member Bastian Greshake Tzovaras’ term expires this year and he would like to stand for another term as member-at-large.</li> </ul> <h3 id="voting-by-obf-membership">Voting by OBF membership</h3> <ul> <li>OBF Community Support Sponsorship: a proposed new grant programme, based on the OBF Event Fellowships but aimed at supporting grassroots projects running events in their own communities. Subject to approval by the OBF membership in a formal vote. <ul> <li><a href="https://www.open-bio.org/2021/05/11/obf-community-support-sponsorship/">/2021/05/11/obf-community-support-sponsorship/</a></li> <li><a href="https://github.com/OBF/obf-docs/issues/86">https://github.com/OBF/obf-docs/issues/86</a></li> </ul> </li> <li>Code of Conduct: BOSC has a code of conduct, as part of the parent conference, but OBF does not yet have its own code of conduct. This pull request lays out a Code of Conduct for the OBF that, if approved by a membership vote, will replace the content on /code-of-conduct/. <ul> <li><a href="https://github.com/OBF/obf-docs/pull/78">https://github.com/OBF/obf-docs/pull/78</a></li> </ul> </li> </ul> <h3 id="minutes">Minutes</h3> <p>After the meeting, the meeting minutes will be made available in the <a href="https://github.com/OBF/obf-docs">obf-docs GitHub repository</a>.</p>https://www.open-bio.org/2021/08/18/obf-event-fellowship-second-call-2021/Wed, 18 Aug 2021 18:45:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/08/18/obf-event-fellowship-second-call-2021/<p>The call for application for the second round of this year&rsquo;s <a href="https://www.open-bio.org">Open Bioinformatics Foundation</a> (OBF) Event Fellowship is open. Please submit your application before <strong>October 1, 2021</strong> (save a calendar reminder).</p> <p>Just announced: deadline extended to October 4, 2021!</p> <p><strong>Please apply via this Google application form: <a href="https://forms.gle/7ocmgvypiFHeFNfy7">https://forms.gle/7ocmgvypiFHeFNfy7</a>.</strong></p> <p>The OBF Event Fellowship program is aimed at increasing diverse participation at events promoting open science practices such as open source bioinformatics resource development and dissemination in the biological research community. These fellowships are available to support both in-person and remote (virtual) participation at events such as conferences, workshops, training courses or collaborative development sprints. See more details on <a href="https://www.open-bio.org/event-awards/">our webpage</a>.</p> <p>Like the previous three rounds, we are continuing to invite applications from individuals seeking financial support to attend or host virtual events.</p> <p>In the previous rounds, we have offered fellowships to participants in bioinformatics, open research and life science-related projects or conferences. This fellowship supported their participation as a speaker, poster presenter or new learners of these particular topics. You can <a href="https://www.open-bio.org/blog/">read blogposts</a> from their participation.</p> <p>If multiple members of a group are applying for this fellowship, please send your applications separately as the OBF Event Fellowship is aimed at supporting <strong>individual applicants only</strong>. For more information, please contact the OBF Event Fellowship chair by emailing: <a href="mailto:board@open-bio.org">board@open-bio.org</a>.</p>https://www.open-bio.org/2021/06/07/sona-charles-glbio2021/Mon, 07 Jun 2021 09:16:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/06/07/sona-charles-glbio2021/<p><em>The</em> <a href="https://www.open-bio.org/"><em>Open Bioinformatics Foundation (OBF)</em></a> <em>Event Fellowship program supports and encourages diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. <strong>Sona Charles</strong>, a Scientist (Bioinformatics) at ICAR-Indian Institute of Spices Research, India, was supported to participate in the</em> <a href="https://www.iscb.org/glbio2021"><em>Great Lakes Bioinformatics (GLBIO) 2021 Conference</em></a> <em>by this award granted to her in the application round-1 of 2021. Find more information</em> <a href="https://www.open-bio.org/travel-awards/"><em>here.</em></a></p> <p>In this pandemic stricken world when all conferences are taking place virtually and don’t require traveling, it has become more accessible for international participants like me. However, the cost for registration, video-conferencing accessories and childcare remain the same. Luckily, I came across the Open Bioinformatics Foundation Event Fellowship, when I was hoping to attend the Great Lakes Bioinformatics (GLBIO) 2021 Conference. I had already submitted a poster entitled “ <a href="https://doi.org/10.5281/zenodo.4892737">Sequence-Based Prediction of Phytophthora- Host Interaction Using Machine Learning Methods</a>” to the conference, which was accepted. I went ahead and applied for the event fellowship at Open Bioinformatics Foundation for its first round of 2021. Two weeks later (after the application review phase), I was informed by the Chair of OBF Event Fellowship that I was awarded the fellowship.</p> <p><strong>Day 1 of GLBIO 2021</strong></p> <p>The GLBIO conference commenced on 13 May 2021 with the workshops, which is undoubtedly my favourite attraction for attending a conference. Out of all the options for workshops, I chose two: (1) Machine Learning on Microbiome Data: Theory and Practice and Introduction to Deep Learning, and (2) Creating Neural Networks in Python and R. All the code for the workshop as well as the required packages were shared much earlier so that it would be easy for us to follow. As a beginner in Machine Learning, the two workshops enabled me to gain more knowledge on the topics in which I anticipate working in the coming days.</p> <p><strong>Day 2 of GLBIO 2021</strong></p> <p>The keynote talk “Variable Selection and Interpretability in ‘Black Box’ Statistical models” took place on 14 May 2021 by Dr Lorin Crawford (screenshot of his title slide below). He introduced the various concepts in Biologically Annotated Neural Networks and their applications in Multiscale genomic inference.</p> <p><img src="https://lh4.googleusercontent.com/WeQrTCiB2bemdNwLL-5FM79AzlwyPtZCoXnminBihW6i6rhaLigy9tXqkTpHfUOkijtLEOmALm7Oqt5s3ZHYr5vGaVWW7A36Mn2q5YEyCE1_gJ56xKcSkvz69oLGEA" alt=""></p> <p>On the same day, I attended four sessions on Knowledge Guided Machine Learning (KGML) in Bio. As a beginner in this area, I really appreciated this session and wanted to learn more about the applications. The session-1 included two talks on predicting the promiscuity of enzymes and Predicting RNA Pseudouridine Sites in Nanopore Sequencing Data. The session-2 included the talks “Knowledge-based Meta-Learning for Cancer Prediction and Survival Analysis” and “Learning to align with differentiable dynamic programming” by Aidong Zhang and Michiel Stock respectively. The session-3 had three informative talks on new machine learning approaches for estimating the functional consequence of mutations in diverse human populations, for diagnostic screening of cardiovascular disease using gut microbiome data and for gut microbiome-based detection of inflammatory bowel diseases. The final session included three talks: (1) Gene signatures of COVID-19 infection severity identified using graph convolutional neural networks on single-cell RNA-Seq data, (2) Machine learning on knowledge graphs and ontologies, and (3) Supervised prediction of ageing-related genes from a weighted dynamic protein-protein interaction network. An EDI panel survey discussion was held between the sessions followed by the poster session. Day 2 of the conference was highly informative and I had a lot of take-home messages and ideas.</p> <p><strong>Day 3 of GLBIO 2021</strong></p> <p>Day 3 started with the keynote lecture titled “Methodological advancements to improve metagenomics for surveillance of antimicrobial resistance” by Dr Noelle Noyes (screenshot from her talk).</p> <p><img src="https://lh4.googleusercontent.com/y3iL0NIlPhJFqjIvLeK8x553_Zlz5_stKXGwU8pznhXzJmYmRQlq2KO5-GZzqT3z7qslQr6fQFWO2pSe_wMBZQsOpqK-Y1jsA-nGfG1w4aSbNfS0JRBagemy3sjnxg" alt=""></p> <p>Metagenomics is one of the areas of interest in my research institute and I attended the Microbiome and Multi-omics analysis sessions. I also attended two sessions on Algorithms and Machine Learning. Another keynote by Michael Osterholm attracted the attention of researchers interested in SARS-Cov2 epidemiology.</p> <p><img src="https://lh3.googleusercontent.com/E0I0-6uZ-72zSTn3dj8R7WXxKlft0krCa9_k7RDLUHhGzflmQyDjvvXQ3WUA9RqYOHurfCu_f9aEyUmkbFtu1gB8Mvv66G0OCM1YYAgm2niq3BJdqgq_x34ECmzUAA" alt=""></p> <p>It was followed by a session on SARS-CoV2 analysis and a session on proteomics and metadata. The last keynote of GLBIO2021 was on Predicting the evolution of syntenies with closing remarks by Aïda Ouangraoua.</p> <p>On Day-3, a second poster session was organised where I presented my work titled “ <a href="http://doi.org/10.5281/zenodo.4892738">Sequence-based prediction of Phytophthora-host interaction using machine learning</a>” (Sona Charles, &amp; Sreekumar J., 2021, DOI: 10.5281/zenodo.4892738). I got to interact with many researchers and receive feedback from a global audience working in the area of machine learning.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2021/06/image-2.png" alt="">Screenshot of the top section of my poster titled: Sequence-based prediction of Phytophthora-host interaction using machine learning, available on Zenodo under CC-BY 4.0 license, <a href="http://doi.org/10.5281/zenodo.4892738">http://doi.org/10.5281/zenodo.4892738</a></p> <p>Overall the conference was excellent and all data of the conference will be available as an open source resource on YouTube on the <a href="https://www.youtube.com/channel/UCN9kqT7pfOzZddPJHqWSuyA">ISCB TV channel</a>. I am extremely thankful to the OBF for funding my participation related cost for the conference. I will be able to cover my registration and connection related costs. Since the conference was conducted during lockdown it would have been practically impossible for me to attend the conference if the childcare grant was not awarded for the entire duration of the conference. Since the time zones were overlapping from 21:30 to 03:00 Indian Standard Time (IST), child care was the most essential resource for me for attending the conference throughout the night.</p> <p>I express my heartfelt thanks for the opportunity to present my research at a reputed international conference with the support of the OBF Event Fellowship. As part of this fellowship, I will soon be depositing my work in my GitHub repository, developed under a CC-BY license ( <a href="https://github.com/sonacharles">GitHub</a>).</p>https://www.open-bio.org/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/2021/02/15/seeking-volunteers-for-obf-2021/Mon, 15 Feb 2021 19:02:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/15/seeking-volunteers-for-obf-2021/<p><em>TL;DR: Nominate candidates or yourself for the OBF board via this <a href="https://forms.gle/PJZLoPXGqKQsEYGJA">form</a> or work with OBF in other volunteer capacities.</em></p> <p><strong>Nominations are welcome for the OBF Board</strong> <strong>election</strong></p> <p>OBF is committed to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The roles and functions of OBF have evolved over the last 20 years, and currently include:</p> <p>- hosting and sponsoring the annual events, Bioinformatics Open Source Conference - running open source events like CodeFests and Google Summer of Code (GSoC) - offering Event fellowships to promote diversity of underrepresented community members at open source events - onboarding and supporting OBF member projects by providing financial management support (e.g., reimbursements and payments and advertising) - maintaining OBF website, social media and newsletter for information dissemination - advocating through policy and public statements</p> <p>OBF board members are elected through public nomination and voting. As board member Yo Yehudi (see <a href="https://www.open-bio.org/2021/02/12/title-would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/">this post</a>) reaches the end of her term, we are reflecting on the need to recruit new and more diverse board members.</p> <p>In particular, we would like to invite members from low-tech/low-income communities or historically marginalised groups to bring new perspectives to the OBF community and highlight new areas of interest. Elected members of the OBF Board will be instrumental in steering OBF’s work to address urgent challenges and needs in open source bioinformatics communities that we might not have yet recognized.</p> <p>If the OBF’s goals and values resonate with you, we encourage you to nominate yourself or someone else (please check with them first!) who would be a good addition to the OBF board. Please fill out this form by 1 April 2021: <a href="https://forms.gle/PJZLoPXGqKQsEYGJA">https://forms.gle/PJZLoPXGqKQsEYGJA</a>.</p> <p>An election for new board members will be held at the next public board meeting (around May or June 2021 - exact data will be announced soon).</p> <p><strong>Working with OBF in other volunteer capacity</strong></p> <p>In addition to the projects mentioned earlier, we are grateful to the members of the OBF community who participate in other community initiatives including (but not limited to) organising BOSC annually, handling GSoC mentorship activities and building capacity (skill development and training) and advocacy around open source in bioinformatics.</p> <p>These tasks could not have been accomplished without the support of our community members. If you would like to be involved in OBF but don’t want to nominate yourself for a position on the Board, we would be delighted talk to you about how you could get involved with these or other projects:</p> <p>- <a href="https://github.com/obf/newsletter">Curate and edit our quarterly (approximately) newsletter</a>, time commitment approximately 4 hours per issue - Help maintain and update our website: <a href="https://www.open-bio.org">https://www.open-bio.org</a> (WordPress, HTML, CSS skills) - Help manage our social channels (such as <a href="https://twitter.com/obf_news">Twitter</a>) - <a href="https://www.open-bio.org/events/gsoc/">Become a GSoC</a> mentor or organisation admin - Volunteer at the Bioinformatics Open Source Conference</p> <p>We appreciate that many of these roles may be new to you and we would offer mentorship and support if it is your first time occupying this type of position - please don’t feel that inexperience should stop you from applying!</p> <p>OBF also offers support for individuals and groups to promote open source practices and build bioinformatics skills. Here are a few opportunities that you can benefit from:</p> <p>- <a href="https://www.open-bio.org/event-awards">Apply for the OBF Event fellowship</a>, 2 deadlines on 1 April and 1 October 2021 - <a href="https://www.open-bio.org/membership">Become an OBF member to participate in the community</a> - Apply to become an affiliate project by discussing with the board ( <a href="https://www.open-bio.org/projects/#affiliated-projects">see currently affiliated projects</a>) - Apply for the OBF Grassroots Event Sponsorship (will be announced soon)</p> <p>We would also love to hear your ideas for how you could help boost OBF’s commitments to:</p> <p>- representing interests of bioinformatics and open source communities from developing countries - onboarding member projects from low and middle-income backgrounds - supporting individuals and communities who are contributing to policy development - boosting grassroots projects that can benefit from OBF’s support - spreading awareness of OBF Event Fellowship and affiliation programs</p> <p>Sound interesting? If so, please get in touch with the board by emailing <a href="mailto:board@open-bio.org">board@open-bio.org</a>. If you want more information, or want to talk to one of us about being on the board or in the OBF community in general, see the <a href="https://www.open-bio.org/board/">OBF Board page</a> for contact information.</p>https://www.open-bio.org/2021/02/12/would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/Fri, 12 Feb 2021 15:46:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2021/02/12/would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/<p>About three years ago I nervously responded to a <a href="https://www.open-bio.org/2017/11/14/obf-visioning-2017/">blog post from the OBF looking for board member applications</a> from people who were interested in leading open science related initiatives. This went as well as I possibly could have hoped - both myself and the other applicant, Bastian Greshake Tzovaras, <a href="https://www.open-bio.org/2018/03/20/welcome-to-our-new-board-members/">officially joined the board in March of 2018</a> for a three-year term.</p> <p>Over the last (nearly) three years, I’ve learned a lot and have participated in many OBF activities I can be proud of. We launched <a href="https://www.open-bio.org/2018/11/05/new-obf-logo/">a new community-designed OBF logo</a> (special thanks to Aleix Lafita-Masip and all the others who contributed!), I mentored the fabulous Deepashree Deshmukh, an <a href="https://www.outreachy.org/">Outreachy</a> intern, to migrate the OBF website from its old mediawiki-based format onto <a href="https://www.open-bio.org/2019/04/08/goodbye-mediawiki-hello-new-website/">a shiny new Wordpress site</a>, I joined the OBF GSoC org admin team alongside Sarthak Sehgal, and we launched <a href="https://github.com/obf/newsletter">an OBF newsletter</a>. We’re still working on preparing an OBF Code of Conduct, which hopefully will be launched soon.</p> <p>As I will step down from the board at the end of my term, I’d like to imagine that my replacement(s?) on the board will achieve even more significant impact. I’d also like to see the OBF leadership become more representative of bioinformatics as a whole, and all the different places and walks of life that bioinformaticians, open source coders, community managers, documentation writers, program managers, and other open science enthusiasts come from.</p> <p>As such, I am excited to announce that the OBF is seeking applications for new board members. If you would like to apply to join the leadership for an organisation that can make a difference in our community, that runs a fantastic yearly conference (BOSC), and has a budget to support fellowships and member projects - <a href="https://www.open-bio.org/2021/02/15/seeking-volunteers-for-obf-2021/">please do apply</a>. I’d especially like to encourage applications from people outside who were born and/or live outside Europe or the United States - we haven’t had enough of your voices in the OBF leadership team to date and I’m certain you would add significant value to the team. I’m also very happy to answer informal queries at a personal level if it helps - feel free to ping me at yochannah [at] gmail dot com.</p>https://www.open-bio.org/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/2020/05/08/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/2020/02/17/travel-fellowship20-round1/Mon, 17 Feb 2020 09:00:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/02/17/travel-fellowship20-round1/<p>We are currently accepting applications for the <strong>first application round for the <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> 2020</strong>. This fellowship aims to promote the conference/event participation of attendees who advocate and present their work related to open-source bioinformatics software development and open science in the biological research community. In 2019, a total of 9 applicants received OBF travel fellowships to attend various conferences across the globe to present their work, gain new skills and promote Open Science practices in their respective areas of life science.</p> <p><strong>Apply for <a href="https://docs.google.com/forms/d/e/1FAIpQLScCYMt_Id9FSKzHtOxyBgiOIXa61CLiveqh5JLx5rQsFoW8fA/viewform">round 1 of 2020 here</a>.</strong></p> <p><img src="https://www.open-bio.org/wp-content/uploads/2020/02/open-1-1-3.jpeg" alt=""></p> <p>(Image on <a href="https://unsplash.com/photos/ZYBl6VnUd_0">Unsplash by @timmossholder</a>)</p> <p>If you are unsure of your eligibility for this fellowship or want to understand the fellowship process better, check the details on our <a href="https://www.open-bio.org/travel-awards/">website</a> and read <a href="https://www.open-bio.org/category/travel-fellowship/">blog posts of past recipients</a>.</p> <p>The <a href="https://www.open-bio.org/events/bosc/">Bioinformatics Open Source Conference (BOSC)</a> will be joining the Galaxy Community Conference at <a href="https://bcc2020.github.io/">BCC2020</a> - the Bioinformatics Community Conference. The main conference will take place from 19 to 21 July 2020 at <a href="https://bcc2020.github.io/location/">Victoria University in Toronto, Canada</a>. The optional pre-conference training day will be 18 July and the CoFest and CoFest Encore days will span from 22 to 25 July. Registration for BCC2020 will open in March 2020 ( <a href="https://bcc2020.github.io/Registration/">see details</a>).</p> <p>The fellowship application deadline for this round is <strong><a href="https://www.timeanddate.com/countdown/to?iso=20200401T23&amp;p0=63&amp;font=cursive&amp;csz=1">1 April 2020, midnight in any part of the world</a></strong>. Those who plan to attend BCC2020 or other conferences related to open source / open science, and whose presence would promote diverse skills and perspectives, are encouraged to <a href="https://www.open-bio.org/travel-awards/">apply</a>.</p>https://www.open-bio.org/2020/01/14/obf-board-elections-december-2019/Tue, 14 Jan 2020 16:47:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2020/01/14/obf-board-elections-december-2019/<p>During the <a href="https://github.com/OBF/obf-docs/pull/71">public OBF Board Meeting held on December 17, 2019</a>, elections were held for five <a href="https://www.open-bio.org/board/">Board members</a> whose terms were about to expire. All five stood for re-election to the Board, though with some changes of officers:</p> <ul> <li>Hilmar Lapp: stepped down after 8 years as President of the Board; elected to At-Large seat.</li> <li>Peter Cock: elected as President of the Board.</li> <li>Heather Wiencko: elected as Treasurer, replacing previous Treasurer Peter Cock.</li> <li>Chris Fields: re-elected as Secretary.</li> <li>Nomi Harris: re-elected as At-Large Board member.</li> </ul> <p>In accordance with the <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">OBF Bylaws</a>, the newly elected Board members and officers will serve a three-year term.</p> <p>The Board thanked Hilmar for his many years as President. Hilmar oversaw or supported many major changes including moving to SPI as a fiscal sponsor, introduction of the Travel Fellowships, and our ongoing work to introduce a code of conduct and formalise our affiliate project policy. We are grateful that Hilmar will continue to contribute to the Board as a member at large.</p>https://www.open-bio.org/2019/11/15/creating-an-obf-wide-code-of-conduct/Fri, 15 Nov 2019 22:14:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/11/15/creating-an-obf-wide-code-of-conduct/<p>Among the core values shared across the OBF community are inclusiveness and welcoming newcomers to contribute, without discrimination. Every year at BOSC, when we ask who is at BOSC for the first time, about half of the audience&rsquo;s hands go up. To signify the importance of this, both to existing and prospective community members, BOSC successfully advocated several years ago for ISMB to adopt a Code of Conduct by ISMB (which applies to BOSC when it is held as part of ISMB).</p> <p>In the near future, OBF plans to adopt an Affiliated Project Policy to provide a transparent and documented mechanism for other open-source projects to formally join the OBF umbrella. To ensure that our larger community supports our core values, a project wishing to join will have to have, or adopt, a Code of Conduct (CoC) aligned with ours. This means that we need to document what our OBF-wide CoC is, i.e., the expectations in conduct that we want to hold ourselves accountable to across our member projects and their communities, whether at BOSC or not.</p> <p>This is in fact not the first time an official CoC has been requested outside the context of BOSC from within our project communities. Interest has been expressed both within member projects (such as Biopython), and in-person at our public board meeting at BOSC 2019. We have now begun an initiative to create, and ultimately get adopted, a Code of Conduct covering both our in-person events (BOSC, CoFest, GSoC meetings, etc) and our online activities (mailing lists, GitHub threads, Gitter conversations, etc), including those of our current and future member projects. We invite our community to engage and provide feedback.</p> <p>Thanks to the work of many other open-source communities, we don’t have to start from scratch. Specifically, having reviewed multiple existing CoC documents, one strong candidate for us is <a href="https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html">The Carpentries Code of Conduct</a>. Another one might be <a href="https://ropensci.org/code-of-conduct/">rOpenSci’s</a>.</p> <p>The OBF would provide member projects and BOSC with a somewhat external CoC point of contact for reporting and tracking any issues, and ensure training as needed. Any new member project would be able to take advantage of this CoC automatically applying to their work and interactions.</p> <p>We welcome suggestions for how to best handle any CoC violation against the OBF board itself, such as a reciprocal arrangement with another society. The Carpentries has a designated ombudsperson in this role.</p> <p>When we hold joint meetings with other organizations (such as BOSC with ISMB or Galaxy) we would expect that a single Code of Conduct is explicitly selected, and applied to the conference.</p> <p>We are inviting feedback on <a href="https://github.com/OBF/obf-docs/issues/67">this GitHub issue</a>, or email privately <a href="mailto:board@open-bio.org">to the board</a> ( <a href="mailto:board@open-bio.org">board@open-bio.org</a>), <strong>by December 1st</strong>, allowing time to put a draft CoC to formal approval at the OBF public board meeting on December 17, 2019, and then OBF member approval by ballot, followed by adoption by the member projects.</p>https://www.open-bio.org/2019/09/30/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/2019/08/17/malvika-sharan-elected-to-obf-board/Sat, 17 Aug 2019 13:36:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/17/malvika-sharan-elected-to-obf-board/<p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/Malvika-cropped-1.jpg" alt="Photo of Malvika Sharan"> At the OBF’s July 2019 <a href="https://www.open-bio.org/2019/08/16/obf-public-board-meeting-july-2019/">public Board meeting</a> (held at BOSC 2019), Malvika Sharan was unanimously elected as a new at-large Board member. Malvika, who earned a PhD in bioinformatics at the University of Würzburg, is a community outreach coordinator at the European Molecular Biology Laboratory (EMBL), Heidelberg. She is passionate about promoting the inclusion of historically underrepresented groups in bioinformatics and STEM in general. Malvika recently won a fellowship from the <a href="https://software.ac.uk/programmes-and-events/fellowship-programme">Software Sustainability Institute</a> to support her research into identifying and developing effective training strategies in low-income research environments (limited resources, lack of funding, etc.). She was also a recipient of an <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> that helped defray her cost of attending BOSC.</p> <p>As a new OBF Board member, Malvika looks forward to helping the organization undertake more efforts to grow and support a vibrant, diverse open science community.</p> <p><img src="https://www.open-bio.org/wp-content/uploads/2019/08/OBF-Board-July-2019-1.jpg" alt="Photo of OBF Board members, July 2019"> Above: OBF Board members Malvika Sharan, Nomi Harris, Bastian Greshake Tzovaras, Hilmar Lapp, Yo Yehudi, Heather Wiencko, Peter Cock. (Not shown: Chris Fields)</p>https://www.open-bio.org/2019/08/16/obf-public-board-meeting-july-2019/Fri, 16 Aug 2019 03:55:21 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/16/obf-public-board-meeting-july-2019/<p>On July 25, 2019, the OBF held a public Board meeting in Basel, Switzerland. Organized as a Birds of a Feather session at BOSC 2019, the meeting was open to all attendees at ISMB. All but one of the current Board members were present (Secretary Chris Fields called in), as well as a number of ISMB/BOSC attendees. At the meeting, Malvika Sharan was elected as a new Board member. Other topics of discussion included the need for a Code of Conduct that applies to member projects as well as covering the yearly BOSC meeting; the policy for accepting new member projects; revisiting the OBF’s mission statement; and considering whether the OBF should issue position statements. The meeting minutes are <a href="https://github.com/OBF/obf-docs/blob/master/minutes/2019-July.md">here</a>. There will be another public Board meeting near the end of 2019 to vote on Board members whose terms are ending.</p>https://www.open-bio.org/2019/08/07/travel-fellowship-deadline-august-15-2019/Wed, 07 Aug 2019 23:12:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2019/08/07/travel-fellowship-deadline-august-15-2019/<p>The <a href="https://www.open-bio.org/travel-awards/">OBF Travel Fellowship</a> program, established in 2016, aims to increase diverse participation at events related to open source bioinformatics. Applications are reviewed three times a year. Applicants may apply for attending any event that develops or promotes open source development and open science in the biological research community. It doesn’t have to be an OBF-related event, and it can be one that you already attended in the recent past. For example, if you attended BOSC 2019 and your travel expenses were not covered by your employer or university, you could apply for a travel fellowship to help defray those expenses (up to a maximum of $1000, in most cases). Travel fellowship awardees are required to write a blog post about their experience attending the event; you can see some past such posts on our <a href="https://www.open-bio.org/tag/travel-fellowship/">blog</a>.</p> <p>The next application deadline is August 15, 2019. We encourage you to apply if you are attending an event that promotes open source bioinformatics software development or open science, and your participation will contribute to diversity in the wider community.</p>https://www.open-bio.org/2019/04/08/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/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/2018/05/25/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/2018/04/24/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/2018/03/20/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/2018/01/30/arun-decano-awarded-obf-travel-fellowship/Wed, 31 Jan 2018 00:40:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2018/01/30/arun-decano-awarded-obf-travel-fellowship/<p><img src="https://news.open-bio.org/wp-content/uploads/2018/01/ArunDecano_profile-300x300.jpg" alt="Arun Decano"> Arun Decano is a PhD research fellow in the Infection Genomics Group at Dublin City University in Dublin, Ireland. Her research, with advisor <a href="https://www.dcu.ie/biotechnology/people/tim-downing.shtml">Dr. Tim Downing</a>, focuses on the phylogenomic study of a multidrug-resistant bacterial population and aims to develop novel infection control strategies using whole genome sequence data.</p> <p>The Open Bioinformatics Foundation awarded Ms. Decano a <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">travel fellowship</a> to help defray the cost of attending the European Galaxy Administrator Workshop ( <a href="https://www.elixir-europe.org/events/european-galaxy-administrator-workshop">https://www.elixir-europe.org/events/european-galaxy-administrator-workshop</a>) in January 2018.</p> <p>The <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship</a> program was launched in 2016 to help increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The next application deadline will be April 15, 2018—see <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md</a> for information and to apply.</p>https://www.open-bio.org/2017/12/15/mailing-list-consolidation/Fri, 15 Dec 2017 19:52:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/12/15/mailing-list-consolidation/<p>The OBF&rsquo;s self-hosted <a href="https://news.open-bio.org/2017/11/12/mailing-list-outage-and-public-board-meeting-update/">mailman server is still struggling</a> right now, so we are looking at migrating the active mailing lists to paid hosting, and as part of this consolidating down to ideally about a dozen mailing lists. Currently we have a <em>lot</em> of mailing lists, but many are dormant or redundant.</p> <p>Some were announcement specific, where nowadays blogs and Twitter work quite well. Others were development specific (including automatic commit logs from central source code repositories), but now most OBF Project discussions are on GitHub. While the main project mailing lists used to have a lot of user support traffic, much of that has moved to external Q&amp;A style sites like BioStars, StackExchange, or StackOverflow. What this means is that the OBF software projects probably only need a single mailing list each.</p> <p>Based on <a href="http://mailman.open-bio.org/mailman/listinfo">http://mailman.open-bio.org/mailman/listinfo</a> here are the current publicly listed OBF hosted mailing lists.</p> <p>Miscellaneous active public lists (propose to retain in some form):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bosc-announce/">Bosc-announce</a> - BOSC meeting announcements and updates ( <a href="http://mailman.open-bio.org/pipermail/bosc-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/gsoc/">GSoC</a> - OBF mentors and students for Google Summer of Code ( <a href="http://mailman.open-bio.org/pipermail/gsoc/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/open-bio-l/">Open-Bio-l</a> - Open Bioinformatics Foundation cross-project dev discussion ( <a href="http://mailman.open-bio.org/pipermail/open-bio-l/">archive</a>)</li> </ul> <p>Miscellaneous active but non-public lists (propose to retain in some form):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioinfo-core/">bioinfo-core</a> - Managers, Staff, and Scientists of Bioinformatics, Data Science and Research IT core facilities ( <a href="http://mailman.open-bio.org/mailman/private/bioinfo-core/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/gsoc-mentors/">Gsoc-mentors</a> - GSoC - mentors only ( <a href="http://mailman.open-bio.org/mailman/private/gsoc-mentors/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/members/">Members</a> - Communication channel to OBF members ( <a href="http://mailman.open-bio.org/mailman/private/members/">private archive</a>)</li> </ul> <p>BioPerl (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bio-phylo-l/">Bio-phylo-l</a> - BioPerl Phylogenetics modules ( <a href="http://mailman.open-bio.org/pipermail/bio-phylo-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-announce-l/">BioPerl-announce-l</a> - Bioperl Project Announcements ( <a href="http://mailman.open-bio.org/pipermail/bioperl-announce-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-dev/">bioperl-dev</a> - BioPerl Developer Core ( <a href="http://mailman.open-bio.org/pipermail/bioperl-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-guts-l/">BioPerl-guts-l</a> - BioPerl internals &amp; bug reports ( <a href="http://mailman.open-bio.org/mailman/private/bioperl-guts-l/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l/">BioPerl-l</a> - Bioperl Project Discussion List ( <a href="http://mailman.open-bio.org/pipermail/bioperl-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-microarray/">bioperl-microarray</a> - Microarrays in BioPerl ( <a href="http://mailman.open-bio.org/pipermail/bioperl-microarray/">archive</a>)</li> </ul> <p>BioJava (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev/">BioJava-dev</a> - BioJava developers list ( <a href="http://mailman.open-bio.org/pipermail/biojava-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l/">BioJava-l</a> - Biojava discussion list ( <a href="http://mailman.open-bio.org/pipermail/biojava-l/">archive</a>)</li> </ul> <p>Biopython (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biopython/">Biopython</a> - Biopython discussion list ( <a href="http://mailman.open-bio.org/pipermail/biopython/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-announce/">Biopython-announce</a> - Biopython announcements and news ( <a href="http://mailman.open-bio.org/pipermail/biopython-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev/">Biopython-dev</a> - Biopython Developers List ( <a href="http://mailman.open-bio.org/pipermail/biopython-dev/">archive</a>)</li> </ul> <p>BioRuby (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioRuby/">BioRuby</a> - BioRuby Project Discussion List ( <a href="http://mailman.open-bio.org/pipermail/bioruby/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioruby-cvs/">BioRuby-cvs</a> - BioRuby CVS commit notices ( <a href="http://mailman.open-bio.org/pipermail/bioruby-cvs/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bioruby-ja/">BioRuby-ja</a> - BioRuby Project Discussion List (in Japanese) ( <a href="http://mailman.open-bio.org/pipermail/bioruby-ja/">archive</a>)</li> </ul> <p>BioSQL (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biosql-guts-l/">BioSQL-guts-l</a> - Commit and Bugzilla messages for BioSQL ( <a href="http://mailman.open-bio.org/pipermail/biosql-guts-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biosql-l/">BioSQL-l</a> - BioSQL Discussion List ( <a href="http://mailman.open-bio.org/pipermail/biosql-l/">archive</a>)</li> </ul> <p>EMBOSS (propose to merge to a single list):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss/">EMBOSS</a> - EMBOSS mailing list ( <a href="http://mailman.open-bio.org/pipermail/emboss/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss-announce/">emboss-announce</a> - EMBOSS Announcements (Releases, etc.) ( <a href="http://mailman.open-bio.org/pipermail/emboss-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss-bug/">emboss-bug</a> - EMBOSS Bug Reports and Support Requests ( <a href="http://mailman.open-bio.org/mailman/private/emboss-bug/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/emboss-dev/">emboss-dev</a> - EMBOSS Development Discussion (Open to all) ( <a href="http://mailman.open-bio.org/pipermail/emboss-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/private/emboss-submit/">emboss-submit</a> - EMBOSS submissions - new packages and apps ( <a href="http://mailman.open-bio.org/pipermail/emboss-submit/">private archive</a>)</li> </ul> <p>DAS (propose to merge to a single list, or close and archive):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/das/">DAS</a> - DAS discussion list ( <a href="http://mailman.open-bio.org/pipermail/das/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/das-announce/">DAS-announce</a> - DAS announcement list ( <a href="http://mailman.open-bio.org/pipermail/das-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/das2/">DAS2</a> - DAS2 Discussion List ( <a href="http://mailman.open-bio.org/pipermail/das2/">archive</a>)</li> </ul> <p>Dormant lists, including legacy projects (propose to close and archive):</p> <ul> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biobiz/">BioBiz</a> - Commercial aspects of open source life science code ( <a href="http://mailman.open-bio.org/pipermail/biobiz/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biocorba-announce-l/">Biocorba-announce-l</a> - BioCorba Announcements ( <a href="http://mailman.open-bio.org/pipermail/biocorba-announce-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biogroovy-l/">biogroovy-l</a> - biogroovy general discussion list ( <a href="http://mailman.open-bio.org/pipermail/biogroovy-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biolib-dev/">BioLib-dev</a> - BioLib Developers List ( <a href="http://mailman.open-bio.org/pipermail/biolib-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/biosoap-l/">Biosoap-l</a> - BioSOAP project ( <a href="http://mailman.open-bio.org/pipermail/biosoap-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/bP-announce/">bp-announce</a> - BioPathways Consortium Announcements ( <a href="http://mailman.open-bio.org/pipermail/bp-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-announce/">Moby-announce</a> - MOBY annoucements ( <a href="http://mailman.open-bio.org/pipermail/moby-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-dev/">MOBY-dev</a> - Core developer announcements ( <a href="http://mailman.open-bio.org/pipermail/moby-dev/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-guts/">MOBY-guts</a> - MOBY CVS Commits Log ( <a href="http://mailman.open-bio.org/pipermail/moby-guts/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/moby-l/">moby-l</a> - MOBY discussion list ( <a href="http://mailman.open-bio.org/pipermail/moby-l/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/obf-developers/">obf-developers</a> - Open-Bio.org members with developer access ( <a href="http://mailman.open-bio.org/pipermail/obf-developers/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/ontologies/">Ontologies</a> - Open Bio Ontologies list ( <a href="http://mailman.open-bio.org/mailman/private/ontologies/">private archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/open-bio-announce/">Open-Bio-Announce</a> - OBF announcements ( <a href="http://mailman.open-bio.org/pipermail/open-bio-announce/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/open-bioinformatics-foundation/">Open-Bioinformatics-Foundation</a> - OBF broadcast list ( <a href="http://mailman.open-bio.org/pipermail/open-bioinformatics-foundation/">archive</a>)</li> <li><a href="http://mailman.open-bio.org/mailman/listinfo/Volunteer/">Volunteer</a> - Open-Bio volunteer coordinator ( <a href="http://mailman.open-bio.org/mailman/private/volunteer/">private archive</a>)</li> </ul> <p>If this affects you directly (e.g. any project leaders we have not been able to contact yet), please write to the OBF board. Since mailman is currently unreliable, board at open-bio.org might not work. Please CC our fall back address of obf-board at Google Groups.</p> <p><strong>Update</strong>: Projects can also get in touch via this <a href="https://github.com/OBF/obf-docs/issues/42">GitHub issue</a>.</p>https://www.open-bio.org/2017/12/07/travel-fellowship-deadline-dec-15/Fri, 08 Dec 2017 00:25:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/12/07/travel-fellowship-deadline-dec-15/<p>The <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> was launched in 2016 to help increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. There are four application deadlines per year; the next will be <strong>December 15, 2017</strong>. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships. More information, including a link to the application form, can be found at <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md</a>.</p>https://www.open-bio.org/2017/11/21/bosc-2017-prague-land-of-stories/Tue, 21 Nov 2017 14:02:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/11/21/bosc-2017-prague-land-of-stories/<p><em>This is a guest blog post from Farah Zaib Khan, who was supported by the ongoing <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> to attend our annual conference BOSC 2017 and its preceding Codefest in Prague, July 2017. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 December 2017, you might want to apply?</em></p> <p>So the journey started back in May 2017 when I met <a href="http://www.commonwl.org/">Common Workflow Language (CWL)</a> co-founder,  <a href="https://orcid.org/0000-0002-2961-9670">Michael R. Crusoe</a> during his visit to our University ( <em>University of Melbourne</em>). I have been working with CWL team since 2015 but it was only then we met in person and discussed various aspects of the CWL standard and how we can collaborate to incorporate principles of Provenance modelling to capture retrospective provenance of CWL workflow enactments. We started working on an idea which led to <a href="https://f1000research.com/posters/6-1547">poster submission</a> and acceptance at <a href="https://www.open-bio.org/wiki/BOSC_2017">Bioinformatics Open Source Conference (BOSC) 2017</a>. I was excited as well as nervous (will explain how this changed later :) ). Excited because this was my very first time attending any BOSC and ISMB conference and nervous because of the feeling that the names that you see at the top of high quality research articles will be there and you get to meet and talk to world class scientists doing wonders.</p> <p>Nervous and excited I prepared for all the travelling which involved applying for a visa of course (going to Sydney for that) and arranging accommodation, conference registration, booking plane ticket and finally receiving the visa 7 days before my flight. The Czech Consulate was very professional and kind to process the visa in just 7 working days. I left Melbourne to attend 2-Day OBF Codefest followed by 2-Day BOSC and remaining ISMB conference. My Airbnb host was waiting for me when I reached and welcomed me warmly. She had the whole day planned for us as I reached at 9 am July 19th and the codefest had to commence on July 20th. She was keen to learn about my culture, home country, language and research too :). During the day we roamed around the City, had lunch and she shared information about the Czech history and how late 80&rsquo;s Velvet Revolution changed the economic conditions of the country.</p> <p>In the evening of my first day, I had a dinner with few members of Seven Bridges team and CWL working group (thanks to Michael for arranging this) at an amazing vegan restaurant in the  Old town. We kick started discussion of our work informally during dinner where SevenBridges team introduced their super cool open source toolkit, <a href="http://rabix.io/launch">Rabix</a> for describing the CWL tools workflows. I presented the idea of CWL provenance module which we had planned to work on during the OBF Codefest the very next day. Mostly it was getting to know the teams and getting ready for the next day while enjoying delicious dinner in the heart of Prague Old town.</p> <p>All geared up, next morning I took a subway from the station right next to Congress center to reach <a href="https://brmlab.cz/">Brmlab</a> which is a non-profit hackerspace self supported by community. The transport system of Prague is commendable as despite the signs written Czech, it was quite straight forward to follow Google maps and take the right subways, trams or buses. When I reached, <a href="https://twitter.com/chapmanb">Brad Chapman</a>, <a href="https://twitter.com/matuskalas">Matúš Kalaš</a> and others were already there making arrangements, providing enough extension cables, arranging food (with many vegan friendly options) and making sure everything is in place. There were more than 60 participants for this open collaborative event to build things and discuss future prospects of research together. The day kick started with introductions and organization into groups to work on related projects. This was followed by coffee and local produce (fruits, bread and pastries) break where people carried on with individual introductions and conversations.</p> <p>[caption id=&ldquo;attachment_1782&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;378&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2017/11/DSC_0553-300x169.jpg" alt=""> &ldquo;Breakfasting&rdquo; in open air outside the lab. Image was originally shared <a href="https://photos.google.com/share/AF1QipNQrGZitpC7yhTozyeX6dWnV5IZzhx1G-fJgkQWfvNpZiwj49qGmPN6azx5gJ7eLg?key=ZTJwdmtGdkV3dGlZWXlZYlg5a2hqaTNkMXRUWkVR">here</a>.[/caption]</p> <p>Various groups started working on different projects from 10 am to 1 pm. These projects include <a href="http://multiqc.info/">MultiQC</a>, <a href="http://biopython.org/">biopython</a>, <a href="https://www.nextflow.io/">nextflow</a>,  <a href="https://github.com/johnfonner/cwltool/tree/feature-singularity">Singularity support in CWL</a>,  <a href="https://github.com/common-workflow-language/cwltool/tree/provenance">Provenance support in CWL</a>,  <a href="https://github.com/common-workflow-language/python-cwlmodel">CWL SDK</a> and <a href="http://rabix.io/launch">Rabix</a>. Our group led by <a href="https://twitter.com/soilandreyes">Stian Soiland-Reyes</a> started working on Provenance analysis and had a very useful discussion about what to capture from a workflow run retrospectively and how to structure the Provenance of a CWL workflow run. To start with, we decided to include a provenance module in reference implementation <a href="https://github.com/common-workflow-language/cwltool/tree/master/cwltool">cwltool</a> developed by CWL team. Nervously I started but now it felt like home and we got to work during 10am-1pm work window. I had guidance through out this time by people around me and I would like to thank them once more :) .</p> <p>[caption id=&ldquo;attachment_1784&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;446&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2017/11/DSC_0582-300x169.jpg" alt=""> Work in Progress for 10am-1pm session[/caption]</p> <p>At 1 pm, we took a lunch break but before going for lunch break all the groups gathered and presented their progress so far. A round of applause for the organizers and sponsors who kept the supply of coffee running through out the day. The lunch was delicious pizza with local flavored soft drinks. Again all dietary requirements were accounted for and everyone seemed to enjoy &quot; <em>across-group</em>&quot; discussion and food. After lunch break the group gathered again and started working from 2 pm to 6 pm before leaving for the group dinner. We kept working on our project idea and all the groups reported at 6 pm presenting their progress and headed out for the group dinner. Our group stayed back as Brad graciously offered to stay back if someone wants to continue working. Luckily brmlab was also open 24/7 so we kept working till 9 pm. Late night dinner and headed to the apartment taking the same subway. The city was awake and happening even later in the night. At last the first very productive day came to an end.</p> <p>July 21st was the second and last day of the Codefest. On my way to brmlab, I stopped at <a href="https://www.copygeneral.cz/">Copy General</a> to get the print of my poster which was required to be displayed the next day. I must admit the staff at this shop was very professional and helpful. They made sure I get the right size of my poster (as it was in landscape orientation) and were quite flexible about the pick up time. Getting done with this important task, I was relaxed and headed to the lab for second day of codefest. The day followed the same pattern as July 20th starting with projects&rsquo; updates, plans to be followed for the day followed by coffee and breakfast. Our organizers collected some best quality local produce from a farmer&rsquo;s market and kept everything organized efficiently.</p> <p>We further worked on the implementation of a basic Research Object generation as a result of CWL workflow run. By the lunch time we were able to complete the set goals and presented out progress. Everyone was excited and engaged in working with their groups and contributing in every way they could. At 6 pm every group leader wrapped up their progress through out these two days and everyone participated in cleaning the space as it is a community-run space shared by everyone. At the end of these two amazing days, I looked back and realized I was nervous for nothing. As Brad Chapman says and  I quote <strong>&quot; <em>BOSC is all about getting people together and learning from each other&quot; .</em></strong></p> <p>I don&rsquo;t think anyone can disagree with this statement and the idea of community led projects and open source bioinformatic software feels real and in practice when one interacts and participates in events like OBF-Codefest and BOSC. The codefest ended with dinner at Zly cafe near the Congress center where the next four days are scheduled.</p> <p>[caption id=&ldquo;attachment_1787&rdquo; align=&ldquo;aligncenter&rdquo; width=&ldquo;482&rdquo;]<img src="https://news.open-bio.org/wp-content/uploads/2017/11/DSC_0614-300x169.jpg" alt=""> Dinner at Zly Cafe[/caption]</p> <p>New day, new tasks.. July 22nd was the first day of BOSC 2017 and at the same time all the posters were required to be hanged in the morning. I rushed to the copy general to collect my poster which was ready the same day. On my way to the shop I met loving and most friendly <a href="https://twitter.com/monimunozto">Monica Munoz-Torres</a> from UC Berkeley who was volunteering as part of organizing committee (presenting Apollo later as well) and was headed to the same copy center. We had good conversation about open source bioinformatics initiatives and her work as volunteer organizing BOSC which she calls her favorite conference :) .</p> <p>Rushed back to the Congress center, arranged the poster on its designated location along with 100s of amazing posters and headed to attend BOSC opening talks. I was impressed by OBF progression and their support for researchers by providing <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">OBF Travel scholarship</a> and participation in organizing Google summer code camps. Brad presented the summary of Codefest afterwards which had a slide we prepared for our part of work [Provenance Support in CWL]. There were many talks related to CWL application and usage during the whole day. Rabix composer, Rabix Executor, CWL Viewer, bcbio and many more CWL oriented work was presented. We organized a Birds of a feather session during lunch time to discuss <em>what should be captured in a Research Object when a CWL workflow is enacted</em>. This session initiated interesting discussion about different levels and views of Provenance.</p> <p>In the afternoon Björn Grüning&rsquo;s talk was very interesting where he empathized on <strong>Findability, Accessibility, Interoperability, and Reusability (FAIR)</strong> principles for tool deployment and resolving tool dependencies using package managers as Conda and BioConda. Later during this and next day <a href="https://twitter.com/search?q=%23BOSC2017%20FAIR%20bingo&amp;src=typd">FAIR bingo</a> became a real thing as part of most of the talks. The highlight of the day was indeed the key note speech <em>&ldquo;Open Sourcing Ourselves&rdquo;</em> by <a href="http://www.madeleineball.net/">Madeleine Ball</a> who is working on the project <a href="https://www.openhumans.org/">Open Humans</a>. She discussed inspiring Dana Lewis&rsquo;s story who is creator of &ldquo;Do-It-Yourself Pancreas System&rdquo; and made her own continuous glucose monitor alarms louder further leading to the foundation of OpenAPS.</p> <p>On the second day of BOSC, we had more talks and updates  starting with the key note speech &quot; <em>Bioinformatics for Personalized Medicine: Looking Beyond the Genome</em>&quot; by <a href="http://epigenomics.cemm.oeaw.ac.at/meg/">Christoph Bock</a>. He presented few examples from cancer research explaining how epigenomic mutations can be mapped to identify the various aspects of cancer. The topic was of my personal interest and indeed very informative. The ultimate goal is to make the dream of personalized medicine a reality using the available technologies including use of CRISPR for modelling epigenomic factors.</p> <p>After the key note speech I attended Monica Munoz-Torres&rsquo;s talk about <em><a href="http://apollo.berkeleybop.org/">Apollo</a></em>, collaborative genomic annotation editor that automatically synchronizes the work of geographically separated research community and establishes a network between the researchers, more like a social network for curators according to Monica. The huge user base working on different genomes interact using Apollo and share the curated genomes. The next talk by  Pjotr Prins was about <em>Journal of Open Source Software (JOSS)</em> , an initiative all available on <a href="https://github.com/openjournals/joss">GitHub</a> for accrediting academic software equipped with documentation.  In this way, software engineers can publish their software without getting to write a paper about it. It will facilitate the users as the software will be better documented when intended to be published.</p> <p>Another impressive talk was about &quot; <em>Distance-based, online bioinformatics training in Africa: the H3ABioNet experience&quot;</em> by Nocola Mulder from University of Cape Town. She described the efforts made to bring bioinformatics training to all the places in Africa using a distributed classroom model. Due to internet connectivity issues and other factors, the lectures were recorded beforehand. The lectures were delivered live (online) as well but if there is a connectivity issue, the recordings were available. In addition, various practical assignments were designed to enhance the learning experience. The combination of live lectures, online classes, recordings and practical exercises together results in connectivity and highly interactive environment. Another highlight from the session was release of open source variant calling toolkit <a href="https://software.broadinstitute.org/gatk/download/beta">GATK4</a> coupled with <a href="https://software.broadinstitute.org/wdl/">WDL</a> and Cromwell.</p> <p>There were many more talks that I attended and enjoyed such as talk by Ted Liefeld about <a href="http://www.genomespace.org/">GenomeSpace</a>, Kai Blin about <a href="https://bitbucket.org/antismash/antismash">anitSMASH</a> and Kenzo-Hugo Hillion about <a href="http://docs.biothings.io/en/latest/">BioThings SDK</a>. Oh and during lunch time I attended the BoF session organized by JOSS (was intrigued after listening to the presentation earlier). Later in the day, the panel discussion was worth attending chaired Madeleine Ball, Prof. <a href="http://www.manchester.ac.uk/research/Carole.goble/">Carole Goble</a>, <a href="http://sulab.org/">Andrew Su</a> and <a href="http://lab.loman.net/">Nick Loman</a>. Carole Goble&rsquo;s point made perfect sense that the young scientists although are willing to share the data and are open to collaborations where as senior scientists (PIs) consider it more effort  with less rewarding results.</p> <p>Day 2 ended with an amazing closing key note speech by <a href="http://lab.loman.net/">Nick Loman</a> who discussed  virus outburst surveillance using the Oxford nanopore minION sequencing technology, using two examples, namely Ebola outburst in Africa in 2015 and the Zika virus in Brazil. &ldquo;If you can&rsquo;t move the subjects and samples to the sequencer, bring the sequencer to the subject&rdquo;.</p> <p>Oh wait the day actually ended with an end of BOSC dinner ..</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/11/DFcPys3WsAIhebp-169x300.jpg" alt=""></p> <p>but before that we stopped at <a href="https://academic.oup.com/gigascience">GigaScience</a>&rsquo;s 5th birthday for cake and free GOT themed <em>&ldquo;Data is coming&rdquo;</em> T shirt which they graciously saved ^_^  (because I reached late). Why did I reach late?</p> <p>Yes I was there for a poster presentation :) . The poster presentation was from 6-7 pm and was a terrific experience talking about my work and progress we made during code fest earlier.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2017/11/21294979_893002990907345_5610908708142841856_n-300x300.jpg" alt=""></p> <p>All in all, everything was amazing, the people, the venue, the city, the knowledge gain, the help you get from peers, the encouragement from fellow researchers. Remember the  nervousness I mentioned at the beginning of this post ? ALL GONE after this fruitful experience. Few things that might be helpful in future: We should work towards resolving the issue of gender imbalance that was seen (and usually seen in conferences), discussed and acknowledged during Code fest and BOSC.  I think we can advertise the Codefest and the objectives in more detail so people can attend even if they don&rsquo;t have a group there to start with. This is by no means a complaint or criticism, just something I observed and felt as there were 3 female participants out of &gt;60 total participants of Codefest. I think in future we can make this better and advertise about the welcoming environment of Codefest and BOSC.</p> <p>Thanks to <a href="https://www.open-bio.org/wiki/Main_Page"><strong>OBF</strong></a> for covering my air fare by refunding through OBF travel funding. I would also like to thank <a href="http://daspos.org/">Data and Software Preservation for Open Science</a> ( <strong>DASPOS</strong>) (working in developing workflow and provenance tracking for high energy physics) for covering the rest of conference related expenses . In the end, this post will be incomplete if I don&rsquo;t thank <em>Michael Crusoe</em> for the mentoring, encouragement, guidance, all the support, connecting me with DASPOS and providing prompt feedback whenever I ask :) .</p> <p><strong><em>Need a shorter version and more pictures</em></strong>?? &ndash;&gt; <a href="//storify.com/farahzk03/bosc-2017-in-the-land-of-stories">View the story &ldquo;BOSC-2017 in the Land of stories&rdquo; on Storify</a></p> <p>P.S. Some other day, I might write about wandering experience in Prague Castle, Old Town, Charles Bridge, local wooden sovereigns, amazing food especially Goats cheese and of course&hellip; lemonades :) .</p>https://www.open-bio.org/2017/11/14/obf-visioning-2017/Tue, 14 Nov 2017 17:08:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/11/14/obf-visioning-2017/<p>TL;DR: The OBF isn&rsquo;t doing enough in public policy and advocacy around Open Science, and we are looking to recruit a new board member who is interested in this role. Is that you? If yes, then <a href="mailto:obf-board@googlegroups.com">contact us</a>.</p> <hr> <p>At our October meeting, the OBF board took some time to think broadly about the OBF, current and future. We tried to answer the questions: What do we say we do? What do we actually do? What more do we wish we could do? We re-read our mission statement and list of public activities from the <a href="https://www.open-bio.org/wiki/Main_Page">OBF main page</a>, listed the current efforts of the board members and affiliates, and assessed how our actual work aligned with the stated goals of the organization. This was motivated by having board members who are new-ish to the OBF, as well as upcoming board elections.</p> <p>Our general mission is fairly broad (&ldquo;promoting the practice and philosophy of Open Source software development and Open Science within the biological research community&rdquo;). We aim to do this through running / sponsoring BOSC and other open source events (codefests and Google Summer of Code); running a travel fellowship program; managing servers, mailing lists, domain names and other assets for our member projects; and by advocacy through policy and public statements.</p> <p>With BOSC being our flagship event, it is not surprising that about 50% of our board time is spent on organizing this meeting, with our remaining effort about equally focused on the travel fellowship, server / domain management, and financials.</p> <p>What more could we be doing? OBF could help facilitate other events, as we do for Google Summer of Code (GSoC). In this model, the board does not directly run the event, but instead provides support with financial management (e.g., reimbursements and payments) and advertising, while the hands-on organization is done by non-board members. In the case of GSoC, Kai Bin has been the OBF GSoC administrator for the past couple of years (thanks, Kai!). So, even though the board members don&rsquo;t have bandwidth to organize other events, we could certainly help in a &lsquo;producer&rsquo; role.</p> <p>The big area where we aren&rsquo;t doing enough is advocacy and communication. There is huge interest in Open Science, reproducibility, software sustainability and other similar topics, but the OBF is surprisingly silent. This doesn&rsquo;t reflect a lack of interest (or opinion!) among the board members, but rather the difficulty in carving out time from other OBF jobs.</p> <p>So, we are looking to recruit a new board member who is interested in policy and advocacy around Open Science. Does that sound like you? If you want to put your name forward, please <a href="mailto:obf-board@googlegroups.com">email the board</a>. The election will be held at the upcoming public board meeting in January. If you want more information, or want to contact one of us to talk about being on the board, see the <a href="https://www.open-bio.org/wiki/Board">OBF Board page</a>.</p>https://www.open-bio.org/2017/11/12/mailing-list-outage-and-public-board-meeting-update/Sun, 12 Nov 2017 09:50:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/11/12/mailing-list-outage-and-public-board-meeting-update/<p>This time of year we&rsquo;d normally be having a public board meeting as part of our commitment to communication with our member projects and the wider OBF community. As per our bylaws we notify the community at least 10 days in advance, and we&rsquo;d also handle election of new board members and leadership changes where appropriate. For a couple of reasons, we&rsquo;re going to postpone that until early 2018.</p> <p>Our mailing list server (which hosts many of our member project lists) has been overwhelmed in the past few days, leading to delayed or blocked communication not just to our members but for our member projects who rely on it. We&rsquo;re looking into options for solving this problem, which might include migrating to a hosted solution.</p> <p>This comes at the same time that the OBF board has been taking a look at how best to direct the organisation as we move forward. We&rsquo;d like to have that conversation with our members <em>after</em> we&rsquo;ve crystallised our thoughts a bit, and we&rsquo;re still in the process of doing that.</p> <p>As we&rsquo;re sorting this out, we decided to push the public meeting back to early 2018 so everyone involved can get the most out of it. We hope you understand, and we&rsquo;re looking forward to hearing from as many of you as we can at that meeting.</p>https://www.open-bio.org/2017/09/05/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/2017/07/29/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/2017/04/07/biopython-1-69-released/Fri, 07 Apr 2017 11:03:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2017/04/07/biopython-1-69-released/<p>Dear Biopythoneers,</p> <p>Source distributions and Windows installers for Biopython 1.69 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the official <a href="http://biopython.org/">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.69">on the Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.7, 3.3, 3.4, 3.5 and 3.6 (we have now dropped support for Python 2.6). It has also been tested on PyPy v5.7, PyPy3.5 v5.7 beta, and Jython 2.7.</p> <p>We have started to dual-license Biopython under both our original liberal &ldquo;Biopython License Agreement&rdquo;, and the very similar but more commonly used &ldquo;3-Clause BSD License&rdquo;. In this release a small number of the Python files are explicitly available under either license, but most of the code remains under the &ldquo;Biopython License Agreement&rdquo; only. See the <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst">LICENSE</a> file for more details.</p> <p>We now expect and take advantage of NumPy under PyPy, and compile most of the Biopython C code modules as well.</p> <p><a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a> now supports the UCSC Multiple Alignment Format (MAF) under the format name &ldquo;maf&rdquo;, using new module Bio.AlignIO.MafIO which also offers indexed access to these potentially large files using SQLite3 (contributed by Andrew Sczesnak, with additional refinements from Adam Novak).</p> <p>Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The underlying format (ABIF) remains the same as AB1 files and so the string &lsquo;abif&rsquo; is the expected format argument in the main SeqIO functions. AbiIO determines whether the file is AB1 or FSA based on the presence of specific tags.</p> <p>The Uniprot parser is now able to parse &ldquo;submittedName&rdquo; elements in XML files.</p> <p>The NEXUS parser handling of internal node comments has been improved, which should help if working with tools like the BEAST TreeAnnotator. Slashes are now also allowed in identifiers.</p> <p>New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue, and cell line ontology (contributed by Steve Marshall).</p> <p>For consistency the Bio.Seq module now offers a complement function (already available as a method on the Seq and MutableSeq objects).</p> <p>The SeqFeature object&rsquo;s qualifiers is now an explicitly ordered dictionary (note that as of Python 3.6 the Python dict is ordered by default anyway). This helps reproduce GenBank/EMBL files on input/output.</p> <p>The Bio.SeqIO UniProt-XML parser was updated to cope with features with unknown locations which can be found in mass spec data.</p> <p>The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type from the LOCUS/ID line explicitly in the record.annotations dictionary. The Bio.SeqIO EMBL parser was updated to cope with more variants seen in patent data files, and the related IMGT parser was updated to cope with IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed. The GenBank output now uses colon space to match current NCBI DBLINK lines.</p> <p>The Bio.Affy package supports Affymetrix version 4 of the CEL file format, in addition to version 3.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the February 2017 release of REBASE.</p> <p>Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default), PDBML/XML and mmtf format protein structures. This is inline with the RCSB recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython already has support for parsing mmCif files.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Rosenfeld</li> <li>Adam Kurkiewicz (first contribution)</li> <li>Adam Novak (first contribution)</li> <li>Adrian Altenhoff (first contribution)</li> <li>Allis Tauri (first contribution)</li> <li>Andrew Dalke</li> <li>Andrew Guy (first contribution)</li> <li>Andrew Sczesnak (first contribution)</li> <li>Ben Fulton</li> <li>Bernhard Thiel (first contribution)</li> <li>Bertrand Néron</li> <li>Blaise Li (first contribution)</li> <li>Brandon Carter (first contribution)</li> <li>Brandon Invergo</li> <li>Carlos Pena</li> <li>Carlos Ríos</li> <li>Chris Warth</li> <li>Emmanuel Noutahi</li> <li>Foen Peng (first contribution)</li> <li>Francesco Gastaldello (first contribution)</li> <li>Francisco Pina-Martins (first contribution)</li> <li>Hector Martinez (first contribution)</li> <li>Jacek Śmietański</li> <li>Jack Twilley (first contribution)</li> <li>Jeroen Van Goey (first contribution)</li> <li>Joshua Meyers (first contribution)</li> <li>Kurt Graff (first contribution)</li> <li>Lenna Peterson</li> <li>Leonhard Heizinger (first contribution)</li> <li>Marcin Magnus (first contribution)</li> <li>Markus Piotrowski</li> <li>Maximilian Greil (first contribution)</li> <li>Michał J. Gajda (first contribution)</li> <li>Michiel de Hoon</li> <li>Milind Luthra (first contribution)</li> <li>Oscar G. Garcia (first contribution)</li> <li>Owen Solberg</li> <li>Peter Cock</li> <li>Richard Neher (first contribution)</li> <li>Sebastian Bassi</li> <li>Sourav Singh (first contribution)</li> <li>Spencer Bliven (first contribution)</li> <li>Stefans Mezulis</li> <li>Steve Bond</li> <li>Steve Marshall (first contribution)</li> <li>Uri Laserson</li> <li>Veronika Berman (first contribution)</li> <li>Vincent Davis</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul> <p>Thank you all.</p> <p><img src="https://news.open-bio.org/wp-content/uploads/2013/12/biopython-300x84.jpg" alt="[Biopython Logo]"></p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a></p> <p>Checksums:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.69.* </span></span><span style="display:flex;"><span>18ad299569eea79febf4641cce840db0 biopython-1.69.tar.gz </span></span><span style="display:flex;"><span>1acfa83d7340d82e248261f8344038be biopython-1.69.win32-py2.7.exe </span></span><span style="display:flex;"><span>ff38a7286b455156619c8c2c4cb45a0e biopython-1.69.win32-py2.7.msi </span></span><span style="display:flex;"><span>e03809050cd862226299ba4285b25615 biopython-1.69.win32-py3.3.exe </span></span><span style="display:flex;"><span>f8605d2e76e60353c776f69991067e07 biopython-1.69.win32-py3.3.msi </span></span><span style="display:flex;"><span>6bc7d291b7482f194f66a91d3eb89cb6 biopython-1.69.win32-py3.4.exe </span></span><span style="display:flex;"><span>0bc8e39ca0c3127b531f1998c91c7233 biopython-1.69.win32-py3.4.msi </span></span><span style="display:flex;"><span>0944a254c079869c481c13ac3bfa6c53 biopython-1.69.win32-py3.5.exe </span></span><span style="display:flex;"><span>567ba8c2b5e069cbcda5b13b558e4b1e biopython-1.69.win32-py3.5.msi </span></span><span style="display:flex;"><span>48549d7083f1dcd37f73acfdbb30c100 biopython-1.69.win32-py3.6.exe </span></span><span style="display:flex;"><span>d3e02e227b6db736bc15f3ce4a08c149 biopython-1.69.win32-py3.6.msi </span></span><span style="display:flex;"><span>a134c5b8e35d6515ca4f9e663000bcb3 biopython-1.69.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.69.* </span></span><span style="display:flex;"><span>169ffa90c3d3ec5678c7a5c99501c0cfeb54c40ca51a619ce6cee5026d3403eb biopython-1.69.tar.gz </span></span><span style="display:flex;"><span>6520ac092f52fd35b48d12c5f264d78c4cd20ede841a4755b73376184c1f9c83 biopython-1.69.win32-py2.7.exe </span></span><span style="display:flex;"><span>505aa27537f358129d096c1cb5b761108c6200a11483d25ad83188b11089b45c biopython-1.69.win32-py2.7.msi </span></span><span style="display:flex;"><span>11a5a04da0d8830789d53fed7d631f5a8a6d3926869241d212265b7b9889b987 biopython-1.69.win32-py3.3.exe </span></span><span style="display:flex;"><span>7e3e764236e29f01fe3b346878801ee9f1166269e4ac557d88201e2f1cd85949 biopython-1.69.win32-py3.3.msi </span></span><span style="display:flex;"><span>c9ee5594e5f865fbf4871be8661e4be559dcb599c64e7fa4922e55b771aab249 biopython-1.69.win32-py3.4.exe </span></span><span style="display:flex;"><span>8426e2b548e594d63bfa7584f39513ee906d2de32037c900af9b6625318e051c biopython-1.69.win32-py3.4.msi </span></span><span style="display:flex;"><span>3025f12b7f8cf81b25823223dc17830d4e0eeda8095e59177069d44fa2be9d32 biopython-1.69.win32-py3.5.exe </span></span><span style="display:flex;"><span>853eb6b75ca84ba703e0c8873d673b49f1580b5b1b9372105fbf9735153ad0dd biopython-1.69.win32-py3.5.msi </span></span><span style="display:flex;"><span>7f11960168e335c1581de2e4a90bef905c92e08d42c67482f25a522db5d7b702 biopython-1.69.win32-py3.6.exe </span></span><span style="display:flex;"><span>4cac457773f251c511ede520f3e8701d8f00e22524103e03d0d1f69a040f95bf biopython-1.69.win32-py3.6.msi </span></span><span style="display:flex;"><span>e71ae4c5ba996cbe01002d55d877bf5eafa053c116012d7ace489dfc41959e05 biopython-1.69.zip </span></span></code></pre></div>https://www.open-bio.org/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/2016/09/07/bioruby-1-5-1-released/Wed, 07 Sep 2016 15:04:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/09/07/bioruby-1-5-1-released/<p>We are pleased to announce the release of BioRuby 1.5.1.</p> <p>In this new release, NCBI Entrez web client classes, Bio::NCBI::REST and Bio::PubMed, are changed to use HTTPS instead of HTTP, to prepare <a href="https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/">NCBI website transitioning to HTTPS</a>.</p> <p>For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.5.1/RELEASE_NOTES.rdoc" title="RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.5.1/ChangeLog" title="ChangeLog">ChangeLog</a>.</p> <p>The archive is available for download from the following links.</p> <ul> <li>Tar.gz file: <a href="http://bioruby.org/archive/bioruby-1.5.1.tar.gz">http://bioruby.org/archive/bioruby-1.5.1.tar.gz</a></li> <li>Gem file: <a href="https://rubygems.org/gems/bio" title="https://rubygems.org/gems/bio">https://rubygems.org/gems/bio</a> or <a href="http://bioruby.org/archive/gems/bio-1.5.1.gem">http://bioruby.org/archive/gems/bio-1.5.1.gem</a></li> </ul> <p>You can easily install by using RubyGems. First, check the version number by using search command:</p> <p><code>% gem search --remote bio</code></p> <p>and find “bio (1.5.1)” in the list. Then,</p> <p><code>% sudo gem install bio</code></p> <p>Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.</p> <p>Because this release is a minor version up, only few changes picked from the <a href="https://github.com/bioruby/bioruby">git head</a> are included.</p> <p>Acknowledgments: Thanks to Dr. Mark Johnson about information of the NCBI website change.</p>https://www.open-bio.org/2016/08/26/biopython-1-68-released/Fri, 26 Aug 2016 16:23:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/08/26/biopython-1-68-released/<p>Dear Biopythoneers,</p> <p>Source distributions and Windows installers for Biopython 1.68 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the official <a href="http://biopython.org/">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.68">on the Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but <strong>this will be our final release to run on Python 2.6.</strong> It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.</p> <p>Bio.PDB has been extended to parse the RSSB&rsquo;s new binary Macromolecular Transmission Format (MMTF, see <a href="http://mmtf.rcsb.org">http://mmtf.rcsb.org</a>), in addition to the mmCIF and PDB file formats (contributed by Anthony Bradley). This requires an optional external dependency on the <a href="https://github.com/rcsb/mmtf-python">mmtf-python library</a>.</p> <p>Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski). It is now faster, addresses some problems with local alignments, and also now allows gap insertions after deletions, and vice versa, inspired by the <a href="http://dx.doi.org/10.1101/031500">preprint from Flouri et al</a>.</p> <p>The two sample graphical tools SeqGui (Sequence Graphical User Interface) and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide transcription, back-transcription and translation into amino acids using Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython. xbbtools is able to open Fasta formatted files, does simple nucleotide operations and translations in any reading frame using one of the NCBI genetic codes. In addition, it supports standalone Blast installations to do local Blast searches.</p> <p>New <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">NCBI genetic code table</a> 26 (Pachysolen tannophilus Nuclear Code) has been added to Bio.Data (and the translation functionality), and table 11 is now also available under the alias Archaeal.</p> <p>In line with <a href="https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/">NCBI website HTTPS changes</a>, Biopython now uses HTTPS rather than HTTP to connect to the NCBI Entrez and QBLAST API.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 and best practice standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Anthony Bradley (first contribution)</li> <li>Ben Fulton</li> <li>Carlos Pena</li> <li>Connor T. Skennerton</li> <li>Iddo Friedberg</li> <li>Kai Blin</li> <li>Kristian Davidsen (first contribution)</li> <li>Markus Piotrowski</li> <li>Olivier Morelle (first contribution)</li> <li>Peter Cock</li> <li>Tiago Antao</li> <li>Travis Wrightsman</li> <li>Uwe Schmitt (first contribution)</li> <li>Xiaoyu Zhuo (first contribution)</li> </ul> <p>Thank you all.</p> <p>P.S. You can follow <a href="https://twitter.com/Biopython">@Biopython on Twitter</a></p> <p>Checksums:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ md5sum biopython-1.68.* </span></span><span style="display:flex;"><span>078e915185485a5327937029b7577ddc biopython-1.68.tar.gz </span></span><span style="display:flex;"><span>362e964543a424a2f7585ea4008ea834 biopython-1.68.win32-py2.6.exe </span></span><span style="display:flex;"><span>772d07d9a6490d674688d00ede2bdfe9 biopython-1.68.win32-py2.7.exe </span></span><span style="display:flex;"><span>fda2d1c8d4a7862f6af85122c86fcd0f biopython-1.68.win32-py2.7.msi </span></span><span style="display:flex;"><span>8de95a90704f15f4c22d5359dbc54b75 biopython-1.68.win32-py3.3.exe </span></span><span style="display:flex;"><span>92f40105761520daeeb9128254a8bc94 biopython-1.68.win32-py3.3.msi </span></span><span style="display:flex;"><span>b1cd3f6b4ad1096347d5019c68128dac biopython-1.68.win32-py3.4.exe </span></span><span style="display:flex;"><span>9403b9b0d01c22b49edb34e2164c31de biopython-1.68.win32-py3.4.msi </span></span><span style="display:flex;"><span>72202792fc387376c07e28997ece181f biopython-1.68.win32-py3.5.exe </span></span><span style="display:flex;"><span>ff0cfc6c835ddf890b69ba872fb46b39 biopython-1.68.win32-py3.5.msi </span></span><span style="display:flex;"><span>adb3e8ce60b02b3b46330bbca68f9732 biopython-1.68.zip </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>$ shasum -a 256 biopython-1.68.* </span></span><span style="display:flex;"><span>d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f biopython-1.68.tar.gz </span></span><span style="display:flex;"><span>09449d7204c65e6010545092f2bc1dc662a0b5f6a873e52a08e19392f935fdb7 biopython-1.68.win32-py2.6.exe </span></span><span style="display:flex;"><span>a7c2fe52ce8dcf503a492e4ee006dd8bc62faa77078d04c92abdbf7713bf2166 biopython-1.68.win32-py2.7.exe </span></span><span style="display:flex;"><span>f92dfefc9a4ee61dda838a61d73a38b55552a1771ce411505009a48702aefd41 biopython-1.68.win32-py2.7.msi </span></span><span style="display:flex;"><span>bce6a4cece7b75650d6a478f4ed9d7d1a5351df42a1820866a0cbd74c254565d biopython-1.68.win32-py3.3.exe </span></span><span style="display:flex;"><span>85bd5d499400e594f77d297966f56c139499711513b9cd24b87fece5a0463fbe biopython-1.68.win32-py3.3.msi </span></span><span style="display:flex;"><span>05c1f59933ef35ecb838649f6fabacb823f2a48c2498ed57ac59a6b3629b5369 biopython-1.68.win32-py3.4.exe </span></span><span style="display:flex;"><span>10928347029bc6b0b76567d5f6026a8a002bd3502a7ceeaded7d566938db4bef biopython-1.68.win32-py3.4.msi </span></span><span style="display:flex;"><span>5d08e4de11f920ec5207e10d264fceb837e2000843a56fd684e0ee2dfb948fe5 biopython-1.68.win32-py3.5.exe </span></span><span style="display:flex;"><span>299888c32b36f32542775952e7b863bd9c3d362f61a69b7d8a136a63aeabec36 biopython-1.68.win32-py3.5.msi </span></span><span style="display:flex;"><span>986a0fa6919d2b51959259011dd0674b115383237e109c5a55c37cb18eef999b biopython-1.68.zip </span></span></code></pre></div><p><em>Updated</em> 29 August 2016 to include the Python 3.5 installer checksums.</p>https://www.open-bio.org/2016/07/21/bosc-2016-in-disney-world-with-donald-docker/Thu, 21 Jul 2016 14:18:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/07/21/bosc-2016-in-disney-world-with-donald-docker/<p>First I would like to congratulate OBF that supports diversity in the community with its <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">travel awards initiative</a>. I was very pleased to be one of the <a href="https://news.open-bio.org/2016/05/23/first-obf-travel-fellowships/">three travel fellowship awardees</a>. Thank you OBF! Ιt was great to attend <a href="https://www.open-bio.org/wiki/BOSC_2016">BOSC 2016</a> and meet remarkable people and know their work.It was one of the most welcoming meetings I have attended and Ι liked that is was active on the social media and the conference materials and speaker presentations were available online. It made it fun and useful and we could focus less on our notebooks and more on the speakers. Τhis also attracted a lot of positive comments from the other Special Interest Groups. So “Bravo” to the organizers!On the scientific part, it was nice to see Docker making an impression on the bioinformatics community. Everyone was talking about it. It is an awesome way to package bioinformatics applications and the fact that it received so much attention got me pretty excited. I am planning to use it to package CollOS, an open source web application I presented at the conference, that tracks, annotates and barcodes biological samples to facilitate wet lab scientists to locate and identify biological samples.Last but definitely not least, I would like to congratulate Mónica Muñoz-Torres and the organizers for their reference to the recent tragic shooting incident in Orlando.Hope to see you next year in Prague!Dimitra</p>https://www.open-bio.org/2016/06/14/new-biojava-logo-design-competition-andreas/Tue, 14 Jun 2016 17:47:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/06/14/new-biojava-logo-design-competition-andreas/<p><a href="https://github.com/biojava/logo">BioJava</a> is organizing a <strong>design competition</strong> to come up with a new logo. Anybody can participate:</p> <ul> <li> <p>The logo should look modern and be better than the current one (yellow circle)</p> </li> <li> <p>The logo should be able to be rendered as a favicon, as well as large (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.</p> </li> <li> <p>Logos shall not look similar in any way to the trademarked Java programming language logo. This means no coffee cups in any way.</p> </li> </ul> <p><strong>Deadline:</strong> Deadline for submissions is July 4th.</p> <p><strong>Announcement of Winner:</strong> The winner of the new logo competition will be announced during BOSC 2016.</p> <p><strong>Prize:</strong> We will print t-shirts with the new logo and the designer will get a free t-shirt.</p> <p>If the designer of the winning new logo will be attending ISMB 2016, the attending BioJava developers will take the winner out for dinner.</p> <p>BioJava will carry the new logo on its homepage and GitHub Profile</p> <p><strong>Details:</strong> For full details of the competition and how to make a submission please view here:</p> <p><a href="https://github.com/biojava/logo">https://github.com/biojava/logo</a> <strong>Result Update:</strong></p> <p>As <a href="http://mailman.open-bio.org/pipermail/biojava-l/2016-July/011488.html">announced via the mailing list</a> and at BOSC 2016, the winning logo was by Aleix Latifa:</p> <p><img src="https://raw.githubusercontent.com/biojava/logo/master/submissions/lafita_4/logo.png" alt=""></p>https://www.open-bio.org/2016/06/08/biopython-1-67-released/Wed, 08 Jun 2016 17:39:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/06/08/biopython-1-67-released/<p>This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure.</p> <p>Source distributions and Windows installers for Biopython 1.67 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">official Biopython website</a>, and the release is also on the <a href="https://pypi.python.org/pypi/biopython/1.67">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but support for Python 2.6 is considered to be deprecated. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.</p> <p>Comparison of SeqRecord objects until now has used the default Python object comparison (are they the same instance in memory?). This can be surprising, but comparing all of the attributes would be too complex. As of this release attempting to compare SeqRecord objects should raise an exception instead. If you want the old behaviour, use id(record1) == id(record2) instead.</p> <p>New experimental module Bio.phenotype is for working with Phenotype Microarray plates in JSON and the machine vendor&rsquo;s CSV format (contributed by Marco Galardini).</p> <p>Following the convention used elsewhere in Biopython, there is a new function Bio.KEGG.read(&hellip;) for parsing KEGG files expected to contain a single record only - the existing function Bio.KEGG.parse(&hellip;) is intended to be used to iterate over multi-record files.</p> <p>When a gap character is defined, Bio.Seq will now translate gap codons (e.g. &ldquo;&mdash;&rdquo;) into a single gap (&quot;-&quot;) in the protein sequence. The gap character is inferred from the Seq object&rsquo;s alphabet, but it can also be passed as an argument to the translate method.</p> <p>The new NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria, has been added to Bio.Data (and the translation functionality).</p> <p>The Bio.Entrez interface will automatically use an HTTP POST rather than HTTP GET if the URL would exceed 1000 characters. This is based on NCBI guidelines and the fact that very long queries like complex searches can otherwise trigger an HTTP Error 414 Request URI too long.</p> <p>Foreign keys are now used when creating BioSQL databases with SQLite3 (this was not possible until SQLite version 3.6.19). The BioSQL taxonomy code now updates the taxon table left/right keys when updating the taxonomy.</p> <p>There have been some fixes to the MMCIF structure parser which now uses identifiers which better match results from the PDB structure parse.</p> <p>The restriction enzyme list in Bio.Restriction has been updated to the May 2016 release of REBASE.</p> <p>The mmCIF parser in Bio.PDB.MMCIFParser has been joined by a second version which only looks at the ATOM and HETATM lines and can be much faster.</p> <p>The Bio.KEGG.REST will now return unicode text-based handles, except for images which remain as binary bytes-based handles, making it easier to use with the mostly text-based parsers in Biopython.</p> <p>Note that the BioSQL test configuration information is now in a new file Tests/biosql.ini rather than directly in Tests/test_BioSQL_*.py as before. You can make a copy of the provided example file Tests/biosql.ini.sample as Tests/biosql.ini and edit this if you wish to run the BioSQL tests.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 standard coding style, and in converting our docstring documentation to use the reStructuredText markup style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Rosenfeld (first contribution)</li> <li>Anders Pitman (first contribution)</li> <li>Barbara Mühlemann (first contribution)</li> <li>Ben Fulton</li> <li>Ben Woodcroft (first contribution)</li> <li>Brandon Invergo</li> <li>Brian Osborne (first contribution)</li> <li>Carlos Pena</li> <li>Chaitanya Gupta (first contribution)</li> <li>Chris Warth (first contribution)</li> <li>Christiam Camacho (first contribution)</li> <li>Connor T. Skennerton</li> <li>David Koppstein (first contribution)</li> <li>Eric Talevich</li> <li>Jacek Śmietański (first contribution)</li> <li>João D Ferreira (first contribution)</li> <li>João Rodrigues</li> <li>Joe Cora (first contribution)</li> <li>Kai Blin</li> <li>Leighton Pritchard</li> <li>Lenna Peterson</li> <li>Marco Galardini (first contribution)</li> <li>Markus Piotrowski</li> <li>Matt Ruffalo (first contribution)</li> <li>Matteo Sticco (first contribution)</li> <li>Nader Morshed (first contribution)</li> <li>Owen Solberg (first contribution)</li> <li>Peter Cock</li> <li>Steve Bond (first contribution)</li> <li>Terry Jones (first contribution)</li> <li>Vincent Davis</li> <li>Zheng Ruan</li> </ul> <p>Again this list of contributors is longer than usual, which is good, but partly reflects the delay since our last release. My apologies.</p>https://www.open-bio.org/2016/05/23/first-obf-travel-fellowships/Mon, 23 May 2016 16:05:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/05/23/first-obf-travel-fellowships/<p>The first round of the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation travel fellowship program</a> has granted funds to three open source bioinformatics software developers to help them attend the <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC) 2016</a> in Orlando, Florida, this July. The travel fellowship program ( <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">announced 1 May 2016</a>) aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Applications for the first round in 2016 were due on April 15, with two more due dates this year on August 15 and December 15.</p> <p>Out of more than a dozen applicants from four different continents, the OBF Board chose the following three recipients:</p> <ul> <li><a href="https://github.com/dimitras">Dimitra Sarantopoulou</a> of the University of Pennsylvania is an open source bioinformatics developer who focuses on web applications for proteomic analysis.</li> <li>Michael R. Crusoe ( <a href="https://twitter.com/biocrusoe">@biocrusoe</a>) is the Co-founder &amp; Community Engineer for the <a href="http://www.commonwl.org/">Common Workflow Language (CWL)</a>, and previously was the lead developer of <a href="https://github.com/dib-lab/khmer">khmer</a>.</li> <li><a href="http://wurmlab.github.io/team/priyam/">Anurag Priyam</a> is a self-taught bioinformaticst who has created several successful open source tools, including  <a href="https://github.com/wurmlab/sequenceserver">SequenceServer</a> and <a href="https://github.com/wurmlab/oswitch">oswitch</a>, a Docker-based virtual environment switcher.</li> </ul> <p>The OBF Board congratulates the three winners!</p> <p>This first round has also shown several points of improvement, both for the program description and the application form. We are in the process of making small adjustments to both, and expect to reopen the application form for the next round of funding at the latest by the time BOSC 2016 rolls around (July 8). We encourage others for whom travel costs are a barrier to participating in open source bioinformatics events to apply for this next round (due date is August 15, 2016).</p>https://www.open-bio.org/2016/04/25/welcome-gsoc-2016-students/Mon, 25 Apr 2016 08:13:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/04/25/welcome-gsoc-2016-students/<p>The Open Bioinformatics Foundation is participating in the Google Summer of Code 2016 program, and last Friday the selected students were announced. Congratulations to all of you, and welcome. I also want to use this opportunity to thank all students who applied. Resources are limited and your proposals did not make it easy to select our finalists. We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one after all.</p> <p>The Open Bioinformatics Foundation gets to host <a href="https://summerofcode.withgoogle.com/organizations/5693436329984000/#projects">eight student projects this</a> year:</p> <ul> <li><a href="https://github.com/AlishaMechtley/treematcher/wiki/Blog">Alisha Mechtley</a> will work with the ETE toolkit on tree searching using regular-expression-like queries.</li> <li><a href="https://anton-khodak.github.io/argparse2cwl-blog/2016/08/11/gentle-introduction.html">Anton Khodak</a> will work on the Common Workflow Language, creating an automated tool wrapper/converter for CWL.</li> <li><a href="https://chfi.se/posts/2016-08-22-gsoc-final.html">Christian Fischer</a> will work on the GeneNetwork Genome Browser.</li> <li><a href="https://sxibolet.2pitau.org/gsoc.html">Graham Dyer</a> will work on openSNP, extending the quantified-self support.</li> <li><a href="https://github.com/bionode/gsoc16/blob/8a155a14c34d820a3a77d15b3600d4adf225f179/README.md">Julian Mazzitelli</a> will work on a workflow engine for streamed data analysis in Bionode.</li> <li><a href="https://bitbucket.org/mnave/gsoc-blog/">Mariana Nave</a> will improve the prediction for RiPP clusters in antiSMASH.</li> <li><a href="http://mateusjabour.github.io/gsoc-code-submission">Mateus Jabor</a> will work on improving the user experience in openSNP.</li> <li><a href="http://raivivek.in/programming/gsoc-16-wrap-up.html#main">Vivek Rai</a> will work on linking phenotypes to SNPs in openSNP.</li> </ul> <p>Please join me in welcoming all of them in the Open Bioinformatics Foundation community and the respective subprojects. It looks like this will be a great summer.</p> <p>Kai Blin</p> <p>OBF administrator for GSoC 2016</p> <p><em>P.S. We have retrospectively updated this post to add links to the students&rsquo; blog posts.</em></p>https://www.open-bio.org/2016/04/18/phylosoc-supports-obf-travel-fellowships/Mon, 18 Apr 2016 16:01:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/04/18/phylosoc-supports-obf-travel-fellowships/<p>The Open Bioinformatics Foundation is pleased to announce a gift of USD 18,125 from the Phyloinformatics Summer of Code toward the <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">OBF travel fellowship program</a>. The program, <a href="https://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/">announced earlier this year on March 1</a>, aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The program includes but is not limited to the annual <a href="https://www.open-bio.org/wiki/BOSC">Bioinformatics Open Source Conference</a> (BOSC), OBF’s flagship event.</p> <p>The funds for this gift are a legacy of the seven years during which the National Evolutionary Synthesis Center ( <a href="https://www.nescent.org/">NESCent</a>) served as a mentoring organization in the <a href="https://developers.google.com/open-source/gsoc/">Google Summer of Code</a> ™. Over the years, NESCent’s program, the <a href="http://informatics.nescent.org/wiki/Main_Page#Phyloinformatics_Summer_of_Code">Phyloinformatics Summer of Code</a>, supported dozens of students for three-month paid internships developing open source software for evolutionary and biodiversity informatics.  Each year, Google made a small award to Duke University, NESCent’s administrative home, to support the program, and when NESCent ceased operations in 2015, the funds for this gift remained.</p> <p>Todd Vision, former Associate Director of Informatics at NESCent, says &ldquo;With this gift, OBF will carry on the legacy of the Phyloinformatics Summer of Code in building a diverse and collaborative open source bioinformatics community.&rdquo;</p> <p>OBF has only been able to underwrite the Travel Fellowship program for an initial 3 years, for at most a handful of awards each year. As Hilmar Lapp, President of OBF’s Board, and former Assistant Director of Informatics at NESCent, explains, “This program is a signature part of our commitment to inclusivity and growing our community, and we are keen to make it a sustained effort. This gift is a key step in that direction, and I hope that we can convince other donors to follow.”</p> <p>The gift is specifically earmarked for awards to increase diversity at bioinformatics community events. “By targeting travel costs, we hope to remove one barrier to participation. Meeting face to face can be a critical step to becoming part of an existing community.”, says Karen Cranston, OBF Board Member, who ran the Phyloinformatics Summer of Code program for several years while at NESCent.</p> <p>There have been long-standing ties between the Phyloinformatics Summer of Code and OBF. They have shared project ideas and mentors, and some graduates from the summer program have subsequently taken on prominent roles in OBF’s projects and community. A student from the 2011 summer program, Sarah Hird, even <a href="https://news.open-bio.org/2015/01/04/bosc-welcomes-sarah-hird/">served as the Outreach Coordinator for BOSC 2015</a>, the theme of which was Increasing Diversity.</p> <p><strong><em>About OBF:</em></strong> The <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a> (OBF) is a nonprofit volunteer run organization founded in 2001 with a mission to promote the practice and philosophy of open-source software development and open science within the biological research community. OBF is incorporated as an affiliate project of <a href="http://www.spi-inc.org/">Software in the Public Interest</a>, Inc., a 501(c)(3) fiscal sponsorship organization.</p> <p><strong><em>About NESCent:</em></strong> The <a href="https://www.nescent.org/">National Evolutionary Synthesis Center</a> (NESCent) was a science center dedicated to cross-disciplinary research in evolution, jointly operated by Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University from 2004-2015, with support largely from the National Science Foundation. In 2015, it transitioned to the <a href="http://tricem.org">Triangle Center for Evolutionary Medicine</a> (TriCEM).</p>https://www.open-bio.org/2016/03/28/bosc-codefest-2016/Mon, 28 Mar 2016 13:56:07 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/28/bosc-codefest-2016/<p>The <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC)</a> is a two day meeting focused on open source bioinformatics. We aim to encourage and support a friendly, open and productive community that helps us work together to answer hard biological questions. We&rsquo;ll get together this summer, July 8-9, in Orlando, Florida.</p> <p>Abstracts for BOSC 2016 talks and posters are due this Friday, April 1st. We want to hear about your research and encourage everyone to <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">submit an abstract</a>. We love talks from newcomers to BOSC as well as established projects: no idea is too big or small. We also offer <a href="https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/">Travel Fellowships for speakers</a> if money would be a barrier to attending.</p> <p>Prior to BOSC, we organize a free two day collaborative working session called <a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest</a>. We&rsquo;ll establish friendships and collaborations while helping new members find fun work and extending existing projects. It&rsquo;s a time to learn, teach, develop and grow. This year we&rsquo;re kindly hosted by the <a href="https://familab.org/">FamiLAB workspace</a> in Orlando. So in addition to getting to work with fellow OpenBio members, you&rsquo;ll have the chance to learn about the Orlando maker community.</p> <p>We hope you&rsquo;ll join us in Orlando this summer for Codefest and BOSC. Please send in your abstracts before Friday and sign up on the Codefest page.</p>https://www.open-bio.org/2016/03/22/bosc-2016-keynote-speakers/Tue, 22 Mar 2016 12:10:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/22/bosc-2016-keynote-speakers/<p>We&rsquo;re delighted to announce the keynote speakers for the <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference, BOSC 2016</a>:</p> <h1 id="jennifer-gardy">Jennifer Gardy</h1> <p><a href="https://www.open-bio.org/wiki/File:JenniferGardy.jpg" title="Jennifer Gardy"><img src="https://www.open-bio.org/w/images/thumb/0/04/JenniferGardy.jpg/240px-JenniferGardy.jpg" alt="Jennifer Gardy"></a></p> <p>Dr. Jennifer Gardy is both a scientist and science communicator. She holds a PhD in Bioinformatics, and is an Assistant Professor of Population and Public Health at the University of British Columbia and a Senior Scientist at the British Columbia Centre for Disease Control (BCCDC). At the BCCDC, she pioneered a new way of investigating outbreaks of infectious diseases – &ldquo;genomic epidemiology&rdquo;, which uses a pathogen&rsquo;s genome sequence as a tool for understanding how an infectious disease spreads. Her group was the first to use genome sequencing to reconstruct a large outbreak of tuberculosis, and she is continuing to apply this novel technique to other outbreak scenarios. She is also involved in other genomics-related research, including replacing traditional laboratory microbiology protocols with single genomic analyses. In 2014, she was appointed the Canada Research Chair in Public Health Genomics, and is Senior Editor at the new open data, open access journal Microbial Genomics.</p> <p>In addition to her career as a research scientist, Dr. Gardy is known for her work in science communication and education, both in print and on TV. She has made regular appearances on CBC&rsquo;s documentary series The Nature of Things, has hosted CBC&rsquo;s eight-part science series Project X, and is a regular guest host on Discovery Channel’s Daily Planet science show. She has written and blogged for the Globe and Mail, has written a children’s book – It’s Catching! The Infectious World of Germs and Microbes – and runs a series of workshops on how to communicate science effectively.</p> <p>Dr. Gardy&rsquo;s keynote topic is “The open-source outbreak: can data prevent the next pandemic?”</p> <p><em>Every century, something comes along that shakes up public health – vaccines, sanitation, antibiotics – and data promises to be the great disrupter of 21st century infectious disease epidemiology. In the last 5-6 years, genomics has dramatically changed how public health agencies diagnose and investigate diseases from food poisoning to tuberculosis, giving us a new tool to understand and control infections. The change is also apparent at a cultural level – genomics and bioinformatics researchers have largely come from an open data, collaborative space and have brought new ways of thinking to public health laboratories, previously secret, closed organizations. In this talk, we’ll explore some of the dramatic changes in public health microbiology that genomics and bioinformatics has facilitated, and look at how future data sharing efforts in areas such as digital disease detection might be the key to preventing future pandemics.</em></p> <p>Homepage: <a href="http://www.jennifergardy.com">Jennifer Gardy</a>, Twitter: <a href="https://twitter.com/jennifergardy">@JenniferGardy</a></p> <hr> <h1 id="steven-salzberg">Steven Salzberg</h1> <p><a href="https://www.open-bio.org/wiki/File:StevenSalzberg.jpg" title="Steven Salzberg"><img src="https://www.open-bio.org/w/images/thumb/3/3b/StevenSalzberg.jpg/210px-StevenSalzberg.jpg" alt="Steven Salzberg"></a></p> <p>Dr. Steven Salzberg is the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics and the Director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. From 2005-2011, he was the Director of the Center for Bioinformatics and Computational Biology and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world&rsquo;s leading DNA sequencing centers at the time.</p> <p>Salzberg&rsquo;s lab currently focuses on next-generation sequence alignment, genome assembly, and microbiome analysis.They have produced several popular systems for alignment of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems. All of the group&rsquo;s software is free and open source, and their systems have been downloaded hundreds of thousands of times.</p> <p>Dr. Salzberg is a Fellow of the American Association for the Advancement of Science (AAAS) and a Fellow of the International Society for Computational Biology (ISCB). He was the 2013 winner of the Benjamin Franklin Award for Open Access in the Life Sciences, in recognition of his many contributions to open access bioinformatics software and his strong advocacy for open access to data, software and publications.</p> <p>Dr. Salzberg will speak about &ldquo;Open source, open access, and open data: why science moves faster in an open world&rdquo;.</p> <p><em>The Human Genome Project established a practice of sharing data rapidly, prior to publication, that has since become a model for many projects in genomics. Data sharing has been slow to penetrate other fields because of many factors, some of which I will discuss in this talk. Nevertheless, sharing of methods, data, and results helps science move ahead faster, and openness is essential for the continual process of checking and self-correction that good science requires. I will discuss some of the successes as well as some noteworthy mistakes that have been discovered thanks to open science.</em></p> <p>Homepage: <a href="https://salzberg-lab.org/">Steven Salzberg</a>, Twitter: <a href="https://twitter.com/StevenSalzberg1">@StevenSalzberg1</a></p> <hr> <p>The <a href="https://www.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/">BOSC 2016 call for abstracts is currently open</a>, and <a href="https://www.iscb.org/ismb2016-registration">BOSC/ISMB 2016 registration</a> will open next week. We hope to see you in Florida!</p>https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/Tue, 01 Mar 2016 20:52:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/<p>We are very pleased to announce our new <a href="https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md">Open Bioinformatics Foundation (OBF) Travel Fellowship program</a>. The program is designed to enable people, whether long-standing members of our community or newcomers, to participate in eligible events for which costs would otherwise be prohibitive. This includes our annual <a href="https://www.open-bio.org/wiki/BOSC">Bioinformatics Open Source Conference (BOSC)</a>.</p> <p>Although not limited to specific groups of people, the program constitutes another major step for us in our ongoing efforts to increase the diversity in our communities in particular, and in the open source / open science bioinformatics community in general. As explained in the just published <a href="http://dx.doi.org/10.1371/journal.pcbi.1004691">BOSC 2015 report</a>, inclusivity was one of the founding principles of the Bio* open-source project communities that came together under the OBF umbrella, and thus also of BOSC, our flagship event. <a href="https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md">OBF&rsquo;s bylaws</a> have included a nondiscrimination clause from the outset. OBF&rsquo;s major member projects have not only always welcomed new participants to their communities, but embraced passing on leadership to people who hadn&rsquo;t been part of the &ldquo;inner circle&rdquo; from the beginning.</p> <p>However, being on the &ldquo;inside&rdquo; can hide the barriers to joining a community as a newcomer. In practice, the demographics of our member community, and therefore also of BOSC, have mirrored the <a href="http://floss2013.libresoft.es/results.en.html">low diversity observed</a> for open-source project communities in general.</p> <p>We&rsquo;ve committed ourselves to address this. We simply owe it to our mission, which is predicated on being inclusive. For BOSC 2015 we chose to make increasing diversity the main theme, including the <a href="https://news.obf.io/2015/06/05/bosc-2015-panel-increasing-diversity/">BOSC 2015 panel discussion</a>. When asked for a show of hands of who was there for the first time, nearly half of the attendees&rsquo; hands went up! We believe firmly that with enough dedicated and sustained attention, our community <em>can</em> include everyone who shares our mission. We also believe that eventually more diversity at our community events <em>will</em> trickle down to increasing the diversity of participants in our member projects.</p> <p>To fund the OBF Travel Fellowship program, we have for now committed an annual budget of $5,000 from our existing assets. At this level, we should be able to sustain the program for a minimum of 3 years.  We would like to do more, and to commit to the program for at least 10 years. To help us accomplish that, we are <a href="https://www.open-bio.org/wiki/Donate">calling on donors</a> and BOSC sponsors. You can earmark your contribution to be used specifically for funding this program – simply <a href="mailto:board@open-bio.org">email the Board</a> if the donation form does not leave enough space.</p> <p>Special thanks for bringing this program to life go to Karen Cranston, who joined the OBF Board in spring 2015 and shepherded the effort from inception to launch.</p>https://www.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/Tue, 01 Mar 2016 17:42:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/<p>Call for Abstracts for the 17th Annual Bioinformatics Open Source Conference (BOSC 2016), a Special Interest Group (SIG) of <a href="https://www.iscb.org/ismb2016">ISMB 2016</a>.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2016"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]"></a></p> <ul> <li>Dates: July 8-9, 2016</li> <li>Location: Orlando, FL</li> <li>Web site: <a href="https://www.open-bio.org/wiki/BOSC_2016">/wiki/BOSC_2016</a></li> <li>Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></li> <li>BOSC announcements mailing list: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a></li> <li>Twitter: <a href="https://twitter.com/OBF_BOSC" title="OBF Bioinformatics Open Source Conference (BOSC)">@OBF_BOSC</a> and <a href="https://twitter.com/OBF_news" title="Open Bioinformatics Foundation (OBF) News">@OBF_News</a></li> </ul> <p>Important Dates:</p> <p><a href="http://www.iscb.org/ismb2016"><img src="https://news.obf.io/wp-content/uploads/2016/03/ismb2016.png" alt="[ISMB 2016 logo]"></a></p> <ul> <li>Call for one-page abstracts opens: March 1, 2016</li> <li><a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">Abstract submission</a> deadline: April 1, 2016 - <em>extended to Monday 4 April 2016</em></li> <li>Travel fellowship application deadline: April 15, 2016</li> <li>Authors notified: May 6, 2016</li> <li><a href="https://www.open-bio.org/wiki/Codefest_2016">Codefest 2016</a>: July 6-7, 2016, Orlando, FL (confirming venue)</li> <li><a href="https://www.open-bio.org/wiki/BOSC_2016">BOSC 2016</a>: July 8-9, 2016, Orlando, FL</li> <li><a href="https://www.iscb.org/ismb2016">ISMB 2016</a>: July 8-12, 2016, Orlando, FL</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. It is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results and software.</p> <p>We welcome one-page abstracts on any topic of relevance to open source bioinformatics and open science. Presentation formats are lightning talks, longer talks, and/or posters. We plan to offer a limited number of travel fellowships to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC – please see the <a href="https://www.open-bio.org/2016/03/01/obf-travel-fellowship-program/">OBF Travel Fellowship announcement</a> for more information.</p> <p>Session topics include:</p> <ul> <li>Open Science and Reproducible Research</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Visualization</li> <li>Translational Bioinformatics</li> <li>Bioinformatics Open Source Libraries and Projects</li> </ul> <p>If your company or organization is interested in helping to sponsor BOSC 2016, please contact us! Sponsors in 2015 included <a href="http://www.google.com/">Google</a>, <a href="http://www.gigasciencejournal.com/">GigaScience</a>, <a href="http://curoverse.com/">Curoverse</a> and <a href="http://bina.com/">Bina</a> – we thank them for their support.</p> <p>BOSC 2016 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko</p>https://www.open-bio.org/2015/12/10/online-membership-form/Thu, 10 Dec 2015 05:35:13 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/12/10/online-membership-form/<p>The Open Bioinformatics Foundation (OBF) is pleased to announce that we’ve finally entered the 21st century and upgraded our membership form from paper (yep!) to an <a href="https://goo.gl/l6WJ23" title="OBF membership form">online form</a>.</p> <p><a href="https://www.open-bio.org/wiki/Membership">Membership in the OBF</a> is free, and is open to anyone who has attended BOSC or can otherwise demonstrate commitment to <a href="https://www.open-bio.org/wiki/Main_Page#About_Us">OBF&rsquo;s goals</a>. The information you enter on the form, including your email address, will be treated confidentially - we are in the business of promoting open source and open science, not in selling email addresses.</p> <p>If you have any questions about OBF or OBF membership, you can contact us at <a href="mailto:board@open-bio.org">board@open-bio.org</a> and/or tweet to <a href="https://twitter.com/obf_news">@OBF_News</a>.</p>https://www.open-bio.org/2015/10/21/biopython-1-66-released/Wed, 21 Oct 2015 19:55:16 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/10/21/biopython-1-66-released/<p>Source distributions and Windows installers for Biopython 1.66 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">official Biopython website</a> and from the <a href="https://pypi.python.org/pypi/biopython/1.66">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, although support for Python 2.6 is now deprecated. It has also been tested on PyPy 2.4 to 2.6, PyPy3 version 2.4, and Jython 2.7.</p> <p>Further work on the <code>Bio.KEGG</code> and <code>Bio.Graphics</code> modules now allows drawing KGML pathways with transparency.</p> <p>The <code>Bio.SeqIO &quot;abi&quot;</code> parser now decodes almost all the documented fields used by the ABIF instruments - including the individual color channels.</p> <p><code>Bio.PDB</code> now has a <code>QCPSuperimposer</code> module using the Quaternion Characteristic Polynomial algorithm for superimposing structures. This is a fast alternative to the existing <code>SVDSuperimposer</code> code using singular value decomposition.</p> <p>Bio.Entrez now implements the NCBI Entrez Citation Matching function (ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings. <code>Bio.Entrez.parse(...)</code> now supports NCBI XML files using XSD schemas, which will be downloaded and cached like NCBI DTD files.</p> <p>A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand were parsed into CompoundLocations was fixed: <code>complement(join(...))</code> as used by NCBI worked, but <code>join(complement(...),complement(...),...)</code> as used by EMBL/ENSEMBL gave the CompoundLocation parts in the wrong order. A related bug when taking the reverse complement of a SeqRecord containing features with CompoundLocations was also fixed.</p> <p>Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work on conforming to the Python PEP8 standard coding style.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alan Medlar (first contribution)</li> <li>Anthony Mathelier (first contribution)</li> <li>Antony Lee (first contribution)</li> <li>Anuj Sharma (first contribution)</li> <li>Ben Fulton (first contribution)</li> <li>Bertrand Néron (first contribution)</li> <li>Brandon Invergo</li> <li>Carlos Pena</li> <li>Christian Brueffer</li> <li>Connor T. Skennerton (first contribution)</li> <li>David Arenillas (first contribution)</li> <li>David Nicholson (first contribution)</li> <li>Emmanuel Noutahi (first contribution)</li> <li>Eric Rasche (first contribution)</li> <li>Fabio Madeira (first contribution)</li> <li>Franco Caramia (first contribution)</li> <li>Gert Hulselmans (first contribution)</li> <li>Gleb Kuznetsov (first contribution)</li> <li>João Rodrigues</li> <li>John Bradley (first contribution)</li> <li>Kai Blin</li> <li>Kian Ho (first contribution)</li> <li>Kozo Nishida (first contribution)</li> <li>Kuan-Yi Li (first contribution)</li> <li>Leighton Pritchard</li> <li>Lucas Sinclair</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Saket Choudhary</li> <li>Sunhwan Jo (first contribution)</li> <li>Tarcisio Fedrizzi (first contribution)</li> <li>Tiago Antao</li> <li>Vincent Davis</li> </ul> <p>This is a longer list than usual, which is good, but in part this reflects the fact that this release is long overdue. Sorry, that was my fault.</p>https://www.open-bio.org/2015/07/02/bioruby-1-5-0-released/Thu, 02 Jul 2015 14:03:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/07/02/bioruby-1-5-0-released/<p>We are pleased to announce the release of BioRuby 1.5.0. This new release includes support of recent Ruby versions (Ruby 2.0.0, 2.1 and 2.2),  improvement of codes, and bug fixes.</p> <p>Here is a brief summary of changes.</p> <ul> <li>Ruby 2.0.0, 2.1, 2.2 support.</li> <li>Some features are removed because of remote service discontinuance or difficulty of code maintenance.</li> <li>Refactoring of code.</li> <li>Bio::SPTR is renamed as Bio::UniProtKB.</li> <li>Bug fixes.</li> </ul> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.5.0/RELEASE_NOTES.rdoc" title="RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.5.0/ChangeLog" title="ChangeLog">ChangeLog</a>.</p> <p>The archive is available for download from the following links.</p> <ul> <li>Tar.gz file: <a href="http://bioruby.org/archive/bioruby-1.5.0.tar.gz" title="http://bioruby.org/archive/bioruby-1.5.0.tar.gz">http://bioruby.org/archive/bioruby-1.5.0.tar.gz</a></li> <li>Gem file: <a href="https://rubygems.org/gems/bio" title="https://rubygems.org/gems/bio">https://rubygems.org/gems/bio</a> or <a href="http://bioruby.org/archive/gems/bio-1.5.0.gem" title="http://bioruby.org/archive/gems/bio-1.5.0.gem">http://bioruby.org/archive/gems/bio-1.5.0.gem</a></li> </ul> <p>You can easily install by using RubyGems. First, check the version number by using search command:</p> <p><code>% gem search --remote bio</code></p> <p>and find “bio (1.5.0)” in the list. Then,</p> <p><code>% sudo gem install bio</code></p> <p>Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2015/06/05/bosc-2015-panel-increasing-diversity/Fri, 05 Jun 2015 10:29:46 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/06/05/bosc-2015-panel-increasing-diversity/<p>Every year, BOSC includes a panel discussion that offers all attendees the chance to engage in conversation with the panelists and each other. Two months ago <a href="http://news.open-bio.org/news/2015/04/bosc-2014-diversity/">we announced the theme</a> of the BOSC 2015 panel would be &quot; <em>Open Source, Open Door: increasing diversity in the bioinformatics open source community&quot;</em>. Our complete list of panellists is:</p> <ul> <li>Panel chair <strong>Mónica Muñoz-Torres</strong> ( <a href="https://twitter.com/monimunozto">@monimunozto</a>) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). She is part of the development teams for Web Apollo (a web-based annotation editor designed to support community-based curation of genomes) and the tools of the Gene Ontology (GO) Consortium. She co-leads the Community Curation group within the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5K Initiative), and is a member of the Executive Committee of the International Society for Biocuration (ISB). As a graduate student, Monica founded the first Southeastern Chapter of the Society for Advancement of Hispanics/Chicanos and Native Americans in Science (SACNAS) at Clemson University; the chapter has since been actively involved in outreach activities to local high schools in an attempt to inspire students to pursue careers in STEM. She is currently working on forming the first professional chapter of SACNAS in the San Francisco Bay area.</li> <li><strong>Holly Bik</strong> ( <a href="https://twitter.com/hollybik">@hollybik</a>) is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes.</li> <li><strong>Michael R. Crusoe</strong> ( <a href="https://twitter.com/biocrusoe">@biocrusoe</a>) is the lead for the k-h-mer project at C. Titus Brown&rsquo;s Lab for Data Intensive Biology at the University of California, Davis in the School of Veterinary Medicine. A community-minded bioinformatics research software engineer and Software Carpentry instructor, he is also a member of the Debian Med software packaging team. Michael&rsquo;s social justice background includes a prior seat on the board for the Phoenix, Arizona chapter of GLSEN, the Gay, Lesbian, and Straight Education Network and he is proud to be a supporter of the Ada Initiative.</li> <li><strong>Aleksandra Pawlik</strong> ( <a href="https://twitter.com/aleksandrana">@aleksandrana</a>) is a Training Lead at the Software Sustainability Institute at Manchester University, UK. She coordinates training activities and helps develop strategies and curricula for teaching computational lab skills to researchers across disciplines at all stages of their research career. She is a member of the Steering Committees for Data Carpentry and Software Carpentry Foundation, and supports the development of both initiatives. Currently, Aleksandra is collaborating on training with the ELIXIR project supporting the bioinformatics community. As a certified Software and Data Carpentry instructor Aleksandra has taught at a number of workshops, including Software Carpentry for Women in Science and Engineering, which she co-organised.</li> <li><strong>Jason Williams</strong> ( <a href="https://twitter.com/JasonWilliamsNY">@JasonWilliamsNY</a>) is the Lead of the iPlant Collaborative’s Education, Outreach, Training (EOT) group, based at Cold Spring Harbor Laboratory, where he has worked for over 10 years. He is also a Lead Instructor of “The Science Institute” at Yeshiva University High School for Girls, and the Treasurer of the Software Carpentry Foundation. His background is in molecular biology and bioinformatics. Diversity is a focus of Jason&rsquo;s work at the DNA Learning Center and with iPlant, where he works to target outreach along the entire spectrum of underrepresented and underserved groups ranging from minorities in urban communities to first-generation college students at rural institutions.</li> </ul> <p>In addition the BOSC 2015 co-chairs <strong>Nomi Harris</strong> and <strong>Peter Cock</strong> will be on hand, along with other Open Bioinformatics Foundation (OBF) Board Members and BOSC organising committee members, to comment on what BOSC and the OBF are trying to do to improve diversity in the open source bioinformatics community, and listen to suggestions.</p> <p>P.S. Today is the deadline for discounted early <a href="https://www.iscb.org/ismbeccb2015-registration#registrationfee" title="ISMB/ECCB 2015 registration, including BOSC">registration</a>, and the deadline to submit a late breaking lightning talk or poster abstract. See <a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a> for more details.</p>https://www.open-bio.org/2015/05/01/public-obf-board-meeting/Fri, 01 May 2015 21:46:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/05/01/public-obf-board-meeting/<p>The next public Board of Directors Meeting of the OBF will take place on May 12th, 2015, at 17:00 UTC (1pm EDT, 10am PDT, 19:00 CEST, see <a href="http://#" title="OBF Meeting in World Clock">World Clock</a>). The developing <a href="https://www.open-bio.org/wiki/Minutes:2015_May_ConfCall" title="Board Meeting agenda">agenda for the meeting</a> is posted, as are the dial-in details.</p> <p>We will have Board elections at this meeting. The terms of Directors Jason Stajich and Chris Dagdigian expire, and they will both step down from the Board. As most of you will know, both have provided truly extraordinary service to the OBF, from the earliest beginnings of the organization and in fact the very community around it. They provided leadership when few others did, and they were there during the most challenging times of OBF.  If you won&rsquo;t be able to attend the meeting, please still find the time to express your appreciation to them for their service, and the work they continue to volunteer.</p> <p>We also have a candidate, Karen Cranston, running for a seat on the Board. If you have not yet met her, Karen (Github, Twitter) is the Training Coordinator and Informatics Project Manager at the National Evolutionary Synthesis Center (NESCent). She is an evolutionary biologist interested in phylogenetic methods and is the lead PI of Open Tree of Life, an NSF-funded project to synthesize published evolutionary trees. She&rsquo;s helped organize many events for open source and data interoperability in biology, including Phyloinformatics Summer of Code, iEvoBio, hackathons, and Data / Software Carpentry workshops.</p> <p>I look forward to the Board meeting, and to seeing many of you in July at the <a href="https://www.open-bio.org/wiki/BOSC_2015" title="BOSC 2015">2015 BOSC</a> in Dublin.</p> <p><a href="http://termpaperhelponline.com/term-papers-for-sale">term papers for sale</a></p> <p>Hilmar Lapp, President, OBF Board of Directors</p> <p><em><strong>Update:</strong></em> Karen Cranston was elected to the board at the <a href="https://www.open-bio.org/wiki/Minutes:2015_May_ConfCall" title="meeting minutes">12 May Public OBF Board Meeting</a>.</p>https://www.open-bio.org/2015/04/02/bosc-2014-diversity/Thu, 02 Apr 2015 22:09:39 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/04/02/bosc-2014-diversity/<p>The <a href="https://www.open-bio.org/wiki/BOSC_2015">Bioinformatics Open Source Conference (BOSC)</a> has always been about community. Launched in 2000, BOSC aims to provide a forum for both bioinformatics developers and users to share ideas and code and learn about the latest developments in open source bioinformatics and open science.</p> <p>Our goal this year is to welcome even greater participation, opening the door even wider to participants who have historically been underrepresented in the world of open source bioinformatics and, therefore, at BOSC. This includes (but is by no means limited to) women, people who aren&rsquo;t white, older people, people from outside North America and Europe, and non-programmers.</p> <p>During a Birds of a Feather (BoF) session held at <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a>, we discussed ways to increase the diversity of BOSC attendees, and gathered many useful suggestions from the participants, some of which we have already acted upon.</p> <p>One of the suggestions from the 2014 BoF was to add someone to the organizing committee to focus on outreach and community-building. In January 2015, <a href="http://news.open-bio.org/news/2015/01/bosc-welcomes-sarah-hird/">we welcomed Dr. Sarah Hird as our new Outreach Coordinator</a>. Sarah is currently a UC Davis Chancellor&rsquo;s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity. Sarah is also known for her focus on <a href="https://sites.google.com/site/sarahhird/diversity-in-stem">promoting diversity in STEM</a>.  &quot; <em>I am personally and professionally interested in how we can make “the Academy&quot; a more representative sample of the world around us,</em>&quot; she says.</p> <p>During the 2014 BoF, we were asked whether BOSC planned to adopt a Code of Conduct. We felt that this should be an ISCB-wide effort, not one that is limited to a single SIG. Our advocacy efforts with the ISCB were successful with a <a href="https://www.iscb.org/ismbeccb2015-general-info/ismbeccb2015-coc">code of conduct published on the ISMB/ECCB 2015 website</a>. We are very pleased that ISCB joins us in wanting to foster a collegial and productive environment for everyone who attends the conferences. The code of conduct will also be announced in the ISCB April Newsletter.</p> <p>The high price of travel and registration can make it hard for some people to attend BOSC. We are trying to lower this barrier by offering free or half-price registration to a limited number of accepted speakers - please indicate in the Comments section of your abstract submission if you would like to apply for this. We also award Student Travel Fellowships to the authors of the three best student abstracts each year; these provide $250 to offset travel costs, as well as granting free registration to BOSC.</p> <p>Every year, the agenda at BOSC includes a panel that gives all participants the opportunity to engage each other in discussion. This year, our panel discussion will focus on increasing diversity in our community and at our conferences. The panel will be chaired by <em>Monica Munoz-Torres</em> and will include panellists <em>Holly Bik</em> and <em>Jason Williams</em> (see bios below).</p> <ul> <li> <p>Dr. Monica Munoz-Torres (Twitter: @monimunozto) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). She is part of the development teams for Web Apollo (a web-based annotation editor designed to support community-based curation of genomes) and the tools of the Gene Ontology (GO) Consortium. She co-leads the Community Curation group within the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5K Initiative), and is a member of the Executive Committee of the International Society for Biocuration (ISB).</p> </li> <li> <p>Dr Holly Bik (Twitter: @hollybik) is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes.</p> </li> <li> <p>Jason Williams (Twitter: @JasonWilliamsNY) is the Lead of the iPlant Collaborative&rsquo;s Education, Outreach, Training (EOT) group, based at Cold Spring Harbor Laboratory, where he has worked for over 10 years. He is also a Lead Instructor of &ldquo;The Science Institute&rdquo; at Yeshiva University High School for Girls, and the Treasurer of the Software Carpentry Foundation. His background is in molecular biology and bioinformatics.</p> </li> </ul> <p>We are looking for two more panellists, and have some ideas - but your suggestions are welcome! Please [email the BOSC committee](mailto:bosc@open-bio.org?subject=BOSC 2015 Panelists) or just tweet panellist ideas at @OBF_BOSC.</p> <p><a href="http://termpapersnetwork.com/">term paper writing service</a></p> <p>Finally, please spread the word about BOSC! The deadline for <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">submitting abstracts</a> for regular-length talks is tomorrow (Friday, April 3 <em>- update: extended to Tuesday, April 7 due to Easter/Passover weekend</em>), but there will also be opportunities for last-minute lightning talks and posters.</p>https://www.open-bio.org/2015/04/01/gsoc-project-sambamba-published-in-scientific-journal/Wed, 01 Apr 2015 15:21:30 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/04/01/gsoc-project-sambamba-published-in-scientific-journal/<p><em>(This is a repost of a BLOG on Google Open Source news about Google&rsquo;s open source student programs and software releases)</em></p> <p>One of our goals with GSoC is to inspire young developers to participate in open source development, hopefully continuing well beyond the summer. Pjotr Prins from the Open Bioinformatics Foundation shared this story with us about a GSoC 2012 student who has continued leading the development of a software tool used in laboratories around the world. That tool, Sambamba, was recently featured in an Oxford University Press scientific journal. The Open Bioinformatics Foundation (OBF) participated in Google Summer of Code (GSoC) in 2012 and again in 2014. One of our projects,Sambamba, enables users to rapidly process large sequence alignment files in the SAM, BAM and CRAM formats using parallel processing. Sambamba, which means “parallel” in Swahili, was recently the subject of a paper published in Bioinformatics Journal by GSoC alumnus Artem Tarasov. Since the tool is now used in DNA sequencing centres around the world, Artem has become well known in the bioinformatics community as Sambamba’s creator.</p> <p>When we participated in GSoC 2012, we accepted five students, one of whom was Artem. His project was to “write the fastest parallelized BAM parser in D” as an alternative to the existing SAMtools software written in single-threaded C. I consider the D language to be particularly well-suited to bioinformatics given its modern hybrid OOP/functional syntax with close-to-the-metal performance optimizations.</p> <p>Even before GSoC started that year, Artem was doing research and cranking out code. In his blog, he wrote about learning the D language, dealing with parallel executing code, and the sometimes-buggy compiler and garbage collector. The file formats he was working with are complicated and contain many assumptions, but he made wise choices which led to a very effective piece of software: people tend to rave about Sambamba when they use it the first time. Artem and I continued working on Sambamba after GSoC and before long, I found that he was the one mentoring me!</p> <p>Since then, Artem has been invited to visit the Cuppen sequencing lab in the Netherlands where he added depth analysis to Sambamba. This is also when we started work on the manuscript for the Bioinformatics Journal. Later, the OBF was able to sponsor a second trip to the European Bioinformatics Institute in Cambridge, UK where he and I took part in a Codefest and met with other bioinformatics researchers and developers, including some OBF contributors.</p> <p>Artem isn’t our only GSoC student who has continued making a difference in open source. Four of our five GSoC 2012 students are still active FOSS committers on GitHub, with three of them continuing in the bioinformatics space. Although GSoC can be competitive and we haven’t been accepted into the program every year, we’re grateful for the opportunities it has given us. Organizations like OBF and SciRuby are proof that GSoC and scientific projects work really well together. Without GSoC, Artem and I would probably not have ever met. He and I both hope to introduce more students to scientific open source projects in the future. By Pjotr Prins, Sambamba GSoC Mentor</p>https://www.open-bio.org/2015/03/26/bosc-2015-keynote-speakers/Thu, 26 Mar 2015 16:05:48 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/03/26/bosc-2015-keynote-speakers/<p>Announcing the keynote speakers for the <a href="https://www.open-bio.org/wiki/BOSC_2015">Bioinformatics Open Source Conference, BOSC 2015</a>:</p> <h1 id="holly-bik">Holly Bik</h1> <p><a href="https://www.open-bio.org/wiki/File:HollyBik.png" title="Holly Bik"><img src="https://www.open-bio.org/w/images/thumb/3/37/HollyBik.png/180px-HollyBik.png" alt="Holly Bik"></a> Dr Holly Bik is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. She obtained her Ph.D. in molecular phylogenetics at the University of Southampton, UK (working in conjunction with the Natural History Museum, London), followed by subsequent postdoctoral appointments at the Hubbard Center for Genome Studies at the University of New Hampshire and the UC Davis Genome Center.</p> <p>Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes. Holly&rsquo;s keynote talk topic is &ldquo;Bioinformatics: Still a scary world for biologists&rdquo;.</p> <p><em>Many biological disciplines remain staunchly traditional, where high-throughput DNA sequencing and bioinformatics have not yet become widely adopted. In this talk, I&rsquo;ll discuss the ongoing challenges and barriers facing biologists in the age of &lsquo;Omics, based on my experiences in transitioning from nematode taxonomy to computational biology research.</em></p> <p>Homepage: <a href="http://www.hollybik.com/about/">Holly Bik</a>, Twitter: <a href="https://twitter.com/hollybik">@hollybik</a></p> <hr> <h1 id="ewan-birney">Ewan Birney</h1> <p><a href="https://www.open-bio.org/wiki/File:EwanBirney2.jpg" title="Ewan Birney"><img src="https://www.open-bio.org/w/images/thumb/0/08/EwanBirney2.jpg/230px-EwanBirney2.jpg" alt="Ewan Birney"></a> Dr Ewan Birney is Joint Associate Director of EMBL-EBI, as well as Interim Head of the Centre for Therapeutic Target Validation. Together with Dr Rolf Apweiler, he has strategic responsibility and oversight for bioinformatics services at EMBL-EBI.</p> <p>Ewan played a vital role in annotating the genome sequences of the human, mouse, chicken and several other organisms; this work has had a profound impact on our understanding of genomic biology. He led the analysis group for the ENCODE project, which is defining functional elements in the human genome. He was also one of the leaders of the BioPerl project. Ewan’s main areas of research include functional genomics, assembly algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences) and compression of sequence information.</p> <p>He has received a number of prestigious awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics. He was elected a Fellow of the Royal Society in 2014.</p> <p>Ewan was a cofounder of the <a href="https://www.open-bio.org/" title="Main Page">Open Bioinformatics Foundation</a>, the organization that sponsors BOSC, and has been involved in BOSC since the first conference in 2000. He chaired the meeting in 2001, and gave one of the keynote talks in 2002. We are delighted to have him back as a keynote speaker for 2015.</p> <p>Ewan&rsquo;s talk topic will be announced soon.</p> <p>Homepage: <a href="https://www.ebi.ac.uk/%7Ebirney/">Ewan Birney</a>, Twitter: <a href="https://twitter.com/ewanbirney">@ewanbirney</a></p> <hr> <p>The <a href="http://news.open-bio.org/news/2015/03/bosc-2015-call-for-abstracts/">BOSC 2015 call for abstracts is currently open</a>, and <a href="https://www.iscb.org/ismbeccb2015-registration">BOSC/ISMB/ECCB 2015 registration</a> has also just opened. We hope to see you in Dublin!</p>https://www.open-bio.org/2015/03/05/bosc-2015-call-for-abstracts/Thu, 05 Mar 2015 21:00:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/03/05/bosc-2015-call-for-abstracts/<p>Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2015"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]"></a></p> <ul> <li>Dates: 10-11 July, 2015</li> <li>Location: Dublin, Ireland</li> <li>Web site: <a href="https://www.open-bio.org/wiki/BOSC_2015">/wiki/BOSC_2015</a></li> <li>Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></li> <li><a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">BOSC announcements mailing list</a></li> <li>Twitter: <a href="https://twitter.com/OBF_BOSC" title="OBF Bioinformatics Open Source Conference (BOSC)">@OBF_BOSC</a> and <a href="https://twitter.com/OBF_news" title="Open Bioinformatics Foundation (OBF) News">@OBF_News</a></li> </ul> <p>Important Dates:</p> <p><a href="http://www.iscb.org/ismbeccb2015"><img src="https://news.obf.io/wp-content/uploads/2015/03/ismb_eccb_2015_dublin.png" alt="ismb_eccb_2015"></a></p> <ul> <li>March 24, 2015: Registration opens for ISMB and BOSC ( <a href="https://www.iscb.org/ismbeccb2015-registration">https://www.iscb.org/ismbeccb2015-registration</a>)</li> <li>April 3, 2015: Deadline for <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission">submitting BOSC abstracts</a></li> <li>May 3, 2015: Notification of accepted talk abstracts emailed to authors</li> <li>July 8-9, 2015: <a href="https://www.open-bio.org/wiki/Codefest_2015">BOSC Codefest 2015</a>, Dublin</li> <li>July 10-11, 2015: <a href="https://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a>, Dublin</li> <li>July 10-14, 2015: <a href="http://www.iscb.org/ismbeccb2015">ISMB/ECCB 2015</a>, Dublin</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!</p> <p>Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>We invite you to submit one-page abstracts for talks and posters. As mentioned, any topics relevant to open source bioinformatics and open science are welcome. Here are some potential session topics (but please don&rsquo;t feel limited to these!):</p> <ul> <li>Open Science and Reproducible Research</li> <li>Standards and Interoperability</li> <li>Data Science</li> <li>Visualization</li> <li>Translational Bioinformatics</li> <li>Bioinformatics Open Source Libraries and Projects</li> </ul> <p>If your company or organization is interested in being a sponsor for BOSC 2015, please contact us! Sponsors of <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a> included <a href="http://www.google.com/">Google</a>, <a href="http://www.eaglegenomics.com/">Eagle Genomics</a>, <a href="http://www.gigasciencejournal.com/">GigaScience</a>, and <a href="http://curoverse.com/">Curoverse</a> - we thank them for their support.</p> <p>BOSC 2015 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres.</p>https://www.open-bio.org/2015/03/03/sadly-obf-not-accepted-for-gsoc-2015/Tue, 03 Mar 2015 13:30:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/03/03/sadly-obf-not-accepted-for-gsoc-2015/<p>Last year&rsquo;s <a href="http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/">Google Summer of Code 2014 was very productive for the OBF</a> with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted.</p> <p>Google&rsquo;s program is enormously popular, and over-subscribed, meaning Google has had to rotate organisation membership. The OBF is grateful to have been accepted in 2010, 2011, 2012 and 2014. This year any participation will be down to individual projects to find a willing umbrella group from the <a href="https://www.google-melange.com/gsoc/org/list/public/google/gsoc2015">organisations accepted for GSoC 2015</a>. For example, a <a href="http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013">Biopython project was included under NESCent for GSoC 2013</a>.</p> <p>Other organizations with bioinformatics as keyword are <a href="https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2015-Ideas">Ruby Science Foundation</a>, <a href="https://docs.google.com/document/d/1zJGT5AwnKqx8mJLmoeRnM_iZkEk-i6Ky_M4b3Z38w6o/edit">Department of Biomedical Informatics, Stony Brook University</a>, <a href="http://bcb.dfci.harvard.edu/~cerami/gsoc.html">OncoBlocks</a>, <a href="http://helikarlab.org/GSoC.html">University of Nebraska - Helikar Lab</a>. Other organizations related to sciences are <a href="http://ascend4.org/Student_projects">ASCEND</a> , <a href="http://brlcad.org/wiki/Google_Summer_of_Code/Project_Ideas">BRL-CAD</a>, <a href="https://wiki.debian.org/SummerOfCode2015/Projects">Debian Project</a>, <a href="https://wiki.hpccsystems.com/display/hpcc/HPCC+Systems+GSoC+2015+Ideas+List">HPCC Systems®</a>,  <a href="https://www.incf.org/gsoc/2015/proposals">International Neuroinformatics Coordinating Facility</a> , <a href="http://wiki.lmona.de/get_involved/gsoc">lmonade:</a> <a href="http://wiki.lmona.de/get_involved/gsoc">scientific software distribution</a>, <a href="http://wiki.osgeo.org/wiki/Google_Summer_of_Code_2015_Ideas">OSGeo - Open Source Geospatial F</a> <a href="http://wiki.osgeo.org/wiki/Google_Summer_of_Code_2015_Ideas">oundation</a>, <a href="http://concord.org/GSoC">The Concord Consortium</a>, <a href="http://www.vtk.org/Wiki/VTK/GSoC_2015">The Visualization Toolkit</a>. Languages: <a href="https://www.google-melange.com/gsoc/org2/google/gsoc2015/python">Python</a>, <a href="https://www.google-melange.com/gsoc/org2/google/gsoc2015/scalateam">Scala</a>, <a href="https://www.google-melange.com/gsoc/org2/google/gsoc2015/apache">Apache Foundation</a>. Last but not least : <a href="https://docs.google.com/document/d/1PHPDTzD4Z6xVoxN0Q1F8yEPclSri-JA1vLvMTrLYUi8/edit">Global Alliance for Genomics &amp; Health</a>.</p> <p>On behalf of the OBF, we would like to thank our volunteer GSoC Administrators, Raoul Bonnal and Francesco Strozzi, for organising our application - and all our potential mentors across the Bio* projects who put forward potential project suggestions.</p>https://www.open-bio.org/2015/02/23/obf-gsoc-2014-wrapup/Mon, 23 Feb 2015 23:24:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2015/02/23/obf-gsoc-2014-wrapup/<p><a href="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo.jpg"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-300x270.jpg" alt="GoogleSummer_2014logo"></a> In 2014, OBF had six students in the <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code 2014™</a> (GSoC) program mentored under its umbrella of Bio* and related open-source bioinformatics community projects: Loris Cro (Bioruby) with mentors Francesco Strozzi and Raoul Bonnal; Evan Parker (Biopython) with mentors Wibowo Arindrarto and Peter Cock; Sarah Berkemer (BioHaskell) with mentors Christian Höner zu Siederdissen and Ketil Malde; and three students contributed to JSBML: Victor Kofia (mentors: Alex Thomas and Sarah Keating), Ibrahim Vazirabad (mentors: Andreas Dräger and Alex Thomas), and Leandro Watanabe (mentors: Nicolas Rodriguez and Chris Myers).</p> <p>As a change from earlier years in which OBF participated in GSoC as a mentoring organization, in 2014 we purposefully defined our umbrella as much more inclusive of the wider bioinformatics open-source community, bringing it more in line with the annual <a href="https://www.open-bio.org/wiki/BOSC" title="BOSC">Bioinformatics Open-Source Conference</a> (BOSC).  In part this was also motivated by &quot; <a href="http://en.wikipedia.org/wiki/Pay_it_forward" title="Pay It Forward - Wikipedia">paying it forward</a>&quot;, a concept central to growing healthy open-source communities, after the larger domain-agnostic language projects such as <a href="http://sciruby.com/" title="SciRuby project">SciRuby</a> and <a href="https://www.python.org/psf/" title="Python Software Foundation">PSF</a> had extended an open hand to OBF mentors when OBF did not get admitted as a GSoC mentoring organization in 2013. In the end, four out of the six succeeding student applications were for projects outside of the traditional core Bio* projects, a result with which everyone won: We had a terrific crop of students, our community grew larger and stronger, and open-source bioinformatics was advanced in a more diverse way than would have been possible otherwise.</p> <p>In addition to our students, huge kudos also go to our mentors (see above), and to Eric Talevich (Biopython) and Raoul Bonnal (Bioruby), who ran our program participation as administrators. They all invested significant amounts of time on behalf of our community and projects. Thank you!</p> <p>Below follows a short summary of each of the 2014 student projects, starting with the three JSBML students.</p> <h3 id="jsbml-and-gsoc2014">JSBML and GSoC 2014</h3> <p><a href="http://sbml.org/Software/JSBML"><img src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png" alt="JSBML logo"></a> <a href="http://sbml.org/Software/JSBML" title="JSBML website">JSBML</a> is an international community-driven, open-source project to develop a Java API library for reading, writing and manipulating <a href="http://sbml.org" title="SBML website">SBML</a>, a data format for representing and exchanging computational models in systems biology. SBML has been in use for over a decade but continues to evolve and grow, and hence so does JSBML. JSBML holds two annual development-oriented workshops, and the three 2014 JSBML GSoC students had the opportunity to participate in and present their work at the autumn event, <a href="http://co.mbine.org/events" title="COMBINE website">COMBINE</a> (Computational Modeling in Biology Network), which was held in Los Angeles, California, right at the end of GSoC. Furthermore, a scientific publication on a new JSBML release, currently under review at Bioinformatics, highlights some of the work done by the students. Hence, <a href="http://sbml.org/GSoC2014" title="JSBML in 2014 GSoC">JSBML&rsquo;s 2014 participation in GSoC</a> was a great success and experience, both for the students as well as the JSBML project and community.</p> <h3 id="ibrahim-y-vazirabad----improving-the-plugin-interface-for-celldesigner">Ibrahim Y. Vazirabad - &quot; <em>Improving the plugin interface for CellDesigner</em>&quot;</h3> <p><a href="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.52.png"><img src="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.52-300x268.png" alt="CellDesigner UML"></a> CellDesigner is a frequently used program in computational systems biology. It features an easy-to-use GUI, powerful graph editing functions, and a rich simulation functionality, among others. To facilitate rapid prototyping of new algorithms in third-party applications, CellDesigner provides a plug-in interface for Java applications to its robust interface and other features. However, the design and implementation of the plug-in interface made developing software for it very difficult and time consuming. To remedy this, a draft version of a JSBML library had been created to allow developing and testing prospective plug-in modules initially as stand-alone software, which can then be turned into a CellDesigner plug-in with very little effort. The goal of Ibrahim&rsquo;s project was to improve the interface provided by the library, and importantly, to revise it to support access to one of CellDesigner&rsquo;s most interesting features, graphical network layout. As a result of <a href="http://jsbmlcelldesigner2014.blogspot.com/" title="Project blog">Ibrahim&rsquo;s work</a>, new CellDesigner test cases and plugins that use this interface have already been implemented, including one that converts between CellDesigner’s proprietary data format and the official SBML layout extension.</p> <h3 id="leandro-h-watanabe----arrays-package">Leandro H. Watanabe - &quot; <em>Arrays Package</em>&quot;</h3> <p>The arrays and dynamic package extensions to SBML have been proposed to overcome SBML&rsquo;s limitation to static static models, which is in contrast to the inherently dynamic nature of many biological systems. The goal of <a href="http://lhwatanabe.blogspot.com/">Leandro&rsquo;s project</a> was to implement the arrays package in JSBML. Rather than enabling models with new behaviors to be constructed, the purpose of the arrays package is to represent regular constructs more efficiently and more compact than SBML core constructs can. To aid the integration of the arrays package into existing tools, Leandro also implemented the option of flattening an arrayed model to use only SBML core constructs, and a validation procedure for array constructs that checks whether a model violates any of the rules imposed on array constructs. As a consequence, his work helped solidify the Arrays Specification document of the SBML standard.</p> <h3 id="victor-kofia----redesign-the-implementation-of-mathematical-formulas">Victor Kofia - &quot; <em>Redesign the implementation of mathematical formulas</em>&quot;</h3> <p><a href="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.16.png"><img src="https://news.obf.io/wp-content/uploads/2015/02/Screenshot-2015-02-23-16.30.16-300x255.png" alt="Screenshot 2015-02-23 16.30.16"></a> JSBML uses the concept of abstract syntax trees to work with mathematical expressions. For example, the image to the right shows a syntax tree representing the formula k8 · R1. Originally, JSBML implemented different kinds of formula components all in just one complex class with diverse type attributes, which was prone to introducing errors upon code changes and generally made maintenance of the software difficult. <a href="http://kofiav.blogspot.ca/" title="Victor's project blog">Victor implemented a math package</a> for JSBML, in which different kinds of tree nodes that can occur in formulas (e.g., real numbers or algebraic symbols such as &lsquo;plus&rsquo; or &lsquo;minus&rsquo;) are represented with their own, specialized classes. This has made handling of formulas much more straightforward, and also more efficient. In the future, this new representation could even be used for symbolic or numeric calculations.</p> <h3 id="evan-parker----addition-of-a-lazy-loading-sequence-parser-to-biopython">Evan Parker - &quot; <em>Addition of a lazy loading sequence parser to Biopython&rsquo;s SeqIO package</em>&quot;</h3> <p>Though Biopython is already equipped with sequence parsers for a wide array of formats, these generally parsed entire records into memory. For large sequences such as entire chromosomes this quickly degrades performance.  To allow sequences to be loaded on-demand, Evan  designed a general lazy-loading parser by refactoring the existing object model, and then added format-specific modifications to each individual parser. The approach he devised works by pre-indexing the sequence files and then loading only those sequence regions that the user requests. <a href="http://blog.evanaparker.com/2014/08/pre-pull-request-performance-tests-and.html">Benchmarking</a> and <a href="http://blog.evanaparker.com/2014/08/fasta-performance-comparison.html">performance comparisons</a> showed this approach yields significant performance gains when, as is common for genome-scale files, users are interested only in parts of the full sequence. Evan&rsquo;s code is <a href="https://github.com/biopython/biopython/pull/356">currently under review by Biopython core developers</a>, and once merged will make parsing large sequences in Biopython much more tractable.</p> <h3 id="loris-cro----an-ultra-fast-scalable-restful-api-to-query-large-numbers-of-vcf-datapoints">Loris Cro - &quot; <em>An ultra-fast scalable RESTful API to query large numbers of VCF datapoints</em>&quot;</h3> <p>Variant Call Format (VCF) files are commonly generated by genome sequencing projects for sequence variations among different individuals and can get very large. The goal of Loris&rsquo; work was to develop code for Bioruby to determine the common variations (i.e., intersections) between multiple individuals and groups of individuals in a fast and scalable way. In the first phase of the project, Loris tested different technologies for storing large VCF files, from which MongoDB emerged as having superior performance. In the second phase Loris developed the code for efficiently storing VCF data into MongoDB, and then implemented algorithms for performing the intersection queries (see <a href="https://github.com/kappaloris/vcf-mongo" title="Loris Cro 2014 GSoC code repo">Github repo</a> and <a href="http://kappaloris.github.io/GSoC-2014-OBF/" title="Loris Cro 2014 GSoC project blog ">Loris&rsquo; project blog</a>). The code was developed using JRuby and uses the <a href="https://samtools.github.io/htsjdk/" title="HTS-JDK">HTS-JDK library</a> to parse the VCF data. In the course of the project, Loris also provided valuable feedback to the HTS-JDK team that led to improvements of the VCF parser and data model. The result of Loris&rsquo; GSoC work is now available to the community as a Ruby Gem, which has been tested and used already in large international genome re-sequencing projects, including <a href="http://www.gene2farm.eu/" title="Gene 2 Farm Website">Gene2Farm</a> and <a href="http://www.whealbi.eu/" title="WHEAt and barley Legacy for Breeding Improvement">WHEALBI</a>.</p> <h3 id="sarah-berkemer----open-source-high-performance-biohaskell">Sarah Berkemer - &quot; <em>Open source high-performance BioHaskell</em>&quot;</h3> <p>One of the challenges with sequence alignments for the purposes of sequence similarity searches is that for most known genes (i.e., sequences) relatively little is known about their biology, and the few for which a lot is known therefore tend to be only remotely related to a query sequence. <a href="http://dx.doi.org/10.1371/journal.pone.0054422" title="PLoS ONE article on Transitive Alignments">Transitive alignments</a> try to ameliorate this by aligning the query sequence against a large body of known but not deeply understood sequences, the intermediate set, which in turn are then aligned against the core of well-understood sequences. However, in contrast to aligning two sequences, aligning a sequence via a vast intermediate data set to a smaller core set is slow and memory-consuming. As part of her GSoC project, Sarah dug deep into the structure of the algorithm, and rewrote core parts to make use of fusing data structures and efficient tree-like data structures (see <a href="http://biohaskell.org/GSoC_blog" title="Sarah's GSoC project blog">her project blog</a>). <a href="http://biohaskell.org/GSoC_blog/Weeks_12and13" title="Sarah's blog">Her work brought down the runtime</a> for a benchmark by a factor of 3, from 31 to 11 minutes, and, arguably even more important, reduced memory consumption from 53 to 22 gigabytes. This now allows running the program on consumer-grade high-memory PCs. With Sarah having finished her Masters degree (congrats!!) in the meantime, she and her mentors are now in the process of writing a scientific application note and are planning to make the program available as an online web-service.</p> <p>As a rather small family within the much larger OBF umbrella, the chance to have a student contribute to functional programming for computational biology has been a tremendous opportunity and learning experience for the Biohaskell community as well.</p>https://www.open-bio.org/2014/12/17/biopython-1-65-released/Wed, 17 Dec 2014 21:06:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/12/17/biopython-1-65-released/<p>Dear Biopythoneers,</p> <p>Source distributions and Windows installers for Biopython 1.65 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">official Biopython website</a> and from the <a href="https://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>This release of Biopython supports Python 2.6, 2.7, 3.3 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.</p> <p>The most visible change is that the Biopython <em><strong>sequence objects now use string comparison</strong></em>, rather than Python&rsquo;s object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).</p> <p>The Bio.KEGG and Bio.Graphics modules have been expanded with support for the online KEGG REST API, and parsing, representing and drawing KGML pathways.</p> <p>The <em>Pterobranchia</em> Mitochondrial genetic code has been added to Bio.Data (and the translation functionality), which is the new <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">NCBI genetic code</a> table 24.</p> <p>The Bio.SeqIO parser for the ABI capillary file format now exposes all the raw data in the SeqRecord&rsquo;s annotation as a dictionary. This allows further in-depth analysis by advanced users.</p> <p>Bio.SearchIO QueryResult objects now allow Hit retrieval using its alternative IDs (any IDs listed after the first one, for example as used with the NCBI BLAST NR database).</p> <p>Bio.SeqUtils.MeltingTemp has been rewritten with new functionality.</p> <p>The new experimental module Bio.CodonAlign has been renamed Bio.codonalign (and similar lower case PEP8 style module names have been used for the sub-modules within this).</p> <p>Bio.SeqIO.index_db(&hellip;) and Bio.SearchIO.index_db(&hellip;) now store any relative filenames relative to the index file, rather than (as before) relative to the current directory at the time the index was built. This makes the indexes less fragile, so that they can be used from other working directories. <em>NOTE:</em> This change is backward compatible (old index files work as before), however relative paths in new indexes will not work on older versions of Biopython!</p> <p>Behind the scenes, we have done a lot of work applying <a href="https://www.python.org/dev/peps/pep-0008/">PEP8 coding styles</a> to Biopython, and improving the formatting of the source code documentation ( <a href="https://www.python.org/dev/peps/pep-0257/">PEP257 docstrings</a>).</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alan Du (first contribution)</li> <li>Carlos Pena (first contribution)</li> <li>Colin Lappala (first contribution)</li> <li>Christian Brueffer</li> <li>David Bulger (first contribution)</li> <li>Eric Talevich</li> <li>Evan Parker (first contribution)</li> <li>Hongbo Zhu</li> <li>Kai Blin</li> <li>Kevin Wu (first contribution)</li> <li>Leighton Pritchard</li> <li>Leszek Pryszcz (first contribution)</li> <li>Markus Piotrowski</li> <li>Matt Shirley (first contribution)</li> <li>Mike Cariaso (first contribution)</li> <li>Peter Cock</li> <li>Seth Sims (first contribution)</li> <li>Tiago Antao</li> <li>Travis Wrightsman (first contribution)</li> <li>Tyghe Vallard (first contribution)</li> <li>Vincent Davis</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Zheng Ruan</li> </ul> <p>This is a longer list of contributors and changes than usual, but it was also a longer gap since our last release.</p>https://www.open-bio.org/2014/09/18/bosc-2015-will-be-in-dublin/Thu, 18 Sep 2014 09:42:06 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/09/18/bosc-2015-will-be-in-dublin/<p>We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they&rsquo;d like to see, and — most importantly — what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) rather than as an ISMB/ECCB SIG in Dublin (Ireland)..</p> <p>Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. We would have been hosted by <a href="http://www.tgac.ac.uk">The Genome Analysis Centre (TGAC)</a> just after and co-located with the <a href="http://gcc2015.tsl.ac.uk">Galaxy Community Conference 2015</a> (GCC 2015, hosted by <a href="http://www.tsl.ac.uk">The Sainsbury Laboratory</a>). Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority preferred BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin right before ISMB/ECCB 2015.</p> <p>Here is the summary of responses to the questions about the location of BOSC 2015:</p> <p><img src="https://news.obf.io/wp-content/uploads/2014/09/BOSC2015_locations.png" alt="BOSC2015_locations"><img src="https://news.obf.io/wp-content/uploads/2014/09/BOSC2015_GCC.png" alt="BOSC2015_GCC"></p> <p>Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and welcome suggestions of people to invite.) You can reach us at <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></p> <p>Nomi Harris and Peter Cock Co-Chairs, BOSC 2015</p>https://www.open-bio.org/2014/06/19/bosc-2014-video-recording/Thu, 19 Jun 2014 15:56:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/06/19/bosc-2014-video-recording/<p><img src="https://www.open-bio.org/w/images/thumb/b/b0/Pear.png/100px-Pear.png" alt="">We&rsquo;re pleased to publicly announce that we aim to video record <em>all</em> the talks at <a href="https://www.open-bio.org/wiki/BOSC_2014_Schedule">BOSC 2014</a>, and the panel discussion, to be made freely available online after the conference. This is on an opt-out basis, and thus far none of our speakers have declined to be filmed. <a href="https://www.youtube.com/channel/UCNSng3q18VuQ-13RhhKJ5FA" title="OBF videos on YouTube.com"><img src="https://news.obf.io/wp-content/uploads/2014/06/YouTube2.png" alt="YouTube"></a> Last year we managed to record many of the talks - including both keynotes, which you can watch via the YouTube links on the <a href="https://www.open-bio.org/wiki/BOSC_2013_Schedule">BOSC 2013 Schedule</a>. This year we are hiring a professional from <a href="http://nextdayvideo.com/">Next Day Video</a> ( <a href="https://twitter.com/nextdayvideo">@NextDayVideo</a> on Twitter).</p> <p><a href="https://developers.google.com/open-source/" title="Google's Open Source Programs Office "><img src="https://news.obf.io/wp-content/uploads/2014/06/205px-Google-logo11w.png" alt="Google Logo"></a> This is thanks to very generous support from <a href="https://developers.google.com/open-source/">Google&rsquo;s Open Source Programs Office</a> (who also run the amazing <a href="https://developers.google.com/open-source/soc/">Google Summer of Code program</a> which the OBF and its member projects have regularly <a href="https://www.open-bio.org/news/category/google-summer-of-code/">taken part in</a>), a new sponsor for BOSC this year.</p>https://www.open-bio.org/2014/06/15/obf-mailing-list-outage/Sun, 15 Jun 2014 21:39:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/06/15/obf-mailing-list-outage/<p>This is a belated notice that the OBF mailing lists are down due to a server failure. Posting a tweet is easier than writing a blog post, please follow <a href="https://twitter.com/OBF_news">@OBF_news</a> for updates.</p> <p>We have a complete back up and running as a virtual machine hosted on <a href="http://aws.amazon.com">Amazon Web Services (AWS)</a>, which should become live by Monday pending DNS updates etc.</p> <p>Back in later 2012 we previously <a href="http://news.open-bio.org/news/2012/11/server-transition-to-aws/">migrated the OBF websites AWS</a>, and this has proved very reliable and saves us worrying about looking after physical hardware.</p> <p>Update (Monday 16 June 2014): The replacement mailman server is now live, but our apologies for the inconvenience. Some delayed emails should now be delivered, but unfortunately older emails where you received a failure message will have to be resent.</p>https://www.open-bio.org/2014/04/26/obf-gsoc-students-2014/Sat, 26 Apr 2014 18:45:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/04/26/obf-gsoc-students-2014/<p>Hi all, I&rsquo;m pleased to announce the acceptance of OBF&rsquo;s <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code 2014 (GSoC)</a> students: <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2014"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-150x150.jpg" alt="[GSoC 2014 Logo]"></a></p> <ul> <li>Sarah Berkemer - &quot; <em>Open source high-performance BioHaskell</em>&quot; (Mentors: Christian Höner zu Siederdissen, Ketil Malde) ( <a href="http://biohaskell.org/GSoC_blog">blog</a>)</li> <li>Loris Cro - &quot; <em>An ultra-fast scalable RESTful API to query large numbers of VCF datapoints</em>&quot; (Mentors: Francesco Strozzi, Raoul Bonnal &amp; the BioRuby team) ( <a href="http://kappaloris.github.io/GSoC-2014-OBF/">blog</a>)</li> <li>Victor Kofia - &quot; <em>JSBML: Redesign the implementation of mathematical formulas</em>&quot; (Mentors: Alex Thomas, Sarah Keating &amp; the JSBML team) ( <a href="http://kofiav.blogspot.ca/">blog</a>)</li> <li>Evan Parker - &quot; <em>Addition of a lazy loading sequence parser to Biopython&rsquo;s SeqIO package</em>&quot; (Mentors: Wibowo Arindrarto, Peter Cock &amp; the Biopython team) ( <a href="http://evanaparker.com/">blog</a>)</li> <li>Ibrahim Vazirabad - &quot; <em>Improving the Plug-in interface for CellDesigner</em>&quot; (Mentors: Andreas Dräger, Alex Thomas &amp; the JSBML team) ( <a href="http://jsbmlcelldesigner2014.blogspot.com/">blog</a>)</li> <li>Leandro Watanabe - &quot; <em>Dynamic Modeling of Cellular Populations within JSBML</em>&quot; (Mentors: Nicolas Rodriguez, Chris Myers &amp; the JSBML team) ( <a href="http://lhwatanabe.blogspot.co.uk/">blog</a>)</li> </ul> <p>Congratulations to our accepted students!</p> <p>Thanks very much to all the students who applied, we very much appreciate your hard work.</p> <p>We are now in the GSoC Community Bonding Period. Official work starts on May 23rd, and until then, students should prepare for their projects: get on the project mailing lists, solidify your plans, figure out where all the version control repositories are and which branch or fork you&rsquo;ll be working on, and start doing preparatory work.</p> <p>Here&rsquo;s to a great 2014 Summer of Code,</p> <p>Eric &amp; Raoul</p> <p>OBF GSoC 2014 Organization Administrators</p>https://www.open-bio.org/2014/04/02/catering-at-bosc-codefest-2014/Wed, 02 Apr 2014 11:13:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/04/02/catering-at-bosc-codefest-2014/<p>Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!</p> <p>The OBF will be holding the fifth <a href="https://www.open-bio.org/wiki/Codefest">annual BOSC Codefest</a>, an informal two day &ldquo;hackathon&rdquo; or &ldquo;coding festival&rdquo; preceding the <a href="https://www.open-bio.org/wiki/BOSC_2014">Bioinformatics Open Source Conference (BOSC 2014)</a> in Boston (USA).</p> <p>This year, the BOSC Codefest 2014 is being hosted by <a href="http://www.hackreduce.org">hack/reduce</a> (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by <a href="http://curoverse.com">Curoverse</a> (the team behind the open source platform <a href="http://arvados.org">Arvados</a>) and <a href="http://harbinger-partners.com/">Harbinger Partners, Inc.</a><a href="http://www.hackreduce.org/"><img src="https://www.open-bio.org/w/images/4/42/Hack-reduce-logo.png" alt=""></a><a href="http://curoverse.com/"><img src="https://www.open-bio.org/w/images/e/e5/Curoverse.png" alt=""></a><a href="http://harbinger-partners.com/"><img src="https://www.open-bio.org/w/images/a/ac/HP-logo-no-tagline.png" alt=""></a><a href="http://arvados.org/"><img src="https://www.open-bio.org/w/images/4/43/Arvados.png" alt=""></a> Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I&rsquo;m expecting <em>at least</em> coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and <a href="http://en.wikipedia.org/wiki/Jolt_Cola">Jolt Cola</a> doesn&rsquo;t exist in the USA any more&hellip; so I&rsquo;m waiting to see what our local organisers Brad Chapman &amp; Michael Heuer have planned.</p> <p>If you are wondering what happens exactly at a CodeFest, I suggest Brad&rsquo;s <a href="http://bcbio.wordpress.com/2013/07/18/summary-from-bioinformatics-open-science-codefest-2013-tools-infrastructure-standards-and-visualization/">blog post from the BOSC Codefest 2013</a>, or <a href="http://journal.embnet.org/index.php/embnetjournal/article/view/726/998">Möller et al (2013)</a>. Basically these meeting are a chance for developers of open source bioinformatics (not just the OBF&rsquo;s Bio* projects) to get together and work on common interests. Things work best with some pre-meeting planning on the usual project development mailing lists or IRC, but are also a great way to meet other scientists and developers in person with more time to chat than during a conference coffee break.</p> <p>Please note that while there is no registration fee for the <a href="https://www.open-bio.org/wiki/Codefest_2014">BOSC Codefest 2014</a>, please do fill in the registration form to help with the planning/catering.</p> <p>We&rsquo;re hoping all the Codefest participants will stay for the BOSC meeting itself, which requires formal paid registration as one of the big ISCB 2014 conference&rsquo;s SIG satellite meetings. Note that we&rsquo;re offering a <a href="http://news.open-bio.org/news/2014/03/free-student-presenters-bosc-2014/">BOSC fee waiver for student speakers</a>, this year. If you are going to BOSC, please remember to <a href="http://news.open-bio.org/news/2014/03/bosc-2014-call-for-abstracts/">submit your BOSC abstracts</a> this week!</p> <p>Peter</p>https://www.open-bio.org/2014/03/19/free-student-presenters-bosc-2014/Wed, 19 Mar 2014 18:21:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/03/19/free-student-presenters-bosc-2014/<p><a href="https://www.open-bio.org/wiki/BOSC_2014"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt=""></a> To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we&rsquo;re waiving the registration fee for accepted student presenters. When you submit your abstract ( <a href="http://news.open-bio.org/news/2014/03/bosc-2014-call-for-abstracts/">BOSC abstract call open until 4th April</a>), you must tick the student box:</p> <p><em>Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.</em></p> <p>Please note that because BOSC registration is via the ISCB as <a href="https://www.iscb.org/ismb2014-program/ismb2014-sigs-satellite-meetings#bosc">one of the ISCM SIG meetings</a>, eligible students must contact us <strong><em>before</em></strong> filling in their ISCB registration to ensure the BOSC SIG fee is waived. <a href="http://www.eaglegenomics.com/"><img src="https://www.open-bio.org/w/images/thumb/5/5f/Eagle_logo_2013.jpg/120px-Eagle_logo_2013.jpg" alt=""></a></p> <p>Furthermore, as in previous years, BOSC Student Travel Awards sponsored by <a href="http://www.eaglegenomics.com/">Eagle Genomics</a> will be awarded to the top student presentations to help with your travel and accommodation costs.</p> <p><strong>Update (2 May 2014):</strong> We&rsquo;ve just sent out the accepted talk invitations, and are offering a registration fee waiver to four student speakers.</p>https://www.open-bio.org/2014/03/09/obf-gsoc-2014-call-for-student-applications/Mon, 10 Mar 2014 00:54:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/03/09/obf-gsoc-2014-call-for-student-applications/<p><a href="http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2014/about_page"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-300x270.jpg" alt="Google Summer of Code 2014"></a> Are you a university student and interested in spending the summer developing open-source bioinformatics software?</p> <p>(Good! Keep reading.)</p> <p>On Monday, March 10, <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code 2014 (GSoC)</a> will begin accepting student applications to work with mentoring organizations like OBF.</p> <p>Here are the steps for you to prepare an application and apply for GSOC 2014 with OBF:</p> <ol> <li><strong>Check the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas">OBF ideas page</a></strong> for potential projects you&rsquo;d like to work on, and identify one or a few that you&rsquo;re most interested in doing.</li> <li><strong>Read our <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code#Guide_for_prospective_GSoC_students">guide for prospective GSoC students</a></strong> on the OBF wiki. Also see Google&rsquo;s <a href="http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2014/help_page">GSoC FAQ</a> and <a href="http://en.flossmanuals.net/GSoCStudentGuide/">GSoC student guide</a>, if you&rsquo;re with us so far.</li> <li><strong>Introduce yourself</strong> on the <a href="http://lists.open-bio.org/mailman/listinfo/gsoc">OBF GSoC mailing list</a>. Tell us which project(s) you like, any modifications to them you&rsquo;d like to make, or propose your own idea.</li> <li>Once you&rsquo;ve settled on a project or two and contacted your potential mentors, begin preparing a detailed <strong>project timeline</strong> for the summer. This timeline should cover each week of the summer, as far as you can plan it, describing the week&rsquo;s specific goals, coding tasks, anticipated problems and open questions. ( <a href="https://spreadsheets.google.com/pub?key=puFMq1smOMEo20j0h5Dg9fA&amp;single=true&amp;gid=0&amp;output=html">Example 1</a>, <a href="http://informatics.nescent.org/wiki/PhyloSoC:PhyloXML_support_in_BioRuby">Example 2</a>)</li> <li><strong>Submit your application to Google early.</strong> You can keep revising it on the Melange website until the deadline on March 21, but once you&rsquo;ve submitted your basic information we can begin giving you feedback and suggestions to improve your application. In addition to your weekly timeline, you can link to examples of code you&rsquo;ve written (e.g. on GitHub); a small contribution of code (e.g. a bug fix) to the project you&rsquo;re applying to work with would really impress us.</li> </ol> <p>Feel free to contact us on the <a href="http://lists.open-bio.org/mailman/listinfo/gsoc">mailing list</a> or <a href="https://plus.google.com/communities/103096212020630764091">Google Plus</a> if you have any questions.</p>https://www.open-bio.org/2014/03/04/bosc-2014-call-for-abstracts/Tue, 04 Mar 2014 18:18:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/03/04/bosc-2014-call-for-abstracts/<p>Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.</p> <p><a href="https://www.open-bio.org/wiki/BOSC_2014"><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]"></a></p> <ul> <li>Dates: July 11-12, 2014</li> <li>Location: Boston, MA, USA</li> <li>Web site: <a href="https://www.open-bio.org/wiki/BOSC_2014">/wiki/BOSC_2014</a></li> <li>Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a></li> <li><a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">BOSC announcements mailing list</a></li> <li>Twitter: <a href="https://twitter.com/OBF_BOSC" title="OBF Bioinformatics Open Source Conference (BOSC)">@OBF_BOSC</a> and <a href="https://twitter.com/OBF_news" title="Open Bioinformatics Foundation (OBF) News">@OBF_News</a></li> </ul> <p>Important Dates:</p> <ul> <li>March 24, 2014: <a href="https://www.iscb.org/ismb2014-registration">Registration opens for ISMB and BOSC</a></li> <li>April 4, 2014: Deadline for <a href="https://www.open-bio.org/wiki/BOSC_Abstract_Submission" title="BOSC abstract submission">submitting BOSC abstracts</a></li> <li>May 1, 204: Notification of accepted talk abstracts emailed to authors</li> <li>July 9-10, 2014: <a href="https://www.open-bio.org/wiki/Codefest_2014" title="BOSC Codefest 2014">BOSC Codefest 2014</a>, Boston</li> <li>July 11-12, 2014: <a href="https://www.open-bio.org/wiki/BOSC_2014" title="BOSC 2014">BOSC 2014</a>, Boston</li> <li>July 11-15, 2014: <a href="https://www.iscb.org/ismb2014" title="ISMB 2014 conference">ISMB 2014</a>, Boston</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.</p> <p>BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.</p> <p>We invite you to submit one-page abstracts for talks and posters. This year&rsquo;s session topics are:</p> <p><a href="http://www.eaglegenomics.com/"><img src="https://www.open-bio.org/w/images/thumb/5/5f/Eagle_logo_2013.jpg/120px-Eagle_logo_2013.jpg" alt="[Eagle Genomics Logo]"></a></p> <ul> <li>Open Science and Reproducible Research</li> <li>Software Interoperability</li> <li>Genome-scale Data and Beyond</li> <li>Visualization</li> <li>Translational Bioinformatics</li> <li>Bioinformatics Open Source Libraries and Projects</li> </ul> <p><a href="http://www.gigasciencejournal.com/"><img src="https://www.open-bio.org/w/images/thumb/b/bb/Gigascience-07.png/200px-Gigascience-07.png" alt="GigaScience Journal Logo"></a></p> <p>Once again we thank <a href="http://www.eaglegenomics.com/">Eagle Genomics</a> for sponsoring the BOSC Student Travel Awards, and welcome the open access journal <a href="http://www.gigasciencejournal.com/">GigaScience</a> as a new sponsor for BOSC 2014.</p> <p>BOSC 2014 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp</p>https://www.open-bio.org/2014/02/28/obf-accepted-as-a-mentoring-organization-for-google-summer-of-code-2014/Fri, 28 Feb 2014 07:51:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/02/28/obf-accepted-as-a-mentoring-organization-for-google-summer-of-code-2014/<p>Open Bio is officially a <a href="http://www.google-melange.com/gsoc/org2/google/gsoc2014/obf">mentoring organization</a> for Google Summer of Code 2014! See <a href="http://google-opensource.blogspot.com/2014/02/mentoring-organizations-for-google.html">Google&rsquo;s official announcement</a> for more details on what this means in general.</p> <p>What&rsquo;s next? <a href="http://www.google-melange.com/gsoc/events/google/gsoc2014">Google&rsquo;s GSoC timeline</a> lays out what we need to do as a mentoring organization during the coming weeks. Students can apply March 10&ndash;21 through the <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014">official GSoC 2014 website</a> to work with OBF. Up to that point, we&rsquo;ll be reaching out to potential students and mentors, and contining to develop <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas">potential project ideas</a>. If you&rsquo;d like to get involved, introduce yourself on our <a href="https://plus.google.com/communities/103096212020630764091">Google Plus community</a> or on the mailing lists.</p>https://www.open-bio.org/2014/02/17/obf-applies-for-google-summer-of-code-2014/Mon, 17 Feb 2014 19:21:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/02/17/obf-applies-for-google-summer-of-code-2014/<p>On Friday, OBF applied to be a mentoring organization for Google Summer of Code 2014. The core of our application to Google is our <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas">list of project ideas</a> and our team of mentors supporting them. (We also have a separate page for <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">general information about GSoC and OBF&rsquo;s involvement</a>.) As another way to interact with potential GSoC students, we&rsquo;ve created a <a href="https://plus.google.com/115564754756543103019/posts">Google Plus page for OBF</a> and a <a href="https://plus.google.com/communities/103096212020630764091">G+ community for</a> <a href="https://plus.google.com/communities/103096212020630764091">OBF&rsquo;s GSoC activities</a>.</p> <p>Highlights of this year&rsquo;s Ideas list:</p> <ul> <li>All of the Bio* projects (except BioSQL and EMBOSS) are represented. BioPerl contributed the greatest number of ideas.</li> <li>The BioJava team focused on a Java implementation of the Structural Biology Markup Language called JSBML. The JSBML developers created a <a href="http://sbml.org/GSoC2014">SBML-specific list of GSoC ideas</a>, which we&rsquo;ve included under the OBF umbrella. There is also a great opportunity here to support SBML in other languages and Bio* projects through the JVM.</li> <li>We also have a category for <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#Cross-project_ideas">cross-language project ideas</a>, i.e. those involving two or more programming languages or Bio* project communities.</li> </ul> <p>But for now we have a lull, until Feb. 24 when Google announces the accepted mentoring organizations. (Fingers crossed!)</p> <p>Thanks to everyone who helped us pull together this application. We&rsquo;re eager to hear your thoughts on how this process went and how we can keep adapting for future GSoCs.</p>https://www.open-bio.org/2014/02/01/call-for-ideas-for-obfs-2014-google-summer-of-code/Sat, 01 Feb 2014 18:08:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/02/01/call-for-ideas-for-obfs-2014-google-summer-of-code/<p><a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014">Google Summer of Code</a> is on again for 2014, and OBF is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors.</p> <p>Since OBF is an umbrella organization covering several member projects, most of these GSoC ideas will likely be associated with a specific Bio* community. For our GSoC application, and for the convenience of students, we aggregate each Bio* project&rsquo;s ideas on the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">GSoC page of the OBF wiki</a>, but the details of each idea are posted on the specific Bio* project&rsquo;s own wiki. So, if you have an idea for a Summer of Code project, please post your idea on your Bio* project mailing list for discussion and start an outline on the corresponding wiki page. Feel free to reuse or adapt ideas from 2013 or previous years that were not taken on by a student already, if you feel the idea is still viable.</p> <p>We also welcome ideas that fit with OBF&rsquo;s mission but are not part of a single Bio* project, or span multiple projects &ndash; these ideas can be posted on the <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas">OBF wiki page</a> and discussed on the <a href="http://lists.open-bio.org/mailman/listinfo/open-bio-l">OBF mailing list</a>.</p> <p>Potential students, we&rsquo;re interested in your ideas, too! This is a good occasion to introduce yourself to the OBF community.  If you have an idea for something you&rsquo;d particularly like to work on during GSoC 2014, please ask us on the mailing list and we&rsquo;ll try to find a suitable mentor.</p> <p>Here&rsquo;s to another fun and productive Summer of Code!</p>https://www.open-bio.org/2014/01/14/call-for-org-admins-for-obf-2014-gsoc/Wed, 15 Jan 2014 00:04:20 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2014/01/14/call-for-org-admins-for-obf-2014-gsoc/<p><em><strong>Update: The deadline for responding has been extended to January 25.</strong></em> <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2014"><img src="https://news.obf.io/wp-content/uploads/2014/01/GoogleSummer_2014logo-300x270.jpg" alt="GoogleSummer_2014logo"></a> The 2014 Google Summer of Code (GSoC) is coming up soon. The <a href="http://www.google-melange.com/gsoc/events/google/gsoc2014" title="2014 GSoC Timeline">published timeline</a> puts the mentoring organization applications from Feb 3 to 14.</p> <p>OBF participated on behalf of our member projects in <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2010">2010</a>, <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2011">2011</a>, and <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code_2012">2012</a>. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.</p> <p>To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve.</p> <p>An org admin’s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to “keep it together.” Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org’s mentors. The org admin’s responsibilities include:</p> <ul> <li>Representing our online face to GSoC, in particular to GSoC students</li> <li>Shepherding our mentoring organization application, and submitting it.</li> <li>Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises.</li> <li>Knowing GSoC rules and processes, and making sure ours are consistent with them.</li> <li>Reminding participants of rules, and enforcing them in the event it is necessary.</li> <li>Mediating, and sometimes arbitrating between students and mentors when needed.</li> <li>Ensuring that GSoC timelines are met by everyone.</li> </ul> <p>The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener.</p> <p>If you are interested in helping us out in this role, please email us (by Jan 25, 2014) a statement at <a href="mailto:board@open-bio.org">board@open-bio.org</a> explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project’s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects.</p> <p>We are looking forward to hearing from you!</p>https://www.open-bio.org/2013/12/24/bosc-2014-keynote-speakers/Tue, 24 Dec 2013 05:34:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/12/24/bosc-2014-keynote-speakers/<p>Thanks to those who participated in the <a href="http://news.open-bio.org/news/2013/12/bosc-2014-keynote-competition/">BOSC 2014 Keynote Competition</a>! Our winner is Manuel Corpas, who correctly surmised <a href="https://twitter.com/pebourne">Philip Bourne</a>:</p> <p><a href="https://twitter.com/manuelcorpas/status/412520369044463616">https://twitter.com/manuelcorpas/status/412520369044463616</a></p> <p>(In fact, we had already confirmed Philip Bourne as our second keynote speaker <em>before</em> his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to <a href="https://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a>!</p> <p>Dr. Bourne&rsquo;s keynote talk will be entitled &ldquo;Biomedical Research as an Open Digital Enterprise&rdquo;:</p> <blockquote> <p>The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.</p> </blockquote> <p>Our other keynote speaker at BOSC 2014, as already announced, will be <a href="https://twitter.com/ctitusbrown">Titus Brown</a>, whose topic is &ldquo;A History of Bioinformatics (in the Year 2039)&rdquo;.</p>https://www.open-bio.org/2013/12/13/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/2013/11/27/initial-release-of-bioperl-biocommunity-distribution/Thu, 28 Nov 2013 04:02:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/11/27/initial-release-of-bioperl-biocommunity-distribution/<p><strong>Note</strong>: I&rsquo;m reposting here the <a href="http://lists.open-bio.org/pipermail/bioperl-l/2013-November/071290.html">original announcement</a> from Florent Angly on the BioPerl mail list.</p> <hr> <p>Dear all,</p> <p>Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats.</p> <p>Today, I am happy to announce the release of the first version of these modules, which can be obtained from CPAN:</p> <p><a href="http://search.cpan.org/search?query=Bio-Community&amp;mode=dist">http://search.cpan.org/search?query=Bio-Community&amp;mode=dist</a></p> <p>Obviously, this is just the beginning for these modules and I hope that interested developers will join me to expand them.</p> <p>Best,</p> <p>Florent</p>https://www.open-bio.org/2013/11/12/biopython-1-63-beta-released/Tue, 12 Nov 2013 16:20:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/11/12/biopython-1-63-beta-released/<p>Source distributions and Windows installers for <strong>Biopython 1.63 beta</strong> are now available from the <a href="http://biopython.org/wiki/Download" title="Biopython&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; Downloads">downloads page</a> on the <a href="http://biopython.org/" title="Biopython website">official Biopython website</a>.</p> <p>This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. <strong>This was made possible by dropping Python 2.5 (and Jython 2.5).</strong></p> <p>This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.</p> <p>The Biopython Tutorial &amp; Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> from __future__ import print_function </span></span></code></pre></div><p>Similarly we now use the Python 3 style built-in next function in place of the Python 2 style iterators&rsquo; .next() method. This language feature is also available under Python 2.6 and 2.7.</p> <p><strong>Contributors</strong></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Chris Mitchell (first contribution)</li> <li>Christian Brueffer</li> <li>Eric Talevich</li> <li>Josha Inglis (first contribution)</li> <li>Konstantin Tretyakov (first contribution)</li> <li>Lenna Peterson</li> <li>Martin Mokrejs</li> <li>Nigel Delaney (first contribution)</li> <li>Peter Cock</li> <li>Sergei Lebedev (first contribution)</li> <li>Tiago Antao</li> <li>Wayne Decatur (first contribution)</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul>https://www.open-bio.org/2013/08/28/biopython-1-62-released/Wed, 28 Aug 2013 22:14:43 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/08/28/biopython-1-62-released/<p>Source distributions and Windows installers for <strong>Biopython 1.62</strong> are now available from the <a href="http://biopython.org/wiki/Download" title="Biopython Downloads">downloads page</a> on the <a href="http://biopython.org/" title="Biopython website">official Biopython website</a> and ( <em>soon</em>) from the <a href="https://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p><strong>Python support</strong></p> <p>This is our first release of Biopython which <em>officially supports Python 3</em>. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are <em>not</em> supported.</p> <p>We still fully support Python 2.5, 2.6, and 2.7. Support under <a href="http://www.jython.org/">Jython</a> is available for versions 2.5 and 2.7 and under <a href="http://pypy.org/">PyPy</a> for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.</p> <p>Please note that this release marks our last official for support Python 2.5. Beginning from Biopython 1.63, the minimum supported Python version will be 2.6.</p> <p><strong>Highlights</strong></p> <ul> <li>The translation functions will give a warning on any partial codons (and this will probably become an error in a future release). If you know you are dealing with partial sequences, either pad with &ldquo;N&rdquo; to extend the sequence length to a multiple of three, or explicitly trim the sequence.</li> <li>The handling of joins and related complex features in Genbank/EMBL files has been changed with the introduction of a <code>CompoundLocation</code> object. Previously a <code>SeqFeature</code> for something like a multi-exon CDS would have a child <code>SeqFeature</code> (under the <code>sub_features</code> attribute) for each exon. The <code>sub_features</code> property will still be populated for now, but is deprecated and will in future be removed. Please consult the examples in the help (docstrings) and Tutorial.</li> <li>Thanks to the efforts of Ben Morris, the Phylo module now supports the file formats NeXML and CDAO. The Newick parser is also significantly faster, and can now optionally extract bootstrap values from the Newick comment field (like Molphy and Archaeopteryx do). Nate Sutton added a wrapper for FastTree to <code>Bio.Phylo.Applications</code>.</li> <li>New module <code>Bio.UniProt</code> adds parsers for the GAF, GPA and GPI formats from UniProt-GOA.</li> <li>The <code>BioSQL</code> module is now supported in Jython. MySQL and PostgreSQL databases can be used. The relevant JDBC driver should be available in the <code>CLASSPATH</code>.</li> <li>Feature labels on circular <code>GenomeDiagram</code> figures now support the <code>label_position</code> argument (start, middle or end) in addition to the current default placement, and in a change to prior releases these labels are outside the features which is now consistent with the linear diagrams.</li> <li>The code for parsing 3D structures in mmCIF files was updated to use the Python standard library&rsquo;s <code>shlex</code> module instead of C code using flex.</li> <li>The <code>Bio.Sequencing.Applications</code> module now includes a BWA command line wrapper.</li> <li><code>Bio.motifs</code> supports JASPAR format files with multiple position-frequence matrices.</li> </ul> <p>Additionally there have been other minor bug fixes and more unit tests.</p> <p><strong>Contributors</strong></p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Alexander Campbell (first contribution)</li> <li>Andrea Rizzi (first contribution)</li> <li>Anthony Mathelier (first contribution)</li> <li>Ben Morris (first contribution)</li> <li>Brad Chapman</li> <li>Christian Brueffer</li> <li>David Arenillas (first contribution)</li> <li>David Martin (first contribution)</li> <li>Eric Talevich</li> <li>Iddo Friedberg</li> <li>Jian-Long Huang (first contribution)</li> <li>Joao Rodrigues</li> <li>Kai Blin</li> <li>Lenna Peterson</li> <li>Michiel de Hoon</li> <li>Matsuyuki Shirota (first contribution)</li> <li>Nate Sutton (first contribution)</li> <li>Peter Cock</li> <li>Petra Kubincová (first contribution)</li> <li>Phillip Garland</li> <li>Saket Choudhary (first contribution)</li> <li>Tiago Antao</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> <li>Xabier Bello (first contribution)</li> </ul>https://www.open-bio.org/2013/07/17/bosc-2013/Wed, 17 Jul 2013 14:33:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/07/17/bosc-2013/<p>Hello from Berlin, where the pre-BOSC informal <a href="https://www.open-bio.org/wiki/Codefest_2013">CodeFest 2013</a> meeting is already underway. We&rsquo;re looking forward to seeing even more of you on Friday and Saturday for <a href="https://www.open-bio.org/wiki/BOSC_2013">BOSC 2013</a>.</p> <p>BOSC 2013 will be the 14th annual <em>Bioinformatics Open Source Conference</em>, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the <a href="http://www.iscb.org/ismbeccb2013">ISMB/ECCB 2013 is in Berlin</a>, Germany.</p> <p>You can follow <a href="https://twitter.com/OBF_BOSC">BOSC on Twitter @OBF_BOSC</a>, and we&rsquo;ll be using the <a href="https://twitter.com/search?q=%23BOSC2013">Twitter Hashtag #BOSC2013</a>.</p> <p>We also have a low-volume <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">BOSC announcements mailing list</a>, please sign up if you&rsquo;d consider attending or submitting a talk or poster for next year - BOSC 2014 and the ISMB 2014 will be in Boston, USA in July 2014.</p>https://www.open-bio.org/2013/05/27/bioruby-1-4-3-0001-released/Mon, 27 May 2013 12:44:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/05/27/bioruby-1-4-3-0001-released/<p>We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs.</p> <ul> <li>&ldquo;gem install bio&rdquo; failed with Ruby 2.0 or later versions.</li> <li>lib/bio/db/gff.rb script encoding issue</li> <li>Bio::Blast::Default::Report parse error when subject sequence contains spaces.</li> </ul> <p>For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.4.3.0001/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.4.3.0001/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz">http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz</a> Gem file is also available at: <a href="http://bioruby.org/archive/gems/bio-1.4.3.0001.gem">http://bioruby.org/archive/gems/bio-1.4.3.0001.gem</a></p> <p>We also put RubyGems pacakge at RubyGems.org and RubyForge.</p> <p>You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.3.0001)” in the list. Then, % sudo gem install bio</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.</p>https://www.open-bio.org/2013/02/05/biopython-1-61-released/Tue, 05 Feb 2013 21:14:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2013/02/05/biopython-1-61-released/<p>Source distributions and Windows installers for Biopython 1.61 are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>The updated <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> is online ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p><strong>Platforms/Deployment</strong></p> <p>We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and <a href="http://www.jython.org">Jython</a> 2.5 and <a href="http://pypy.org">PyPy</a> 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ‘beta’ installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows.</p> <p>Please note we are phasing out support for Python 2.5. We will continue support for at least one further release (Biopython 1.62). This could be extended given feedback from our users. Focusing on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier.</p> <p><strong>Features</strong></p> <p>GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows an octagonal shape, like the existing BOX sigil but with the corners cut off. JAGGY shows a box with jagged edges at the start and end, intended for things like NNNNN regions in draft genomes. Finally BIGARROW is like the existing ARROW sigil but is drawn straddling the axis. This is useful for drawing vertically compact figures where you do not have overlapping genes.</p> <p>New module Bio.Graphics.ColorSpiral can generate colors along a spiral path through HSV color space. This can be used to make arbitrary &lsquo;rainbow&rsquo; scales, for example to color features or cross-links on a GenomeDiagram figure.</p> <p>The Bio.SeqIO module now supports reading sequences from PDB files in two different ways. The &ldquo;pdb-atom&rdquo; format determines the sequence as it appears in the structure based on the atom coordinate section of the file (via Bio.PDB, so NumPy is currently required for this). Alternatively, you can use the &ldquo;pdb-seqres&rdquo; format to read the complete protein sequence as it is listed in the PDB header, if available.</p> <p>The Bio.SeqUtils module how has a seq1 function to turn a sequence using three letter amino acid codes into one using the more common one letter codes. This acts as the inverse of the existing seq3 function.</p> <p>The multiple-sequence-alignment object used by Bio.AlignIO etc now supports an annotation dictionary. Additional support for per-column annotation is planned, with addition and splicing to work like that for the SeqRecord per-letter annotation.</p> <p>The Bio.Motif module has been updated and reorganized. To allow for a clean deprecation of the old code, the new motif code is stored in a new module Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif.</p> <p><strong>Experimental Code - SearchIO</strong></p> <p>This release also includes <a href="http://biopython.org/wiki/SearchIO">Bow&rsquo;s Google Summer of Code work</a> writing a unified parsing framework for NCBI BLAST (assorted formats including tabular and XML), HMMER, BLAT, and other sequence searching tools. This is currently available with the new <code>BiopythonExperimentalWarning</code> to indicate that this is still somewhat experimental. We&rsquo;re bundling it with the main release to get more public feedback, but with the big warning that the API is likely to change. In fact, even the current name of Bio.SearchIO may change since unless you are familiar with BioPerl its purpose isn&rsquo;t immediately clear.</p> <p><strong>Contributors</strong></p> <ul> <li>Brandon Invergo</li> <li>Bryan Lunt (first contribution)</li> <li>Christian Brueffer (first contribution)</li> <li>David Cain</li> <li>Eric Talevich</li> <li>Grace Yeo (first contribution)</li> <li>Jeffrey Chang</li> <li>Jingping Li (first contribution)</li> <li>Kai Blin (first contribution)</li> <li>Leighton Pritchard</li> <li>Lenna Peterson</li> <li>Lucas Sinclair (first contribution)</li> <li>Michiel de Hoon</li> <li>Nick Semenkovich (first contribution)</li> <li>Peter Cock</li> <li>Robert Ernst (first contribution)</li> <li>Tiago Antao</li> <li>Wibowo &lsquo;Bow&rsquo; Arindrarto</li> </ul>https://www.open-bio.org/2012/11/06/obf-board-meeting-13-nov/Tue, 06 Nov 2012 15:58:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/11/06/obf-board-meeting-13-nov/<p>The Open Bioinformatics Foundation (OBF) will be holding a public <a href="https://www.open-bio.org/wiki/Board">Board of Directors</a> meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT).</p> <p>The meeting will be held online or over conference call. We will post details about how to dial in or connect closer to the date ( <a href="https://www.open-bio.org/wiki/Minutes:2012_Nov_ConfCall">here</a>).</p> <p>On the agenda Richard Holland and Chris Fields are running for election to the Board, and some other items primarily up for discussion, including how to keep our membership roll up-to-date and increasing with the least barriers. We will post a more detailed agenda in advance of the meeting ( <a href="https://www.open-bio.org/wiki/Minutes:2012_Nov_ConfCall">here</a>).</p> <p>OBF members should have already received notice of this meeting via the <a href="http://lists.open-bio.org/mailman/listinfo/members">OBF member’s mailing list</a>.</p>https://www.open-bio.org/2012/11/04/server-transition-to-aws/Mon, 05 Nov 2012 01:10:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/11/04/server-transition-to-aws/<p>Our aging server which has run for 5+ years the OBF sites has finally reached end of its lifespan. We are currently migrating sites to AWS volumes and sites for a temporary period while we decide about how to continue to support these services in the future.  There will be some downtime while the all-volunteer OBF admin team makes time to fix this.</p> <p>Nearly all projects use public source code repositories such as github or sourceforge so no problems with access to the code should be limiting. Mailing lists are still using the old server but will be moved to the AWS site in the next few days and we are working to have little downtime for the lists.  Mediawiki sites are moving in stages and so far Bioperl, Biopython, and the OBF wikis have been migrated.  This news site has also been migrated to AWS and this is the 1st post from it (will it work!?)</p>https://www.open-bio.org/2012/10/12/obf-now-spi-associated/Fri, 12 Oct 2012 19:01:49 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/10/12/obf-now-spi-associated/<p>I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a <a href="http://www.spi-inc.org">Software in the Public Interest (SPI)</a> associated project, rather than its own not-for-profit incorporation.</p> <p>An electronic vote of O|B|F members on whether or not to provisionally approve the invitation from SPI closed yesterday at 19:00 UTC. We had a participation of 39 out of 105 eligible, or 37%, which is far above the quorum of 10%. The tally is 38 for provisionally accepting and 1 against. The tally can be seen (and audited) here: <a href="https://vote.heliosvoting.org/helios/e/OBFjoiningSPI">https://vote.heliosvoting.org/helios/e/OBFjoiningSPI</a></p> <p>The SPI Board vote on resolution <a href="http://www.spi-inc.org/meetings/agendas/2012/2012-10-11/">2012-09-28.jb.1</a> (&ldquo;Open Bioinformatics Foundation as associated project&rdquo;) resulted in 8 yes, 0 no, 0 abstain. Given the result of our election, I accepted the invitation right away.</p> <p>Thanks to everyone who voted. On behalf of the Board, I am thrilled about the turnout!</p> <p>This terminates O|B|F&rsquo;s status as its own corporation, which over the years has been more trouble than gain. As an SPI-associated project, we can now accept donations that are 501(c)3 tax-exempt in the US, aside from other <a href="http://www.spi-inc.org/projects/services/">benefits</a>. In the coming weeks and months we will be articulating what kind of objectives, platforms, and activities we can or should pursue, given our new status. I&rsquo;ll communicate separately about that once it gets off the ground.</p> <p>Finally, please join me in thanking Josh Berkus (SPI &amp; PostgreSQL) for shepherding our joining SPI all the way through. And please also join me in saying hi to the SPI community - as I have done earlier I&rsquo;d like to encourage everyone to consider joining the SPI as well. It&rsquo;s a friendly community, and I like to think we can enrich it.</p> <p>This is a historic day for our organization. Have a drink tonight :-)</p> <p>Cheers,</p> <p>-hilmar</p> <p>Note: This post is based on an email sent yesterday to the <a href="http://lists.open-bio.org/mailman/listinfo/members">OBF member&rsquo;s mailing list</a>.</p>https://www.open-bio.org/2012/08/21/bioruby-1-4-3-released/Tue, 21 Aug 2012 16:47:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/08/21/bioruby-1-4-3-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/">BioRuby</a> 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius.</p> <p>Here is a brief summary of changes.</p> <ul> <li>Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element.</li> <li>Many failures and errors running on JRuby and Rubinius are resolved.</li> <li>Strange behavior related with “circular require” is fixed.</li> <li>Fixed: Genomenet remote BLAST does not work.</li> <li>Fixed: Bio::NucleicAcid.to_re(“s”) typo.</li> <li>Fixed: Bio::EMBL#os raises RuntimeError.</li> <li>Fixed: bin/bioruby: Failed to save object with error message &ldquo;can’t convert Symbol into String&rdquo; on Ruby 1.9.</li> </ul> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.4.3/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.4.3/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.3.tar.gz">http://bioruby.org/archive/bioruby-1.4.3.tar.gz</a></p> <p>Gem file is also available at: <a href="http://bioruby.org/archive/gems/bio-1.4.3.gem">http://bioruby.org/archive/gems/bio-1.4.3.gem</a></p> <p>We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:</p> <p>% gem search &ndash;remote bio</p> <p>and find “bio (1.4.3)” in the list. Then,</p> <p>% sudo gem install bio</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2012/07/30/travis-ci-for-testing/Mon, 30 Jul 2012 13:24:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/07/30/travis-ci-for-testing/<p>Earlier this year <a href="http://bioruby.org">BioRuby</a> and then <a href="http://biopython.org">Biopython</a> and <a href="http://bioperl.org">BioPerl</a> started using <a href="http://travis-ci.org">Travis-CI.org</a>, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their <a href="http://github.com">GitHub</a> repositories are updated:</p> <ul> <li><a href="http://travis-ci.org/bioruby/bioruby/"><img src="https://secure.travis-ci.org/bioruby/bioruby.png?branch=master" alt="BioRuby on Travis-CI.org"></a><a href="http://travis-ci.org/bioruby/bioruby/">BioRuby</a></li> <li><a href="http://travis-ci.org/biopython/biopython/"><img src="https://secure.travis-ci.org/biopython/biopython.png?branch=master" alt="Biopython on Travis-CI.org"></a><a href="http://travis-ci.org/biopython/biopython/">Biopython</a></li> <li><a href="http://travis-ci.org/bioperl/bioperl-live/"><img src="https://secure.travis-ci.org/bioperl/bioperl-live.png?branch=master" alt="BioPerl on Travis-CI.org"></a><a href="http://travis-ci.org/bioperl/bioperl-live/">BioPerl</a></li> </ul> <p>The BioRuby team are also using Travis-CI for automated testing of their new &lsquo;plugin&rsquo; ecosystem, BioRuby Gems, or <a href="http://www.biogems.info/">BioGems</a>.</p> <p>Travis-CI gives us continuous testing, but for the moment only covers <a href="http://about.travis-ci.org/docs/user/ci-environment/">one operating system</a> (currently 32 bit Ubuntu Linux using Virtual Machines). This automated testing is therefore complementary to our existing <a href="http://testing.open-bio.org/">OBF BuildBot server</a> which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.</p> <p>However, Travis-CI are working on a new feature - <a href="http://about.travis-ci.org/blog/announcing-pull-request-support/">automatic testing of pull requests</a>, currently only available on a donation basis - which the OBF was happy to support.</p> <p>What this means is that when a contributor has some code ready for integration, they can issue a <a href="https://help.github.com/articles/using-pull-requests/">GitHub pull request</a>, and then Travis-CI will automatically run the unit tests with those proposed changes. This is something that currently the core-developers would normally do manually as part of evaluating proposed changes, so having this happen automatically should be a big help.</p> <p>We&rsquo;re excited about making more use of Travis-CI for other <a href="https://www.open-bio.org/wiki/Projects">OBF projects</a>. Thus far we&rsquo;ve been really impressed with Travis-CI.</p>https://www.open-bio.org/2012/06/25/biopython-1-60-released/Mon, 25 Jun 2012 18:17:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/06/25/biopython-1-60-released/<p>Source distributions and Windows installers for <strong>Biopython 1.60</strong> are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <h3 id="platformsdeployment">Platforms/Deployment</h3> <p>We currently support Python 2.5, 2.6 and 2.7 and also test under <a href="http://www.jython.org/">Jython</a> 2.5 and <a href="http://pypy.org/">PyPy</a> 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported.</p> <p>Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy). We are now encouraging early adopters to help beta testing on these platforms, and have included a &lsquo;beta&rsquo; installer for Python 3.2 under 32-bit Windows.</p> <h3 id="features">Features</h3> <p>New module <code>Bio.bgzf</code> supports reading and writing BGZF files (Blocked GNU Zip Format), a variant of GZIP with efficient random access, most commonly used as part of the <a href="http://samtools.sourceforge.net/">BAM file format</a> and in <a href="http://samtools.sourceforge.net/tabix.shtml">tabix</a>. This uses Python&rsquo;s <code>zlib</code> library internally, and provides a simple interface like Python&rsquo;s gzip library. Using this the <code>Bio.SeqIO</code> indexing functions now support BGZF compressed sequence files. See this blog post for <a href="http://custom-essay-service-help.co.uk/">more</a> background on <a href="http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html">BGZF and SeqIO</a>.</p> <p>The GenBank/EMBL parser will now give a warning on unrecognized feature locations and continue parsing (leaving the feature&rsquo;s location as None). Previously it would abort with an exception, which was often unhelpful.</p> <p>The <code>Bio.PDB.MMCIFParser</code> is now compiled by default (but is still not available under Jython, PyPy or Python 3).</p> <p>The SFF parser in <code>Bio.SeqIO</code> now decodes Roche 454 &lsquo;universal accession number&rsquo; 14 character read names, which encode the timestamp of the run, the region the read came from, and the location of the well.</p> <p>In the Phylo module, the &ldquo;draw&rdquo; function for plotting tree objects has become much more flexible, with improved support for <a href="http://matplotlib.sourceforge.net/">matplotlib</a> conventions and new parameters for specifying branch and taxon labels. Writing in the <a href="http://www.phyloxml.org/">PhyloXML</a> format has been updated to more closely match the output of other programs. A wrapper for the program <a href="http://sco.h-its.org/exelixis/software.html">RAxML</a> has been added under <code>Bio.Phylo.Applications</code>, alongside the existing wrapper for PhyML.</p> <p>Additionally there have been other minor bug fixes and more unit tests.</p> <h3 id="contributors">Contributors</h3> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Brandon Invergo</li> <li>Eric Talevich</li> <li>Jeff Hussmann (first contribution)</li> <li>John Comeau (first contribution)</li> <li>Kamil Slowikowski (first contribution)</li> <li>Kevin Jacobs</li> <li>Lenna Peterson (first contribution)</li> <li>Matt Fenwick (first contribution)</li> <li>Peter Cock</li> <li>Paul T. Bathen</li> <li>Wibowo Arindrarto</li> </ul>https://www.open-bio.org/2012/04/24/students-selected-for-gsoc/Tue, 24 Apr 2012 09:08:35 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/04/24/students-selected-for-gsoc/<p>Hello all,</p> <p>I&rsquo;m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 5 very capable students to work on OBF projects this summer as part of the <a href="http://code.google.com/soc/">Google Summer of Code (GSoC) program</a>.</p> <p>The accepted students, their projects, and their mentors (in alphabetical order):</p> <ul> <li><strong><a href="http://bow.web.id/blog/tag/gsoc/">Wibowo Arindrarto</a></strong>: <em>SearchIO Implementation in Biopython</em> mentored by Peter Cock</li> <li><strong><a href="http://arklenna.tumblr.com/tagged/gsoc2012">Lenna Peterson</a></strong>: <em>Diff My DNA: Development of a Genomic Variant Toolkit for Biopython</em> mentored by Brad Chapman, Reece Hart, James Casbon</li> <li><strong><a href="http://blog.mpthecoder.com/tagged/gsoc">Marjan Povolni</a></strong>: <em>The worlds fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby</em> mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal</li> <li><strong><a href="http://lomereiter.wordpress.com/tag/gsoc/">Artem Tarasov</a></strong>: <em>Fast parallelized GFF3/GTF parser in C++, with Ruby FFI bindings</em> mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal</li> <li><strong><a href="http://csw.github.com/bioruby-maf/">Clayton Wheeler</a></strong>: <em>Multiple Alignment Format parser for BioRuby</em> mentored by Francesco Strozzi and Raoul Bonnal</li> </ul> <p>As in every year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF&rsquo;s open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.</p> <p>For the accepted students: congratulations! You have risen to the top of a very competitive application process. Now it&rsquo;s time to &ldquo;put your money where your mouth is&rdquo;, as the saying goes. Let&rsquo;s get out there and write some great code this summer!</p> <p>Best regards,</p> <p>Robert Buels OBF GSoC 2012 Organization Administrator</p>https://www.open-bio.org/2012/03/25/obf-summer-of-code-2012/Sun, 25 Mar 2012 21:27:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/25/obf-summer-of-code-2012/<p>Applications due 19:00 UTC, April 6, 2012. <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">/wiki/Google_Summer_of_Code</a></p> <p>The Open Bioinformatics Foundation (OBF) Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the <a href="http://code.google.com/soc/">Google Summer of Code (GSoC)</a>.</p> <p>Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.</p> <p>The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">initial project ideas are listed on the website</a>. These range from sequence search I/O in <a href="http://biopython.org/wiki/Google_Summer_of_Code">Biopython</a> to lightweight sequence objects and lazy parsing in <a href="http://bioperl.org/wiki/Google_Summer_of_Code">BioPerl</a>, a next-generation <a href="http://www.bioruby.org/wiki/Google_Summer_of_Code">BioRuby</a> interface to Ensembl to developing cloud-optimized versions of <a href="http://biojava.org/wiki/Google_Summer_of_Code">BioJava</a> modules. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also particularly welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves.</p> <p><strong>TO APPLY:</strong> Apply online at the Google Summer of Code website (<a href="http://socghop.appspot.com/)">http://socghop.appspot.com/)</a>, where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 26 through Friday, April 6th, 2012.</p> <p><strong>INQUIRIES:</strong></p> <p>We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details.</p> <p>2012 OBF Summer of Code: <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">/wiki/Google_Summer_of_Code</a></p> <p>Google Summer of Code FAQ: <a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs">http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs</a></p> <p>Rob Buels OBF GSoC 2012 Admin</p>https://www.open-bio.org/2012/03/16/obf-accepted-for-gsoc-2012/Fri, 16 Mar 2012 21:53:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/16/obf-accepted-for-gsoc-2012/<p>Google announced today that the <a href="http://open-bio.org/">Open Bioinformatics Foundation (OBF)</a> has been accepted as a mentoring organization for <a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2012">Google Summer of Code 2012</a>!</p> <p><a href="http://code.google.com/soc/"><img src="http://code.google.com/images/GSoC2012_300x200.png" alt="GSoC 2012 Logo"></a><a href="http://code.google.com/soc/">Google Summer of Code (GSoC)</a> is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the <a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs">GSoC 2012 FAQ</a>.</p> <p>Student applications are due April 6, 2012 at 19:00 UTC. Students who are interested in participating should look at the <a href="http://open-bio.org/wiki/Google_Summer_of_Code">OBF&rsquo;s GSoC page</a>, which lists project ideas, and whom to contact about applying.</p> <p>For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project&rsquo;s GSoC wiki page.</p> <p>Thanks to all who helped make OBF&rsquo;s application to GSoC a success, and let&rsquo;s have a great, productive summer of code!</p> <p>Rob Buels OBF GSoC 2012 Administrator</p>https://www.open-bio.org/2012/03/05/call-for-abstracts-for-bosc-2012/Mon, 05 Mar 2012 19:54:28 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/05/call-for-abstracts-for-bosc-2012/<p>Call for Abstracts for the 13th Annual <a href="https://www.open-bio.org/wiki/BOSC_2012">Bioinformatics Open Source Conference (BOSC 2012)</a>, a Special Interest Group (SIG) of <a href="http://www.iscb.org/ismb2012">ISMB 2012</a>.</p> <p>Dates: July 13-14, 2012 Location: Long Beach, California Web site: <a href="https://www.open-bio.org/wiki/BOSC_2012">/wiki/BOSC_2012</a> Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> BOSC announcements mailing list: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a></p> <p>Important Dates:</p> <ul> <li>April 13, 2012: Deadline for submitting abstracts</li> <li>May 7, 2012: Notification of accepted talk abstracts emailed to authors</li> <li>July 11-12, 2012: Codefest 2012 programming session</li> <li>July 13-14, 2012: <a href="https://www.open-bio.org/wiki/BOSC_2012">BOSC 2012</a></li> <li>July 15-17, 2012: <a href="http://www.iscb.org/ismb2012">ISMB 2012</a></li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>We invite you to submit one-page abstracts for talks and posters. This year&rsquo;s session topics are:</p> <ul> <li>Cloud and Parallel Computing</li> <li>Linked Data</li> <li>Genome-scale Data Management</li> <li>Data Visualization and Imaging</li> <li>Translational Bioinformatics</li> <li>Software Interoperability (possibly a joint session with <a href="http://www.broadinstitute.org/software/bsi-sig/">BSI-SIG, the Bioinformatics Software Interoperability SIG</a>)</li> <li>Bioinformatics Open Source Project Updates</li> <li>Interfacing with Industry (panel)</li> </ul> <p>Thanks to generous sponsorship from <a href="http://eaglegenomics.com/">Eagle Genomics</a> and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards. Each winner will be awarded $250 to defray the costs of travel to BOSC 2012.</p> <p>For instructions on submitting your abstract, please visit <a href="https://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts">/wiki/BOSC_2012#Submitting_Abstracts</a></p> <p>BOSC 2012 Organizing Committee: Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice</p>https://www.open-bio.org/2012/03/02/cross-links-in-genomediagram/Fri, 02 Mar 2012 16:56:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/03/02/cross-links-in-genomediagram/<p>I&rsquo;ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in <a href="http://news.open-bio.org/news/2012/02/biopython-1-59-released/">Biopython 1.59</a>. You can now control the start and end points of individual tracks, and you can add cross-links between regions of different tracks, as shown here:</p> <p><a href="https://www.open-bio.org/wp-content/uploads/2012/03/three_track_cl2.png"><img src="https://news.obf.io/wp-content/uploads/2012/03/three_track_cl2-1024x724.png" alt="GenomeDiagram with cross-links between tracks"></a></p> <p>This example attempts a simplified reproduction of Figure 6 in <a href="http://dx.doi.org/10.1128/%E2%80%8BJB.184.21.6026-6036.2002">Proux et al. (2002)</a>, and shows three related phage genomes one above the other. Different classes of genes have been given different colors, while the strength of the red shaded cross-links indicates the percentage identity of the linked genes. Note there are some minor differences in the GenBank annotation we&rsquo;ve used and the genes shown in the original figure.</p> <p>Note while this example is in the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Tutorial HTML</a> and <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a> online, it was not in the zip/tarball for Biopython 1.59, and nor was the <a href="https://github.com/biopython/biopython/blob/master/Doc/examples/Proux_et_al_2002_Figure_6.py">Proux_et_al_2002_Figure_6.py</a> script. It will be in future releases.</p> <p>Another motivating use case for this functionality was to produce vector images of whole genome alignments in the style of the <a href="http://www.sanger.ac.uk/resources/software/act/">Artemis Comparison Tool (ACT)</a> or <a href="http://asap.ahabs.wisc.edu/mauve/">Mauve</a>. We&rsquo;ve got a poster printer in the building just crying out to be used for showing whole genome comparison of a dozen bacteria strains!</p>https://www.open-bio.org/2012/02/24/biopython-1-59-released/Fri, 24 Feb 2012 15:09:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2012/02/24/biopython-1-59-released/<p>Source distributions and Windows installers for <strong>Biopython 1.59</strong> are now available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org/">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <h3 id="platformsdeployment">Platforms/Deployment</h3> <p>We currently support <a href="http://python.org">Python</a> 2.5, 2.6 and 2.7 and also test under <a href="http://jython.org">Jython</a> 2.5 (which does not cover NumPy). Please note that this release will not work on Python 2.4</p> <p>Most functionality is also working under Python 3.1 and 3.2 (including modules using <a href="http://numpy.scipy.org/">NumPy</a>), and under <a href="http://pypy.org/">PyPy</a> (excluding our NumPy dependencies). We are now encouraging early adopters to help beta testing on these platforms.</p> <p>The installation setup.py now supports &lsquo;install_requires&rsquo; when setuptools is installed. This avoids the manual dialog when installing Biopython via easy_install or pip and numpy is not installed. It also allows user libraries that require Biopython to include it in their install_requires and get automatic installation of dependencies.</p> <h3 id="features">Features</h3> <p>New module <code>Bio.TogoWS</code> offers a wrapper for the <a href="http://togows.dbcls.jp/site/en/rest.html">TogoWS REST API</a>, a web service based in Japan offering access to KEGG, DDBJ, PDBj, CBRC plus access to some NCBI and EBI resources including PubMed, GenBank and UniProt. This is much easier to use than the NCBI Entrez API, but should be especially useful for Biopython users based in Asia.</p> <p>The <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html">NCBI Entrez Fetch</a> function <code>Bio.Entrez.efetch</code> has been updated to handle the NCBI&rsquo;s stricter handling of multiple ID arguments in EFetch 2.0 (released February 2012, see this <a href="http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000086.html">announcement</a>), however the NCBI have also changed the <code>retmode</code> default argument so <em>you</em> may need to make this explicit. e.g. add <code>retmode=&quot;text&quot;</code> to your EFetch calls (see this <a href="http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000085.html">announcement</a>).</p> <p>The position objects used in <code>Bio.SeqFeature</code> now act almost like integers, making dealing with fuzzy locations in EMBL/GenBank files much easier. Also the <code>SeqFeature</code>&rsquo;s strand and any database reference are now properties of the <code>FeatureLocation</code> object (a more logical placement), with proxy methods for backwards compatibility.</p> <p><code>Bio.Graphics.BasicChromosome</code> has been extended to allow simple sub-features to be drawn on chromosome segments, suitable to show the position of genes, SNPs or other loci.</p> <p><code>Bio.Graphics.GenomeDiagram</code> has been extended to allow <a href="http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/">cross-links between tracks</a>, and track specific start/end positions for showing regions. This can be used to imitate the output from the <a href="http://www.sanger.ac.uk/resources/software/act/">Artemis Comparison Tool (ACT)</a>. Also, a new attribute circle_core makes it easier to have an empty space in the middle of a circular diagram (see tutorial).</p> <p>Note <code>Bio.Graphics</code> requires the <a href="http://www.reportlab.com/software/opensource/">ReportLab library</a>.</p> <p><code>Bio.Align.Applications</code> now includes a wrapper for command line tool <a href="http://www.clustal.org/omega/">Clustal Omega</a> for protein multiple sequence alignment.</p> <p><code>Bio.AlignIO</code> now supports sequential <a href="http://evolution.genetics.washington.edu/phylip.html">PHYLIP</a> files (as well as interlaced PHYLIP files) as a separate format variant.</p> <p>Additionally there have been other minor bug fixes and more unit tests, and updates to the documentation including the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <h3 id="contributors">Contributors</h3> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Andreas Wilm (first contribution)</li> <li>Alessio Papini (first contribution)</li> <li>Brad Chapman</li> <li>Brandon Invergo</li> <li>Connor McCoy</li> <li>Eric Talevich</li> <li>João Rodrigues</li> <li>Konrad Förstner (first contribution)</li> <li>Michiel de Hoon</li> <li>Matej Repič (first contribution)</li> <li>Leighton Pritchard</li> <li>Peter Cock</li> </ul>https://www.open-bio.org/2011/10/28/obf-annual-meeting-2011/Fri, 28 Oct 2011 20:54:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/10/28/obf-annual-meeting-2011/<p>The annual Board of Directors Meeting of the Open Bioinformatics Foundation will take place on November 8, 2011. As in previous years, it will be held by conference call, estimated to be about 2 hrs long.</p> <p>The meeting will on Tuesday 8 November 2011, at 11am EST, 8am PST, 16:00 UTC/GMT, 17:00 CET, or Wednesday 9 November 1am JST. Note for translating into other time zones that by then both Europe and the US have gone off DST.</p> <p>Note that this meeting, like all O|B|F Board meetings, is public; every member may call in at their leisure. Please see the <a href="https://www.open-bio.org/wiki/Minutes:2011_ConfCall">agenda of the meeting</a> (including dial-in information), see also the <a href="https://www.open-bio.org/wiki/Board">current board</a>.</p>https://www.open-bio.org/2011/10/28/chromosome-diagrams-in-biopython/Fri, 28 Oct 2011 15:44:10 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/10/28/chromosome-diagrams-in-biopython/<p>One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen <a href="http://twitter.com/#!/pjacock/status/121676973054496768">via Twitter</a>. I&rsquo;ve just been updating the Biopython Tutorial (current version <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">here</a>, <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>) to include an example drawing this:</p> <p><img src="https://github.com/biopython/biopython/raw/1574d8112914ea147f4e62c6b980543db1abdc7d/Doc/images/tRNA_chrom.png" alt="tRNA genes in Arabidopsis thaliana"></p> <p>Here&rsquo;s a <a href="https://github.com/biopython/biopython/raw/1574d8112914ea147f4e62c6b980543db1abdc7d/Doc/images/tRNA_chrom.pdf">PDF version</a> too. This example just parses the <em>Arabidopsis thaliana</em> GenBank files to get the chromosome lengths and the tRNA gene placements. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. Here the figure just uses a different color for each chromosome, but you can color each feature individually.</p> <p>This kind of diagram is often used for showing the placement of SNPs or other loci of interest (e.g. disease or breeding markers).</p> <p>P.S. Biopython produces these and other graphics using <a href="http://www.reportlab.com/software/opensource/">ReportLab</a>, an open source Python library capable of outputting PDF, SVG, PNG, etc. Very handy.</p>https://www.open-bio.org/2011/08/26/bioruby-1-4-2-released/Fri, 26 Aug 2011 09:49:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/08/26/bioruby-1-4-2-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/" title="BioRuby">BioRuby</a> 1.4.2. This new release fixes bugs existed in 1.4.1 and adds new features and improvement of performance.</p> <p>Here is a brief summary of changes.</p> <p><strong>Speed-up of Bio::RestrictionEnzyme::Analysis.cut:</strong> The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written by Tomoaki NISHIYAMA and Naohisa Goto.</p> <p><strong>New classes Bio::DDBJ::REST, REST interface for DDBJ Web API for Biology (WABI) web service</strong> in additon to SOAP. Currently, only selected APIs are implemented.</p> <p><strong>Bio::Blast with remote DDBJ server uses REST instead of SOAP</strong> because Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9. We can now use remote DDBJ BLAST server with Ruby 1.9.</p> <p><strong>The Tutorial.rd is updated</strong> by Pjotr Prins and Michael O&rsquo;Keefe.</p> <p><strong>Many unit tests are added</strong> for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB and so on. Most of them are developed by Kazuhiro Hayashi during the Google Summer of Code 2010. <strong>New methods:</strong> Bio::Fastq#to_s, Bio::NCBI::REST::EFetch.nucleotide, Bio::NCBI::REST::EFetch.protein.</p> <p><strong>Bug fixes:</strong></p> <ul> <li>Bio::Blast: Failure of remote BLAST execution is fixed, due to the changes in GenomeNet and DDBJ.</li> <li>Bio::Blast: When executing remote BLAST with &ldquo;genomenet&rdquo; server, options &ldquo;-b&rdquo; and &ldquo;-v&rdquo; are now correctly used to limit the number of hits to be reported.</li> <li>Bio::SPTR (Bio::UniProt): Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines were not correctly parsed.</li> <li>Bio::Reference#pubmed_url: Updated to follow recent NCBI changes.</li> <li>Bio::Newick#reparse failure.</li> <li>Bio::MEDLINE#reference: doi field should be filled.</li> <li>Bio::Reference#endnote fails when url is not set.</li> <li>Bio::FastaFormat#query passes nil to the given factory object.</li> <li>BioRuby Shell: efetch(), getent(), and demo() fail.</li> </ul> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="https://github.com/bioruby/bioruby/blob/1.4.2/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="https://github.com/bioruby/bioruby/blob/1.4.2/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.2.tar.gz">http://bioruby.org/archive/bioruby-1.4.2.tar.gz</a></p> <p>Gem file is also available at:  <a href="http://bioruby.org/archive/gems/bio-1.4.2.gem">http://bioruby.org/archive/gems/bio-1.4.2.gem</a></p> <p>We also put RubyGems pacakge at RubyForge and RubyGems.org. You can easily install by using RubyGems. First, check the version number by using search command: % gem search &ndash;remote bio and find “bio (1.4.2)” in the list. Then, % sudo gem install bio</p> <p>Acknowledgments: Thanks to all persons reporting issues and/or submitting patches. In addition, thanks to <a href="http://biosciencedbc.jp/?lng=en">NDBC</a> / <a href="http://dbcls.rois.ac.jp/en/">DBCLS</a> <a href="http://2011.biohackathon.org/">BioHackathon2011</a> participants and organizers who try BioRuby during the BioHackathon2011.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2011/08/18/biopython-1-58-released/Thu, 18 Aug 2011 17:06:47 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/08/18/biopython-1-58-released/<p>Source distributions and Windows installers for <strong>Biopython 1.58</strong> are available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the <a href="http://biopython.org">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index (PyPI)</a>.</p> <p>A new interface and parsers for the <a href="http://abacus.gene.ucl.ac.uk/software/paml.html">PAML (Phylogenetic Analysis by Maximum Likelihood)</a> package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the <code>Bio.Phylo.PAML</code> module.</p> <p>Bio.SeqIO now includes read and write support for the <a href="http://seqxml.org">SeqXML</a>, a simple XML format offering basic annotation support. See <a href="http://dx.doi.org/10.1093/bib/bbr025">Schmitt et al (2011) in Briefings in Bioinformatics</a>.</p> <p>Bio.SeqIO now includes read support for ABI files (&ldquo;Sanger&rdquo; capillary sequencing trace files, containing called sequence with PHRED qualities).</p> <p>The Bio.AlignIO &ldquo;fasta-m10&rdquo; parser was updated to cope with the marker lines as used in <a href="http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml">Bill Pearson&rsquo;s FASTA</a> version 3.36, without this fix the parser would only return alignments for the first query sequence.</p> <p>The Bio.AlignIO &ldquo;phylip&rdquo; parser and writer now treat a dot/period in the sequence as an error, in line with the official PHYLIP specification. Older verions of our code didn&rsquo;t do anything special with this character. Also, support for &ldquo;phylip-relaxed&rdquo; has been added which allows longer record names as used in <a href="http://wwwkramer.in.tum.de/exelixis/software.html">RAxML</a> and <a href="http://www.atgc-montpellier.fr/phyml/">PHYML</a>.</p> <p>Of potential interest to anyone subclassing Biopython objects, any remaining &ldquo;old syle&rdquo; Python classes have been switched to &ldquo;new style&rdquo; classes. This allows things like defining properties.</p> <p>Bio.HMM&rsquo;s Viterbi algorithm now expects the initial probabilities explicitly.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Aaron Gallagher (first contribution)</li> <li>Bartek Wilczynski</li> <li>Bogdan T. (first contribution)</li> <li>Brandon Invergo (first contribution)</li> <li>Connor McCoy (first contribution)</li> <li>David Cain (first contribution)</li> <li>Eric Talevich</li> <li>Fábio Madeira (first contribution)</li> <li>Hongbo Zhu</li> <li>Joao Rodrigues</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Thomas Schmitt (first contribution)</li> <li>Tiago Antao</li> <li>Walter Gillett</li> <li>Wibowo Arindrarto (first contribution)</li> </ul>https://www.open-bio.org/2011/04/26/announcing-obf-google-summer-of-code-accepted-students/Tue, 26 Apr 2011 19:29:41 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/26/announcing-obf-google-summer-of-code-accepted-students/<p>I&rsquo;m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program.</p> <p>The accepted students, their projects, and their mentors (in alphabetical order):</p> <p>Justinas Vygintas Daugmaudis Michele dos Santos da Silva (2 students!) Mocapy++Biopython: from data to probabilistic models of biomolecules mentored by Thomas Hamelryck and Eric Talevich</p> <p>Chuan Hock Koh BioJava - Amino acids physico-chemical properties calculation mentored by Peter Troshin, Andreas Prlic, and Jay Vyas</p> <p>Michał Koziarski Representing bio-objects and related information with images (BioRuby) mentored by Raoul J.P. Bonnal and Francesco Strozzi</p> <p>Sheena Scroggins Major BioPerl Reorganization mentored by Robert Buels and Chris Fields</p> <p>Mikael Eric Trellet Interface analysis module for BioPython mentored by João Rodrigues and Eric Talevich</p> <p>Once again this year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked.  Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF&rsquo;s open source projects, even without Google funding.  I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.</p> <p>For the accepted students: congratulations!  You have risen to the top of a very competitive application process.  Now it&rsquo;s time to &ldquo;put your money where your mouth is&rdquo;, as the saying goes.  Let&rsquo;s get out there and write some great code this summer!</p>https://www.open-bio.org/2011/04/21/bioperl-db-bioperl-run-bioperl-network-1-6-9-release/Thu, 21 Apr 2011 20:12:53 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/21/bioperl-db-bioperl-run-bioperl-network-1-6-9-release/<p>The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN:</p> <ul> <li><a href="http://search.cpan.org/dist/BioPerl-Run/">BioPerl-Run</a></li> <li><a href="http://search.cpan.org/dist/BioPerl-DB/">BioPerl-DB</a></li> <li><a href="http://search.cpan.org/dist/BioPerl-Network/">BioPerl-Network</a></li> </ul> <p>Please report any bugs to our <a href="https://redmine.open-bio.org/">Redmine server</a>.</p> <p>Enjoy!</p> <p>chris</p>https://www.open-bio.org/2011/04/14/bioperl-1-6-9-released/Thu, 14 Apr 2011 20:03:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/14/bioperl-1-6-9-released/<p><a href="http://search.cpan.org/~cjfields/BioPerl-1.6.900/">BioPerl 1.6.9</a> is now available in CPAN.  In this release:</p> <ul> <li>Refactored Bio::Species/Bio::Tree</li> <li>New SeqIO modules (gbxml, msout, mbsout)</li> <li>Updates for perl 5.12</li> <li>Bio::Assembly support for SAM/BAM, Newbler, ace output</li> <li>Bio::DB::SeqFeature updates</li> <li>PAML updated to work with v. 4.4d</li> <li>lots of various bug fixes, around 50</li> </ul> <p>Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way.  This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make.  In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet).    Please post if there are any problems.</p> <p>Enjoy!</p>https://www.open-bio.org/2011/04/02/biopython-1-57-released/Sat, 02 Apr 2011 12:17:44 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/04/02/biopython-1-57-released/<p>The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website</a> and from the <a href="http://pypi.python.org/pypi/biopython">Python Package Index.</a></p> <p>Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary.</p> <p>Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the ability to run the BLAST tools and save the output as ASN.1 format, and then convert this to any other supported BLAST ouput format (plain text, tabular, XML, or HTML) with the blast_formatter tool. The wrappers were also updated to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.</p> <p>The SeqRecord object now has a reverse_complement method (similar to that of the Seq object). This is most useful to reversing per-letter-annotation (such as quality scores from FASTQ) or features (such as annotation from GenBank).</p> <p>Bio.SeqIO.write&rsquo;s QUAL output has been sped up, and Bio.SeqIO.convert now uses an optimised routine for FASTQ to QUAL making this much faster.</p> <p>Biopython can now be installed with pip. Thanks to David Koppstein and James Casbon for reporting the problem.</p> <p>Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and IMGT output.</p> <p>The Bio.PDB module received several fixes and improvements, including starting to merge João&rsquo;s work from GSoC 2010; consequently Atom objects now know their element type and IUPAC mass. (The new features that use these attributes won&rsquo;t be included in Biopython until the next release, though, so stay tuned.)</p> <p>The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary (previously it was a list of key,value tuples) to better match the standard.</p> <p>Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p> <ul> <li>Brad Chapman</li> <li>Eric Talevich</li> <li>Erick Matsen (first contribution)</li> <li>Hongbo Zhu</li> <li>Jeffrey Finkelstein (first contribution)</li> <li>Joanna &amp; Dominik Kasprzak (first contribution)</li> <li>Joao Rodrigues</li> <li>Kristian Rother</li> <li>Leighton Pritchard</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Peter Thorpe (first contribution)</li> <li>Phillip Garland</li> <li>Walter Gillett (first contribution)</li> </ul> <p>Feedback is most welcome on the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a>, or <a href="http://redmine.open-bio.org/projects/biopython">redmine</a>.</p>https://www.open-bio.org/2011/03/18/obf-gsoc-2011/Fri, 18 Mar 2011 21:44:22 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/18/obf-gsoc-2011/<p>Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer&rsquo;s Google Summer of Code!</p> <p>GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see <a href="http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs">GSoC 2011 FAQ</a>.</p> <p>Student applications are due April 8, 2011 at 19:00 UTC. Students who are interested in participating should look at the <a href="http://open-bio.org/wiki/Google_Summer_of_Code">OBF&rsquo;s GSoC page</a>, which lists project ideas, and whom to contact about applying.</p> <p>For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on the <a href="http://open-bio.org/wiki/Google_Summer_of_Code">OBF wiki page</a>, and on the relevant project&rsquo;s GSoC wiki page.</p> <p>Thanks to all who helped make OBF&rsquo;s application to GSoC a success, and let&rsquo;s have a great, productive summer of code!</p> <p>Rob Buels OBF GSoC 2011 Administrator</p>https://www.open-bio.org/2011/03/17/introduction-of-openid-logins-for-obf-wikis/Thu, 17 Mar 2011 17:29:38 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/17/introduction-of-openid-logins-for-obf-wikis/<p>Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding <a href="http://openid.net/">OpenID</a> logins for the OBF wikis (BioPerl <a href="http://www.bioperl.org/w/index.php?title=Special:OpenIDLogin&amp;returnto=Main_Page">example</a>). User account creation via the old login system will be disabled and OpenID will be the default path for new accounts so users to make wiki changes.  This currently appears to have cut the incidence of spam significantly.  We will be adding information to the login pages to redirect new users to the new login page.</p> <p>We also have one wiki ( <a href="http://biolib.open-bio.org">BioLib</a>) that is testing out manual account approval via a wiki bureaucrat in case we have to take more extreme measures, though we would like to leave the barrier to community involvement with projects at the lowest possible level.</p>https://www.open-bio.org/2011/03/17/obf-redmine-server-now-available/Thu, 17 Mar 2011 17:07:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/17/obf-redmine-server-now-available/<p>The OBF now has a sparkly new <a href="http://redmine.open-bio.org">Redmine instance</a> running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly).  Bugs and user names (along with email contacts) from our old <a href="http://bugzilla.open-bio.org">Bugzilla</a> v2 server have been migrated over, though some links need to be <a href="http://redmine.open-bio.org/issues/3183">fixed</a>.</p> <p><a href="http://www.redmine.org">Redmine</a> is a project management web application that has <a href="http://www.redmine.org/projects/redmine/wiki/Features">several nice features</a> over other systems, including issue tracking, multiple project management, wikis, forums, and calendaring.</p> <p>Previous Bugzilla users will need to either <a href="http://redmine.open-bio.org/account/lost_password">reset their password</a> using their original Bugzilla login (an email address) or contact the OBF Helpdesk to get their password.</p>https://www.open-bio.org/2011/03/04/bosc-2011-abstract-call/Fri, 04 Mar 2011 15:42:59 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2011/03/04/bosc-2011-abstract-call/<p><img src="https://www.open-bio.org/w/images/b/b0/Pear.png" alt="[BOSC Logo]">Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( <a href="https://www.open-bio.org/wiki/BOSC_2011">BOSC 2011</a>), an <a href="http://www.iscb.org/ismbeccb2011-program/satellite-meetings">ISMB 2011 Special Interest Group (SIG)</a>.</p> <p>Dates: July 15-16, 2011 Location: Vienna, Austria Web site: <a href="https://www.open-bio.org/wiki/BOSC_2011">/wiki/BOSC_2011</a> Email: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> BOSC announcements mailing list: <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a></p> <p>Important Dates:</p> <ul> <li>April 18, 2011: Deadline for submitting abstracts to BOSC 2011</li> <li>May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors</li> <li>July 13-14, 2011: <a href="https://www.open-bio.org/wiki/Codefest_2011">Codefest 2011</a> programming session</li> <li>July 15-16, 2011: BOSC 2011</li> <li>July 17-19, 2011: ISMB 2011</li> </ul> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation (O|B|F)</a>, a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>We invite you to submit abstracts for <em>talks and posters</em>. Sessions include:</p> <ul> <li>Approaches to parallel processing</li> <li>Cloud-based approaches to improving software and data accessibility</li> <li>The Semantic Web in open source bioinformatics</li> <li>Data visualization</li> <li>Tools for next-generation sequencing</li> <li>Other Open Source software</li> </ul> <p>In addition to the above sessions, there will be a panel discussion about <em>&ldquo;Meeting the challenges of inter-institutional collaboration&rdquo;</em>. We are also working to arrange a joint session with one of the other ISMB SIGs.</p> <p>Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three <em>Student Travel Awards</em> for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011.</p> <p>For instructions on submitting your abstract, please visit <a href="https://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information">/wiki/BOSC_2011#Abstract_Submission_Information</a></p> <p>BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor</p>https://www.open-bio.org/2010/12/21/bosc-2010-proceedings-published-today-in-bmc-bioinformatics/Tue, 21 Dec 2010 19:29:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/12/21/bosc-2010-proceedings-published-today-in-bmc-bioinformatics/<p>On behalf of the BOSC 2010 Organizing Committee, I am pleased to announce that the <a href="http://www.biomedcentral.com/1471-2105/11?issue=S12">BOSC 2010 Proceedings</a> has been published today in BMC Bioinformatics.  Special thanks go to the abstract and proceedings reviewers who helped make this possible.</p>https://www.open-bio.org/2010/10/22/bioruby-1-4-1-released/Fri, 22 Oct 2010 06:36:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/10/22/bioruby-1-4-1-released/<p>We are pleased to announce the release of <a href="http://bioruby.org/" title="BioRuby">BioRuby</a> 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added.</p> <p>Here is a brief summary of changes.</p> <p><strong>PAML Codeml support is significantly improved:</strong> PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins.</p> <p><strong>KEGG PATHWAY and KEGG MODULE parsers are added:</strong> The code is developed by Kozo Nishida and Toshiaki Katayama.</p> <p><strong>Bio::KEGG::GENES and Bio::KEGG::GENOME and bug fixes and new methods:</strong> Some of them are due to the file format changes.</p> <p><strong>Test codes are added and improved:</strong> Test codes are added and improved. Tney are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince, and Naohisa Goto.</p> <p><strong>Bug fixes in Bio::Tree:</strong> somemethods did not work correctly.</p> <p><strong>Platform-dependent bug when calling external programs:</strong> Detection of platform is improved not to call fork(2) on platforms that do not support it (e.g. JRuby).</p> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="http://github.com/bioruby/bioruby/blob/1.4.1/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="http://github.com/bioruby/bioruby/blob/1.4.1/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.1.tar.gz">http://bioruby.org/archive/bioruby-1.4.1.tar.gz</a></p> <p>Gem file is also available at:  <a href="http://bioruby.org/archive/gems/bio-1.4.1.gem">http://bioruby.org/archive/gems/bio-1.4.1.gem</a></p> <p>We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.1)” in the list. Then, % sudo gem install bio</p> <p>Finally, we are sorry that many new features are waiting to be merged to BioRuby, including  HMMER3 support. These will be included in the next major release version.</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2010/08/31/biopython-1-55-released/Tue, 31 Aug 2010 22:49:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/08/31/biopython-1-55-released/<p>The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable release ( <a href="http://news.open-bio.org/news/2010/05/biopython-release-154/">Biopython 1.54</a>) and the <a href="http://news.open-bio.org//news/2010/08/biopython-1-55-beta-released/">beta release</a> earlier in August.</p> <p>A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn&rsquo;t notice any changes ;)</p> <p>In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated <a href="http://www.biopython.org/wiki/Documentation">documentation</a>.</p> <p>Additionally GenBank and EMBL parsing has been sped up, the <a href="http://www.biopython.org/wiki/BioSQL">BioSQL</a> classes act more like Python dictionaries, and Bio.PDB should handle model numbers and a missing element column better.</p> <p>Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution).</p> <p>(At least) 12 people have contributed to this release, including 6 new people - thank you all:</p> <ul> <li>Andres Colubri (first contribution)</li> <li>Carlos Rios Vera (first contribution)</li> <li>Claude Paroz (first contribution)</li> <li>Cymon Cox</li> <li>Eric Talevich</li> <li>Frank Kauff</li> <li>Joao Rodrigues (first contribution)</li> <li>Konstantin Okonechnikov (first contribution)</li> <li>Michiel de Hoon</li> <li>Nathan Edwards (first contribution)</li> <li>Peter Cock</li> <li>Tiago Antao</li> </ul> <p>Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website (biopython.org)</a>.</p> <p>As usual, feedback is most welcome on the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/08/26/bioruby-paper-published/Fri, 27 Aug 2010 00:13:15 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/08/26/bioruby-paper-published/<p>After 10 years of development, the BioRuby paper is finally published in the <a href="http://bioinformatics.oxfordjournals.org/"><em>Bioinformatics</em></a> journal.  The article is open access, so please take a look.</p> <p>BioRuby: Bioinformatics software for the Ruby programming language Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama <em>Bioinformatics</em> 2010; <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq475">doi: 10.1093/bioinformatics/btq475</a></p>https://www.open-bio.org/2010/08/18/biopython-1-55-beta-released/Wed, 18 Aug 2010 20:52:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/08/18/biopython-1-55-beta-released/<p>We&rsquo;ve just released a <em>beta</em> of Biopython 1.55 for user testing.</p> <p>Since <a href="http://news.open-bio.org/news/2010/05/biopython-release-154/">Biopython 1.54</a> was released three months ago, we&rsquo;ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we&rsquo;ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we&rsquo;ve accidentally broken things - which is why we&rsquo;re doing this beta release.</p> <p>In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated <a href="http://www.biopython.org/wiki/Documentation">documentation</a>.</p> <p>Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution).</p> <p>(At least) 10 people have contributed to this release (so far), including 5 new people:</p> <ul> <li>Andres Colubri (first contribution)</li> <li>Carlos Rios Vera (first contribution)</li> <li>Claude Paroz (first contribution)</li> <li>Eric Talevich</li> <li>Frank Kauff</li> <li>Joao Rodrigues (first contribution)</li> <li>Konstantin Okonechnikov (first contribution)</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Tiago Antao</li> </ul> <p>Source distributions and Windows installers are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a> on the <a href="http://www.biopython.org">Biopython website (biopython.org)</a>.</p> <p>So, please let us know what works and what doesn’t through the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/05/20/biopython-release-154/Thu, 20 May 2010 19:04:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/05/20/biopython-release-154/<p>The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes.</p> <p>This is the first stable release to feature the new <a href="http://www.biopython.org/wiki/Phylo" title="Bio.Phylo documentation on the wiki">Bio.Phylo</a> module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and <a href="http://www.phyloxml.org/" title="PhyloXML decription">PhyloXML</a> formats. The module is the result of Eric Talevich&rsquo;s Google Summer of Code project which was supported by <a href="http://www.nescent.org/index.php">The National Evolutionary Synthesis Center (NESCent)</a>.</p> <p>Biopython now supports the reading, writing and indexing of Standard Flowgram Format (SFF) files produced in 454 sequencing. Jose Blanca (the brains behind the widely used <a href="http://bioinf.comav.upv.es/sff_extract/" title="sff_extract homepage">sff_extract</a> tool) provided code to handle SFF files and Peter Cock has integrated that code with <code>Bio.SeqIO</code>. Adding SFF support to <code>SeqIO</code> makes it possible to convert these files to the FASTQ, FASTA and QUAL formats (as trimmed or untrimmed reads).</p> <p>As well as adding features the new release tweaks and extends some of the core modules:</p> <ul> <li>Both <code>Bio.SeqIO</code> and <code>Bio.AlignIO</code> will accept filenames as well as handles, <a href="http://news.open-bio.org/news/2010/04/biopython-seqio-and-alignio-easier/">as detailed here</a>.</li> <li>The multiple sequence alignment object that underlies Bio.AlignIO has been improved.</li> <li><code>Bio.SeqIO</code> can read and write EMBL nucleotide files.</li> <li>The dictionary-like objects returned by <code>Bio.SeqIO.index()</code> have a new method &quot; <code>get_raw</code>&quot; that gets unparsed data from a file as a string, <a href="http://news.open-bio.org/news/2010/04/partial-seq-files-biopython/">as detailed here</a>.</li> <li><code>Bio.Entrez</code> includes some more DTD files, in particular <code>eLink_090910.dtd</code>, used by our NCBI Entrez Utilities XML parser.</li> </ul> <p>Binaries and source files for Biopython 1.54 are available from the <a href="http://www.biopython.org/wiki/Download">downloads page</a>. The <a href="http://www.biopython.org/wiki/Documentation" title="Biopython Documentation">documentation</a> has been updated to include the changes made since our last release.</p> <p>A big thanks to every one who tested our beta release or submitted bugs since <a href="http://news.open-bio.org/news/2009/12/biopython-release-153/">Biopython 1.53</a>. And an especially big thanks to everyone who contributed to this release, including five first time contributors:</p> <ul> <li>Anne Pajon (first contribution)</li> <li>Brad Chapman</li> <li>Christian Zmasek</li> <li>Diana Jaunzeikare (first contribution)</li> <li>Eric Talevich</li> <li>Jose Blanca (first contribution)</li> <li>Kevin Jacobs (first contribution)</li> <li>Leighton Pritchard</li> <li>Michiel de Hoon</li> <li>Peter Cock</li> <li>Thomas Holder (first contribution)</li> </ul>https://www.open-bio.org/2010/05/14/bioperl-has-moved-to-github/Fri, 14 May 2010 04:18:33 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/05/14/bioperl-has-moved-to-github/<p>BioPerl has migrated to <a href="http://git-scm.com/">git</a> and <a href="http://github.com/bioperl">GitHub</a>!  We have also set up a mirror set of several key repositories at the great public git hosting site <a href="http://repo.or.cz/w">repo.or.cz</a>.</p> <p>If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID.  Also, add the extra email <a href="https://www.open-bio.org/wp-content/uploads/2010/05/generic.jpg"><img src="https://www.open-bio.org/wp-content/uploads/2010/05/generic.jpg" alt=""></a> (where &lsquo;DEVNAME&rsquo; is your <strong>original Subversion account ID</strong>).  This should map any previous commits from the older Subversion and CVS repository to your new GitHub account.</p> <p>The following are ways everyone can download the latest code.</p> <h2 id="using-git">Using git</h2> <p>Note you can replace &lsquo;bioperl-live.git&rsquo; with any of the repository names (bioperl-db, bioperl-run, etc).  For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone git@github.com:bioperl/bioperl-live.git </span></span></code></pre></div><div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone https://bioperl@github.com/bioperl/bioperl-live.git </span></span></code></pre></div><p>The open read-only link (for everyone):</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone git://github.com/bioperl/bioperl-live.git </span></span></code></pre></div><p>or using the mirror site:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> git clone git://repo.or.cz/bioperl-live.git </span></span></code></pre></div><h2 id="using-svn-read-only">Using SVN (read-only)</h2> <p>We will also support read-only access to GitHub with Subversion.  We may allow write support at some later point.  To use svn:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span> svn checkout http://svn.github.com/bioperl/bioperl-live.git </span></span></code></pre></div><h2 id="direct-downloads">Direct downloads</h2> <p>Tagged releases can be found here:</p> <p><a href="http://github.com/bioperl/bioperl-live/downloads">http://github.com/bioperl/bioperl-live/downloads</a></p> <p>The latest source code here:</p> <p><a href="http://github.com/bioperl/bioperl-live/archives/master">http://github.com/bioperl/bioperl-live/archives/master</a></p> <h2 id="forking-bioperl-and-pull-requests"><strong>Forking BioPerl and Pull Requests</strong></h2> <p>We intend on using git and GitHub to their fullest.  With that in mind, we encourage users to <a href="http://help.github.com/forking/">fork</a> BioPerl code, make changes, commit them to your forked repository, and submit <a href="http://github.com/guides/pull-requests">pull requests</a>.</p> <h2 id="documentation">Documentation</h2> <p>We&rsquo;re also in the process of updating our local developer documents for help with those who haven&rsquo;t used git before.  In particular, we have a <a href="http://www.bioperl.org/wiki/Using_Git">Using Git</a> page, and have added <a href="http://www.bioperl.org/wiki/Tracking_Git_commits">RSS feeds</a> for our repository commits.</p> <p>Enjoy!</p> <p>chris</p> <p><strong>Update:</strong> SVN version fixed, thanks to DaveMessina++ for pointing it out.</p>https://www.open-bio.org/2010/05/02/obf-google-summer-of-code-accepted-students/Sun, 02 May 2010 19:37:03 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/05/02/obf-google-summer-of-code-accepted-students/<p>I&rsquo;m pleased to announce the acceptance of <a href="https://www.open-bio.org/wiki/Google_Summer_of_Code">OBF&rsquo;s 2010 Google Summer of Code</a> students, listed in alphabetical order with their project titles and primary mentors:</p> <p>Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms</p> <p>Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins</p> <p>Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby</p> <p>Sara Rayburn (PM Christian Zmasek) - Implementing Speciation &amp; Duplication Inference Algorithm for Binary and Non-binary Species Tree</p> <p>Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython&rsquo;s Structural Biology module</p> <p>Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring</p> <p>Congratulations to our accepted students!</p> <p>All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google.  Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate.  We received a lot of really excellent proposals, the decisions were not easy.</p> <p>Thanks very much to all the students who applied, we very much appreciate your hard work.</p> <p>Here&rsquo;s to a great 2010 Summer of Code, I&rsquo;m sure these students will do wonderful work.</p> <p>Rob Buels O|B|F GSoC 2010 Administrator</p>https://www.open-bio.org/2010/04/30/illumina-q2-trim-fastq/Fri, 30 Apr 2010 07:49:45 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/30/illumina-q2-trim-fastq/<p>In another quirk to the <a href="http://news.open-bio.org/news/2009/12/nar-fastq-format/">FASTQ story</a>, recent Illumina FASTQ files don&rsquo;t actually use the full range of PHRED scores - and a score of 2 has a special meaning, <em>The Read Segment Quality Control Indicator</em> (RSQCI, encoded as &lsquo;B&rsquo;).</p> <p>Hats off to <em>Dr Torsten Seemann</em> for raising awareness of this issue in <a href="http://seqanswers.com/forums/showpost.php?p=17491&amp;postcount=3">his post on the seqanswers.com forum</a>, referring to a presentation by <em>Tobias Mann</em> of Illumina which says:</p> <blockquote> <p><em>The Read Segment Quality Control Indicator:</em></p> <p><em>- At the ends of some reads, quality scores are unreliable. Illumina has an algorithm for identifying these unreliable runs of quality scores, and we use a special indicator to flag these portions of reads</em></p> <p><em>- A quality score of 2, encoded as a &ldquo;B&rdquo;, is used as a special indicator. A quality score of 2 does not imply a specific error rate, but rather implies that the marked region of the read should not be used for downstream analysis.</em></p> <p><em>- Some reads will end with a run of B (or Q2) basecalls, but there will never  be an isolated Q2 basecall.</em></p> </blockquote> <p>So, armed with this knowledge, you might want to apply a simple trimming criteria to any Illumina FASTQ files - remove anything after and including a PHRED quality score of 2 (encoded as ASCII &lsquo;B&rsquo;).</p> <p>We could do this with the rich object orientated <code>SeqRecord</code> based API in Biopython, but when <a href="http://news.open-bio.org/news/2009/09/biopython-fast-fastq/">dealing with massive FASTQ files</a> this overhead matters. Instead we&rsquo;ll stick with plain Python strings:</p> <p><code>from Bio.SeqIO.QualityIO import FastqGeneralIterator handle = open(&quot;B_trimmed.fastq&quot;, &quot;w&quot;) min_length = 10 for title, seq, qual in FastqGeneralIterator(open(&quot;untrimmed.fastq&quot;)) : #Find the location of the first &quot;B&quot; (PHRED quality 2) trim = qual.find(&quot;B&quot;) if trim == -1: #No need to trim handle.write(&quot;@%sn%sn+n%sn&quot; % (title, seq, qual)) elif trim &gt;= min_length: #Take everything up to the first B handle.write(&quot;@%sn%sn+n%sn&quot; % (title, seq[:trim], qual[:trim])) handle.close()</code></p> <p>In practice the above can trim too much - you can still get isolated &ldquo;B&rdquo; characters in the middle of a read, where it is just a low quality score. Instead, we can trim any trailing &ldquo;B&rdquo; characters - which will do the same thing on RSQCI based FASTQ files where the &ldquo;B&rdquo; should only appear at the end:</p> <p><code>from Bio.SeqIO.QualityIO import FastqGeneralIterator handle = open(&quot;B_trimmed.fastq&quot;, &quot;w&quot;) min_length = 10 for title, seq, qual in FastqGeneralIterator(open(&quot;untrimmed.fastq&quot;)) : qual = qual.rstrip(&quot;B&quot;) #Remove any trailing B characters length = len(qual) if length &gt;= min_length: seq = seq[:length] #trim to match handle.write(&quot;@%sn%sn+n%sn&quot; % (title, seq, qual)) handle.close()</code></p> <p>You could easily modify this example to read from stdin and write to stdout (see this <a href="http://www.biopython.org/wiki/Reading_from_unix_pipes">cookbook example</a>), or take filenames as command line arguments to turn this into a general purpose &ldquo;FASTQ B-trimming script&rdquo;.</p>https://www.open-bio.org/2010/04/27/partial-seq-files-biopython/Tue, 27 Apr 2010 13:03:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/27/partial-seq-files-biopython/<p>This is another blog post to highlight one of the neat tricks you&rsquo;ll be able to do with Biopython 1.54 (which you can help test with the <a href="http://news.open-bio.org/news/2010/04/biopython-1-54-beta-released/">Biopython 1.54 beta</a> release).</p> <p>It is often useful to be able to extract a few records from a larger sequence file - for example, some sequences of interest from a full UniProt or GenBank dump. One obvious way to try to do this is to parse the file into an object representation (i.e. <code>SeqRecord</code> objects using <code>Bio.SeqIO.parse(...)</code>), filter to pick out the entries you want, and then write them back to disk (using <code>Bio.SeqIO.write(...)</code>). However, for complex file formats like GenBank this can be lossy ( <code>Bio.SeqIO</code> does not support a 100% identical round trip), and Biopython don&rsquo;t currently support writing out the SwissProt plain text format used by UniProt. So, that approach won&rsquo;t work.</p> <p><a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a> introduced a new <a href="http://news.open-bio.org/news/2009/09/biopython-seqio-index/">indexing function</a>, <code>Bio.SeqIO.index(...)</code>, which allows a large multi-sequence file to be treated like a Python dictionary - parsing requested records on request. This has been enhanced for Biopython 1.54 with a method <code>get_raw(...)</code> to extract the raw for a record as a string.</p> <p>How is this useful? Well, take your large (UniProt) file, index it, then extract the records you want and write them to your output file unmodified:</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;-webkit-text-size-adjust:none;"><code class="language-fallback" data-lang="fallback"><span style="display:flex;"><span>from Bio import SeqIO </span></span><span style="display:flex;"><span>uniprot = SeqIO.index(&#34;uniprot_sprot.dat&#34;, &#34;swiss&#34;) </span></span><span style="display:flex;"><span>handle = open(&#34;selected.dat&#34;, &#34;w&#34;) </span></span><span style="display:flex;"><span>for acc in [&#34;P33487&#34;, &#34;P19801&#34;, &#34;P13689&#34;, &#34;Q8JZQ5&#34;, &#34;Q9TRC7&#34;]: </span></span><span style="display:flex;"><span> handle.write(uniprot.get_raw(acc)) </span></span><span style="display:flex;"><span>handle.close() </span></span></code></pre></div><p>Another neat use of this functionality would be to sort entries in a sequential file format, and there is an example of that in the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p>https://www.open-bio.org/2010/04/07/reminder-bosc-abstract-deadline-april-15/Wed, 07 Apr 2010 05:46:00 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/07/reminder-bosc-abstract-deadline-april-15/<p>Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15.  See the BOSC web site at /wiki/BOSC_2010 for details.  Submissions will only be accepted electronically at <a href="http://events.open-bio.org/BOSC2010/openconf.php">http://events.open-bio.org/BOSC2010/openconf.php</a>.</p> <p>Graduate students, don&rsquo;t forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award.</p> <p>We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. <a href="http://www.sanger.ac.uk/" title="http://www.sanger.ac.uk/">http://www.sanger.ac.uk/</a></p> <p>On behalf of the BOSC 2010 organizing committee, I hope to see you there!</p>https://www.open-bio.org/2010/04/05/biopython-seqio-and-alignio-easier/Mon, 05 Apr 2010 16:37:11 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/05/biopython-seqio-and-alignio-easier/<p>One of the small changes coming in Biopython 1.54 (which you can try out already using the <a href="http://news.open-bio.org/news/2010/04/biopython-1-54-beta-released/">Biopython 1.54 beta</a>) is to <a href="http://www.biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://www.biopython.org/wiki/AlignIO">Bio.AlignIO</a>. Previously the input and output functions had required file <em>handles</em>, but they will now also accept <em>filenames</em>.</p> <p>This is a case of <em>practicality beats purity</em> (to quote <a href="http://www.python.org/dev/peps/pep-0020/">the Zen of Python</a>), and is particularly handy when doing very short scripts or working at the Python prompt.</p> <p>For example, filtering a FASTA file to take only entries with a minimum length of 100 can be done like this (with handles):</p> <p><code>from Bio import SeqIO in_handle = open(&quot;example.fasta&quot;, &quot;rU&quot;) out_handle = open(&quot;long.fasta&quot;, &quot;w&quot;) records = (rec for rec in SeqIO.parse(in_handle, &quot;fasta&quot;) if len(rec)&gt;100) SeqIO.write(records, out_handle, &quot;fasta&quot;) in_handle.close() out_handle.close()</code></p> <p>Using filenames it becomes much more concise - just three lines:</p> <p><code>from Bio import SeqIO records = (rec for rec in SeqIO.parse(&quot;example.fasta&quot;, &quot;fasta&quot;) if len(rec)&gt;100) SeqIO.write(records, &quot;long.fasta&quot;, &quot;fasta&quot;)</code></p> <p>This also means Python and Biopython beginners can postpone learning about file handles a little longer, although that may not be an entirely good thing ;)</p>https://www.open-bio.org/2010/04/02/biopython-1-54-beta-released/Fri, 02 Apr 2010 17:19:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/04/02/biopython-1-54-beta-released/<p>A <em>beta</em> release for Biopython 1.54 is now available for download and testing.</p> <p>Since <a href="http://news.open-bio.org/news/2009/12/biopython-release-153/">Biopython 1.53</a> was released at the end of last year, several new features and more documentation have been added, plus the usual bug fixes. For full details see the <a href="http://biopython.open-bio.org/SRC/biopython/NEWS">NEWS file</a>.</p> <p>All the new features have been tested by the dev team but it’s possible there are cases that we haven’t been able to foresee and test, especially for the updated multiple sequence alignment object (which is what you&rsquo;ll now get when parsing alignments with <a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a>), the <a href="http://biopython.org/wiki/Phylo">new Bio.Phylo module</a>, and the <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> support for Standard Flowgram Format (SFF) files.</p> <p>Source distributions and Windows installers are available from the <a href="http://biopython.org/wiki/Download">downloads page</a> on the Biopython website ( <a href="http://biopython.org/">biopython.org</a>).</p> <p>We are interested in getting feedback on the beta release as a whole, but especially on the new features and the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>).</p> <p>(At least) 10 people contributed to this release (so far), which includes 4 new people:</p> <ul> <li> <p>Anne Pajon (first contribution)</p> </li> <li> <p>Brad Chapman</p> </li> <li> <p>Christian Zmasek</p> </li> <li> <p>Eric Talevich</p> </li> <li> <p>Jose Blanca (first contribution)</p> </li> <li> <p>Kevin Jacobs (first contribution)</p> </li> <li> <p>Leighton Pritchard</p> </li> <li> <p>Michiel de Hoon</p> </li> <li> <p>Peter Cock</p> </li> <li> <p>Thomas Holder (first contribution)</p> </li> </ul> <p>So, gather your courage, download the release, try it out and please let us know what works and what doesn’t through the <a href="http://biopython.org/wiki/Mailing_lists">mailing lists</a> (or <a href="http://bugzilla.open-bio.org/">bugzilla</a>).</p>https://www.open-bio.org/2010/03/21/obf-in-google-summer-of-code/Sun, 21 Mar 2010 18:26:52 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/03/21/obf-in-google-summer-of-code/<p>The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer&rsquo;s Google Summer of Code.  Our list of project ideas and mentors is linked from the <a href="http://open-bio.org/wiki/Google_Summer_of_Code" title="O|B|F GSoC">O|B|F GSoC page</a>.</p> <p>Student applications must be submitted to Google by <strong>April 9, 2010,</strong> see the <a href="http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs">official GSoC 2010 FAQ</a>. That is less than three weeks away!</p> <p>Students, have a look at that wiki page, contact the project you&rsquo;re interested in working with, and get rolling on that application post-haste.  A good GSoC application takes quite a bit of thought and effort to put together.  <strong>Students are encouraged to get help from mentors to put together a good application.</strong></p> <p>Current developers on O|B|F projects, have a look through the <a href="http://en.flossmanuals.net/GSoCMentoringGuide">GSoC Mentoring Guide</a>, and if it looks like something you want to do, there&rsquo;s still time to volunteer as a prospective mentor.  Just add your name to the O|B|F and project wiki pages, and contribute your project ideas.  Even if you don&rsquo;t have project ideas of your own, it&rsquo;s good to volunteer.</p> <p>Google Summer of Code is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents).   Students are paid a $5,000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the <a href="http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs">official GSoC 2010 FAQ</a>.</p> <p>Thanks to all who helped make OBF&rsquo;s application to GSoC a success, and let&rsquo;s have a great, productive summer of code!</p> <p>Rob Buels O|B|F GSoC 2010 Administrator</p>https://www.open-bio.org/2010/03/02/bosc-2010-call-for-abstracts/Wed, 03 Mar 2010 01:19:29 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/03/02/bosc-2010-call-for-abstracts/<p>**Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open.**<strong>At-a-glance</strong> BOSC is an ISMB 2010 Special Interest Group (SIG) Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: <a href="https://www.open-bio.org/wiki/BOSC_2010">/wiki/BOSC_2010</a> Abstract submission via Open Conference System site:  <a href="http://events.open-bio.org/BOSC2010/openconf.php">http://events.open-bio.org/BOSC2010/openconf.php</a> E-mail: <a href="mailto:bosc@open-bio.org">bosc@open-bio.org</a> Bosc-announce list:  <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a> <strong>Important Dates</strong> <strong>April 15: Abstract deadline</strong> May 5:  Notification of accepted abstracts May 28: Early Registration Discount Cut-off date July 8-9:  Codefest 2010 <strong>July 9-10: BOSC 2010</strong> August 15:  Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics</p> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>We have some exciting things planned this year, including:</p> <ul> <li>Codefest 2010 programming session for the two days preceeding BOSC:  See <a href="https://www.open-bio.org/wiki/Codefest_2010">/wiki/Codefest_2010</a> for details.</li> <li>OpenBio Solution Challenge:  See session description below and <a href="https://www.open-bio.org/wiki/SolutionChallenge">/wiki/SolutionChallenge</a> for details.</li> <li>Student Travel Fellowships:  Through generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2010. Each winner will be awarded $250 to defray the costs of travel to BOSC 2010.  See <a href="https://www.open-bio.org/wiki/BOSC_2010#Student_Travel_Awards">/wiki/BOSC_2010#Student_Travel_Awards</a> for details.</li> <li>First-ever BOSC Proceedings will be published in the Open Access journal, BMC Bioinformatics.  Manuscripts will be due after BOSC on August 15.  See <a href="https://www.open-bio.org/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings">/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings</a> for details.</li> <li>Sessions on approaches to analyzing high-throughput &lsquo;omics data, cloud-based approaches to improving software and data accessibility, the semantic web in open source bioinformatics, see below:</li> </ul> <p>We invite abstracts for talks at the following sessions: <strong>OpenBio SolutionChallenge</strong> -- Bioinformatics library providers: please join us in a friendly competition to solve a shared biological problem, demonstrating the utility of your toolkit alongside other developers. Instead of the traditional Bio* updates that we&rsquo;ve had at previous conferences, this year, we&rsquo;re planning to organize these talks around a central theme: the OpenBio Solution Challenge. We start with a biological question of general interest, and the project talks will focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). Specific challenges are being discussed on the SolutionChallenge page and through the various Bio* mailing lists. Alternately, each project could highlight a challenge that they particularly do well, focusing tutorial-style on how to solve a particular problem.</p>https://www.open-bio.org/2010/01/18/bioperl-at-gmod-meeting-2010/Tue, 19 Jan 2010 03:58:58 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2010/01/18/bioperl-at-gmod-meeting-2010/<p>BioPerl developers and users attended the <a href="http://www.bioperl.org/wiki/GMOD_2010_Meeting">BioPerl satellite meeting</a> on January 13th, just prior to the <a href="http://gmod.org/wiki/January_2010_GMOD_Meeting">GMOD Meeting</a>.  Several items were covered on the agenda:</p> <ul> <li>In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB backend (i.e. Bio::DB::SeqFeature::Store or similar).  We are also contemplating adding lazy parsing for some parsers, possibly using the Bio::PullParserI methods (or similar) that Sendu Bala created.</li> <li>After a final  1.6 branch point release, we may &lsquo;freeze&rsquo; BioPerl in a maintenance mode, primarily so that we can reorganize core into several more easily installed subdistributions on a branch.  New modules will essentially be additional separate repos that will depend on BioPerl core.  This reorganization has been discussed for a few years now, and as we edge closer to starting this (probably this spring) we&rsquo;ll announce more details.</li> <li>Some initial thoughts on how to handle circular genomes more efficiently.  We essentially do this already, but it isn&rsquo;t full-proof.</li> <li>Need some significant time dedicated towards GFF3-based coding (reimplement FeatureIO but allow some flexibility).  Rob Buels had started the initial run at splitting out FeatureIO, so next step is a true reimplementation.</li> <li>We don&rsquo;t plan on including Moose support for the immediate future, feeling that it would be better to reimplement some of the classes from scratch using Moose and similar as a BioPerl 2.0, or possibly await the impending Rakudo Perl 6 alpha and start afresh using that instead of Moose.</li> </ul> <p>Anything we missed?  Anything you would like to address?  Please add comments and we&rsquo;ll discuss them on list.</p>https://www.open-bio.org/2009/12/29/bioruby-1-4-0-released/Tue, 29 Dec 2009 10:22:25 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/29/bioruby-1-4-0-released/<p>We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements.</p> <p><strong>PhyloXML support:</strong> Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with the National Evolutionary Synthesis Center (NESCent).</p> <p><strong>FASTQ file format support:</strong> Support for reading and writing FASTQ file format is added. All of the three FASTQ format variants are supported. The code is written by Naohisa Goto, with the help of discussions in the open-bio-l mailing list. The prototype of Bio::Fastq class was first developed during the BioHackathon 2009 held in Okinawa.</p> <p><strong>DNA chromatogram support:</strong> Support for reading DNA chromatogram files are added. SCF and ABIF file formats are supported. The code is developed by Anthony Underwood.</p> <p><strong>MEME (motif-based sequence analysis tools) support:</strong> Support for running MAST (Motif Alignment &amp; Search Tool, part of the MEME Suite, motif-based sequence analysis tools) and parsing its results are added,  developed by Adam Kraut.</p> <p><strong>Improvement of KEGG parser classes:</strong> Some new methods are added to parse new fields added to some KEGG file formats. Unit tests for KEGG parsers are also added and improved. These are contributed by Kozo Nishida.</p> <p><strong>Many sample scripts are added:</strong> Many sample scripts showing demonstrations of usages of classes are added. They were originally primitive test codes written in the &ldquo;if __FILE__ == $0&rdquo; convention.</p> <p><strong>Unit tests can test installed BioRuby:</strong> Mechanism to load library and to find test data in the unit tests are changed, and target library path and test data path can be changed with environment variables.</p> <p><strong>Incompatible change: Bio::NCBI::REST needs email address:</strong> NCBI announced that all Entrez Utilities (E-utilities)  requests must contain email and tool parameters, and requests without them will return error after June 2010. In BioRuby, to set default email address and tool name, following methods are added.</p> <ul> <li>Bio::NCBI.default_email=(email)</li> <li>Bio::NCBI.default_tool=(tool_name)</li> </ul> <p>Note that no default email address is preset in BioRuby. Library users must set their own email address or implement to get user&rsquo;s email address in some way (from input form, configuration file, etc).</p> <p>In addition, many changes have been made, including incompatible changes. For more information, see <a href="http://github.com/bioruby/bioruby/blob/1.4.0/RELEASE_NOTES.rdoc">RELEASE_NOTES.rdoc</a> and <a href="http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog">ChangeLog</a>.</p> <p>The archive is available at: <a href="http://bioruby.org/archive/bioruby-1.4.0.tar.gz">http://bioruby.org/archive/bioruby-1.4.0.tar.gz</a></p> <p>Gem file is also available at:  <a href="http://bioruby.org/archive/gems/bio-1.4.0.gem">http://bioruby.org/archive/gems/bio-1.4.0.gem</a></p> <p>We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search &ndash;remote bio and find &ldquo;bio (1.4.0)&rdquo; in the list. Then, % sudo gem install bio</p> <p>Hope you enjoy.</p>https://www.open-bio.org/2009/12/18/bosc-2010-request-for-input/Sat, 19 Dec 2009 01:39:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/18/bosc-2010-request-for-input/<p>BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010.  The BOSC 2010 web site can be accessed here:  <a href="https://www.open-bio.org/wiki/BOSC_2010">/wiki/BOSC_2010</a>.</p> <p>The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community.  You may send your suggestions to the <a href="mailto:bosc@open-bio.org" title="mailto:bosc@open-bio.org">bosc@open-bio.org</a> e-mail address  or add suggestions to the BOSC 2010 talk/discussion wiki page at: <a href="https://www.open-bio.org/wiki/Talk:BOSC_2010.%A0">/wiki/Talk:BOSC_2010.</a> Please respond to any or all of the questions below:</p> <p>1.  For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions.  Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:</p> <ul> <li><strong>Tutorials</strong> where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier.  <strong>Would you be willing to organize/lead such a session for your project?</strong></li> <li><strong>Discussion</strong> following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The &ldquo;speaker&rdquo; would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them.  <strong>Would you be willing to organize/lead such a session for your project?</strong></li> <li><strong>Mini-hackathon</strong> either before, during, or after the 2-day BOSC.  The subject of the hackathon would need to be organized by the individual project leaders/teams.  Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal.  <strong>Would you be willing to organize/lead this type of session?</strong></li> <li>Organizing/creating a <strong>LiveCD</strong> or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community.  <strong>Would you be willing to organize/lead this type of session?</strong></li> <li>What <strong>session topics</strong> would you like to see represented for traditional talks?</li> <li>Who would you like to hear as a <strong>keynote speaker</strong>?</li> </ul> <p>2.  The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC.  If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000?  We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.</p> <p>3.  Call for <strong>volunteers</strong>.  Organizing tutorial/hackathons and such will only be possible if individuals step forward to lead these sessions.  Please let us know if you would be willing to serve in any capacity.  We also need volunteers to review abstracts for the more &ldquo;traditional&rdquo; sessions, please let us know if you are willing to do this as well.</p> <p><strong>Timeline:</strong> We are planning on putting out the Call for Abstracts in mid-January.  To be on track, we would like to receive your input by <strong>Friday, January 8</strong>.  If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.</p> <p>Thanks and Happy Holidays!</p> <p>Kam Dahlquist Chair, BOSC 2010 on behalf of the BOSC 2010 Organizing committee: Brad Chapman, Michael Heur, Darin London, Anton Nekrutenko, Steffen Moeller, Jim Procter And the O|B|F Board: Chris Dagdigian, Nomi Harris, Hilmar Lapp, Jason Stajich</p>https://www.open-bio.org/2009/12/17/nar-fastq-format/Thu, 17 Dec 2009 16:28:55 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/17/nar-fastq-format/<p>I&rsquo;m delighted to announce an open access publication in <em>Nucleic Acids Research</em> describing the FASTQ file format based on the conventions agreed by the OBF projects:</p> <blockquote> <p><a href="http://dx.doi.org/10.1093/nar/gkp1137">The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants</a> Peter J. A. Cock ( <a href="http://www.biopython.org">Biopython</a>), Christopher J. Fields ( <a href="http://www.bioperl.org">BioPerl</a>), Naohisa Goto ( <a href="http://www.bioruby.org">BioRuby</a>), Michael L. Heuer ( <a href="http://www.biojava.org">BioJava</a>) and Peter M. Rice ( <a href="http://emboss.sourceforge.net/">EMBOSS</a>). Nucleic Acids Research, <a href="http://dx.doi.org/10.1093/nar/gkp1137">doi:10.1093/nar/gkp1137</a></p> </blockquote> <p>This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.</p>https://www.open-bio.org/2009/12/14/2009-obf-bod-meeting/Mon, 14 Dec 2009 19:24:08 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/12/14/2009-obf-bod-meeting/<p>The official 2009 Board of Directors meeting is taking place today, Monday Dec 14, at 4pm EST (21:00 UTC) via teleconference. If you are an O|B|F member, you will have received the announcement and dial-in information earlier.</p> <p>O|B|F Board of Director meetings are public - anyone interested in O|B|F business can participate, which is one reason we are holding the meeting over teleconference. The dial-in number is +1-518-825-1400, participant code 279610.</p> <p>All you need to participate is a telephone (this is a US toll number, and if you are located international or outside of the area code, pertinent charges from your phone carrier will apply). Or use SkypeOut, which costs a few cents per minute from many locations (check SkypeOut rates).</p> <p>The <a href="https://www.open-bio.org/wiki/Minutes:2009_ConfCall">agenda for the meeting</a> is on the OBF wiki (and minutes will be posted there later).</p>https://www.open-bio.org/2009/11/22/bioperl-interview-for-floss-weekly/Sun, 22 Nov 2009 20:27:50 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/11/22/bioperl-interview-for-floss-weekly/<p>Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.  The interview is now available <a href="http://www.podtrac.com/pts/redirect.mp3/twit.cachefly.net/floss0096.mp3">as an MP3</a> on the <a href="http://twit.tv/floss96">FLOSS Weekly</a> website; several streaming versions (including podcast) are also available.</p>https://www.open-bio.org/2009/10/10/bioperl-core-1-6-1-ppm-available/Sat, 10 Oct 2009 05:18:40 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/10/10/bioperl-core-1-6-1-ppm-available/<p>BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the <a href="http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows">BioPerl wiki</a>. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.</p>https://www.open-bio.org/2009/10/01/first-alphas-of-bioperl-run-bioperl-db-bioperl-network/Thu, 01 Oct 2009 16:40:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/10/01/first-alphas-of-bioperl-run-bioperl-db-bioperl-network/<p>Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN:</p> <ul> <li><a href="http://search.cpan.org/~cjfields/BioPerl-Run-1.6.1_001/">BioPerl-Run</a></li> <li><a href="http://search.cpan.org/~cjfields/BioPerl-DB-1.6.0_001/">BioPerl-DB</a></li> <li><a href="http://search.cpan.org/~cjfields/BioPerl-Network-1.6.0_001/">BioPerl-Network</a></li> </ul> <p>They can also be downloaded from the BioPerl website:</p> <p><a href="http://bioperl.org/DIST/RC/">http://bioperl.org/DIST/RC/</a></p> <p>This is the first run where we&rsquo;ve switched to a regular Module::Build installation, so expect some initial bumps! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). The other, more serious one, is that the Build.PL script checks for DBI but isn&rsquo;t checking for any compatible DBD::* adaptors for BioPerl-DB (so it fails tests if DBI is installed). We have code in core to check for DBI drivers, so I may adapt that for BioPerl-DB.</p> <p>Enjoy!</p> <p>chris</p>https://www.open-bio.org/2009/09/29/bioperl-1-6-1-released/Tue, 29 Sep 2009 17:55:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/29/bioperl-1-6-1-released/<p>We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl&rsquo;s core code. You can grab it here:</p> <p>Via CPAN:</p> <p><a href="http://search.cpan.org/~cjfields/BioPerl-1.6.1/">http://search.cpan.org/~cjfields/BioPerl-1.6.1/</a></p> <p>Via the BioPerl website:</p> <p><a href="http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2">http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2</a> <a href="http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz">http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz</a> <a href="http://bioperl.org/DIST/BioPerl-1.6.1.zip">http://bioperl.org/DIST/BioPerl-1.6.1.zip</a></p> <p>The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).</p> <p>Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the &lsquo;Changes&rsquo; file included with the distribution.</p> <p>A few highlights:</p> <ul> <li>FASTQ parsing and interconversion of the three FASTQ variants (Sanger, Illumina, Solexa) now works (a concerted OBF effort!)</li> <li>Significant refactoring of Bio::Restriction methods</li> <li>Complete refactoring of Bio::Search-related tiling code, including HOWTO documentation</li> <li>GBrowse-related fixes:</li> <li>- <em>berkeleydb database now autoindexes wig files and locks correctly</em></li> <li>- <em>add Pg, SQLite, and faster BerkeleyDB implementations</em></li> <li>Infernal 1.0 output is now parsed</li> <li>New SearchIO-based parser for gmap -f9 output</li> <li>BLAST XML parsing essentially complete</li> <li>Installation via CPANPLUS should now work</li> <li>For those using Strawberry Perl on Windows, the latest build is expected to pass all tests.</li> <li>&lsquo;raw&rsquo; sequence format now parsed by line or optionally as a single sequence</li> <li>SCF parsing/writing now round-trips</li> <li>Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast</li> <li>Bio::Tools::SeqPattern now has a backtranslate() method</li> <li>Bio::Tree::Statistics now has methods to calculate Fitch-based score, internal trait values, statratio(), sum of leaf distances</li> <li>Scripts</li> <li><em>- update to bp_seqfeature_load for SQLite</em></li> <li><em>- hivq.pl - commmand-line interface to Bio::DB::HIV</em></li> <li><em>- fastam9_to_table - fix for MPI output</em></li> <li><em>- gccalc - total stats</em></li> <li><em>- einfo - simple script to find up-to-date NCBI databases, list field and link values for a specific database</em></li> </ul> <p>We will shortly release updates for BioPerl-db, BioPerl-run, and BioPerl-network. Enjoy!</p> <p>chris</p>https://www.open-bio.org/2009/09/24/biopython-cvs-to-git-migration/Thu, 24 Sep 2009 13:00:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/24/biopython-cvs-to-git-migration/<p>The release of <a href="http://news.open-bio.org/news/2009/09/biopython-release-152/">Biopython 1.52</a> earlier this week marked the end of an era, it was our last release using CVS for source code control.</p> <p>As of now, Biopython is using a <a href="http://github.com/biopython/biopython" title="Biopython on github">git repository</a>, hosted on <a href="http://github.com">github.com</a> who kindly provide git hosting for open source projects free of charge. The <a href="http://bioruby.org">BioRuby project</a> have been <a href="http://github.com/bioruby/bioruby" title="BioRuby on github">using github</a> for some time, so we are in good company.</p> <p>Our existing OBF hosted CVS repository will be maintained in the short to medium term as a backup, but will not be updated.</p> <p>Although many people have been involved in this move, we&rsquo;d like to thank Bartek Wilczynski in particular for handling the CVS to git conversion, and the mirroring our CVS updates to git during the transition period. In the next few weeks hopefully we&rsquo;ll get our <a href="http://biopython.org/wiki/GitUsage">git usage wiki pages</a> perfected, as we start using git for real.</p>https://www.open-bio.org/2009/09/22/biopython-convert-function/Tue, 22 Sep 2009 10:24:57 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/09/22/biopython-convert-function/<p>As per <a href="http://news.open-bio.org/news/2009/09/biopython-seqio-index/" title="Indexing sequence files with Biopython">Peter&rsquo;s recent post</a> we are using this space to show of a couple of the new features in <a href="http://biopython.org">Biopython</a> 1.52 before it is released. In this post we&rsquo;ll look at the new <strong>convert()</strong> function that both <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> and <a href="http://biopython.org/wiki/AlignIO">Bio.AlignIO</a> will get in Biopython 1.52.</p> <p>No one has ever complained that bioinformatics just doesn&rsquo;t have enough file formats - you probably frequently find yourself converting sequence files to suit particular applications with <strong>Bio.SeqIO</strong>. At the moment this is usually a two step process, something like this:</p> <p>`&raquo;&gt; records = SeqIO.parse(in_handle &ldquo;genbank&rdquo;)</p> <blockquote> <blockquote> <blockquote> <p>SeqIO.write(records, out_handle, &ldquo;fasta&rdquo;)`</p> </blockquote> </blockquote> </blockquote> <p>As of Biopython 1.52, you&rsquo;ll be able to achieve the same result in a single step:</p> <p><code>&gt;&gt;&gt; SeqIO.convert(in_handle, &quot;genbank&quot;, out_handle, &quot;fasta&quot;)</code></p> <p>In fact, it&rsquo;s even easier than that because the convert function will accept filename strings as well as file handles for both input and output.</p> <p>Adding the convert function to <strong>Bio.SeqIO</strong> and <strong>Bio.AlignIO</strong> will make your scripts more readable and might even save you a couple of lines of code, but perhaps more importantly it allows for the conversion process to be optimized for the two formats being used. In most cases the same old parse and write functions are called internally, however some key conversions are much faster&hellip;</p> <p>In the above example we are moving from a GenBank file, which probably includes multiple features for each sequence, to a FASTA file, which doesn&rsquo;t include features. If we used the two step process above we&rsquo;d be spending time reading each sequence&rsquo;s features into memory just to skip them when they get passed to the write function. <strong>Bio.SeqIO.convert()</strong> knows that the sequences in the input file are destined to be written to a FASTA file so it can skip over the features and save a bit of time in doing the conversion.</p> <p>Obviously, any optimization is most important when its used on very large files, like those produced in next generation sequencing projects. For example, when converting between each of the FASTQ file formats variants with the &ldquo;SeqIO two step&rdquo; a significant amount of time is taken creating <a href="http://biopython.org/wiki/SeqRecord">SeqRecord objects</a> for each record in the input file and decoding the quality scores into numbers. However, none of the attributes or methods of the SeqRecord object are required to do the conversion. For this reason <strong>Bio.SeqIO.convert()</strong> deals with each record as simple strings. This makes it about five times faster - on a par with converters written in C.</p> <p>The Biopython 1.52 edition of the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial &amp; Cookbook</a> ( <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>) will cover these new convert functions in more detail.</p>https://www.open-bio.org/2009/08/17/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/2009/06/21/ncbi-einfo-biopython/Sun, 21 Jun 2009 21:42:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/06/21/ncbi-einfo-biopython/<p>Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/eutils_help.html">Entrez Programming Utilities</a> called <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/einfo_help.html">Entrez EInfo</a> can help.</p> <p>For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the <a href="http://www.ncbi.nlm.nih.gov/sites/entrez" title="NCBI Entrez">Entrez web interface</a>, for use in a script with <a href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/esearch_help.html%3EESearch%3C/a%3E" title="where you might also download them with &lt;a href=">EFetch</a>.</p> <p>I knew from past experience about using <code>name[ORGN]</code> in Entrez to search for an organism name - but how would you specify just mitochondria? I actually worked this out from the NCBI help and exploring the Entrez website&rsquo;s advanced search - but it took a while.</p> <p>There is an easier way to find out the search fields available in Entrez! Just recently I came across an interesting <a href="http://nsaunders.wordpress.com/2009/05/27/querying-ncbi-entrez-database-fields-using-ruby/">blog post from Neil Saunders</a> (written a couple of weeks ago) showing how Entrez EInfo provides information about the search fields in XML format, and how you can use Ruby to process this.</p> <p><a href="http://biopython.org">Biopython</a> can do this too of course - using <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#chapter:entrez">Bio.Entrez</a> this took just a few lines of Python:</p> <p>`&raquo;&gt; from Bio import Entrez</p> <blockquote> <blockquote> <blockquote> <p>data = Entrez.read(Entrez.einfo(db=&ldquo;genome&rdquo;)) for field in data[&ldquo;DbInfo&rdquo;][&ldquo;FieldList&rdquo;] : &hellip; print &ldquo;%(Name)s, %(FullName)s, %(Description)s&rdquo; % field &hellip; ALL, All Fields, All terms from all searchable fields UID, UID, Unique number assigned to each sequence FILT, Filter, Limits the records WORD, Text Word, Free text associated with record TITL, Title, Words in definition line KYWD, Keyword, Nonstandardized terms provided by submitter AUTH, Author, Author(s) of publication JOUR, Journal, Journal abbreviation of publication VOL, Volume, Volume number of publication ISS, Issue, Issue number of publication PAGE, Page Number, Page number(s) of publication ORGN, Organism, Scientific and common names of organism, and all higher levels of taxonomy ACCN, Accession, Accession number of sequence PACC, Primary Accession, Does not include retired secondary accessions GENE, Gene Name, Name of gene associated with sequence PROT, Protein Name, Name of protein associated with sequence ECNO, EC/RN Number, EC number for enzyme or CAS registry number PDAT, Publication Date, Date sequence added to GenBank MDAT, Modification Date, Date of last update SUBS, Substance Name, CAS chemical name or MEDLINE Substance Name PROP, Properties, Classification by source qualifiers and molecule type SQID, SeqID String, String identifier for sequence GPRJ, Genome Project, Genome Project SLEN, Sequence Length, Length of sequence FKEY, Feature key, Feature annotated on sequence RTYP, Replicon type, Replicon type RNAM, Replicon name, Replicon name ORGL, Organelle, Organelle `</p> </blockquote> </blockquote> </blockquote> <p>That gives us a list of all the fields we can currently search on in the Genome database (and you could use the same code for any of the other NCBI databases in Entrez - they probably all have different searchable fields). Very handy! The ones in bold are discussed below.</p> <p>So for my particular search, using &ldquo;ORGL&rdquo; to filter on organelle looks sensible, and after a bit of trial and error on the website I ended up with <code>mitochondrion[ORGL]</code> as a useful filter (not mitochondrial, or mitochondria).</p> <p>I already knew about using &ldquo;ORGN&rdquo; to filter on the organism, either by species name or with a suitably formatted NCBI taxon ID (which you can get by searching or browsing the Entrez taxonomy database), e.g. <code>txid9443[ORGN]</code> gives <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9443">primates</a>.</p> <p>Putting these together, to get <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&amp;term=txid9443%5BORGN%5D%20AND%20mitochondrion%5BORGL%5D">all the primate mitochondria in the Entrez genome database</a> you could use:</p> <blockquote> <p>txid9443[ORGN] AND mitochondrion[ORGL]</p> </blockquote> <p>Note that you have to use &ldquo;AND&rdquo; in upper case.</p> <p>I think we&rsquo;ll have to add something along these lines to the <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython Tutorial and Cookbook</a> ( <a href="http://www.biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>)&hellip; <em>Update: That&rsquo;s done now and will be included with our next release</em> :)</p> <p>Entrez rocks! (although their documentation could use a few more examples).</p> <p>Peter</p>https://www.open-bio.org/2009/06/01/bosc-schedule-posted-2/Tue, 02 Jun 2009 02:09:18 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/06/01/bosc-schedule-posted-2/<p>The BOSC 2009 schedule of speakers with links to abstracts has been posted at <a href="https://www.open-bio.org/wiki/BOSC_2009_Schedule">/wiki/BOSC_2009_Schedule</a>.</p>https://www.open-bio.org/2009/05/06/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/2009/04/20/biopython-release-150/Mon, 20 Apr 2009 18:58:05 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/20/biopython-release-150/<p>We are pleased to announce Biopython release 1.50, featuring some significant additions since <a href="http://news.open-bio.org/news/2008/09/biopython-release-148/">Biopython 1.49</a> was released late last year.</p> <p><a href="http://bioinf.scri.ac.uk/lp/programs.php#genomediagram">GenomeDiagram</a> by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.</p> <p>A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.SwissProt and Bio.ExPASy and their revised parsers.</p> <p>As noted in a previous news posting, <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> can now read and write <a href="http://news.open-bio.org/news/2009/03/biopython-next-gen-sequencing/">FASTQ and QUAL files</a> used in second generation sequencing work. In connection with this, our <a href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> object has a new dictionary attribute, letter_annotations, for per-letter-annotation information like sequence quality scores or secondary structure predictions. Also, the SeqRecord object can now be sliced to give a new SeqRecord covering just part of the sequence.</p> <p>Biopython 1.50 supports Python 2.3, 2.4, 2.5 and 2.6. However, this is expected to be the final version to support Python 2.3 (see this <a href="http://news.open-bio.org/news/2009/04/2008/11/biopython-and-python-26-and-python-23/">previous announcement</a>). Also, Biopython 1.50 should be the last release to include our old deprecated parsing infrastructure (Martel and Bio.Mindy).</p> <p>We’ve also updated the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html" title="Biopython Tutorial and Cookbook (HTML)">Biopython Tutorial and Cookbook</a> (also available in <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf" title="Biopython Tutorial and Cookbook (PDF)">PDF</a>), and not just by adding <a href="http://biopython.org/wiki/Logo" title="About the Biopython logo">our logo</a> to the cover ;)</p> <p>Thank you to everyone who tested the <a href="http://news.open-bio.org/news/2009/04/biopython-150-beta-released/">Biopython 1.50 beta release</a>, and to all our contributors.</p> <p>Source distributions and Windows installers are available from the <a href="http://biopython.org/wiki/Download">downloads</a> page on the <a href="http://biopython.org/">Biopython website (biopython.org)</a>.</p> <p>-Peter, on behalf of the Biopython developers</p>https://www.open-bio.org/2009/04/10/reminder-abstracts-for-bosc-2009-due-april-13/Fri, 10 Apr 2009 20:41:27 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/04/10/reminder-abstracts-for-bosc-2009-due-april-13/<p>This is a reminder from the BOSC 2009 Organizing committee that abstracts for BOSC are due on Monday, April 13.</p>https://www.open-bio.org/2009/03/27/biopython-on-twitter/Fri, 27 Mar 2009 11:19:56 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/27/biopython-on-twitter/<p>Just to let you all know, <a href="http://twitter.com/Biopython">Biopython is now on twitter</a>. And in case you missed the <a href="https://www.open-bio.org/news/2009/02/hello-twitter-world/">OBF announcement</a> last month, so is the <a href="http://twitter.com/obf_news">O|B|F News feed</a> (and <a href="http://twitter.com/bioperl">BioPerl</a>). You are welcome to follow us (all) on <a href="http://twitter.com/">twitter</a>.</p> <p>I&rsquo;d also like to remind people there are news feeds for the <a href="http://news.open-bio.org/news/category/obf-projects/biopython/">Biopython news posts</a> (as <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/rdf">RDF</a>, <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss/">RSS</a>, <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss2/">RSS2</a>, or <a href="http://news.open-bio.org/news/category/obf-projects/biopython/feed/atom">Atom</a> format). We&rsquo;re planning to have these automatically echoed onto twitter in future&hellip; <em>(update)</em> &hellip;and that seems to be working now :)</p>https://www.open-bio.org/2009/03/26/biopython-next-gen-sequencing/Thu, 26 Mar 2009 16:13:42 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/26/biopython-next-gen-sequencing/<p>Those of you doing next generation sequencing may be pleased to know that the next release of <a href="http://www.biopython.org">Biopython</a> is expected to include support for reading and writing <a href="http://bioperl.org/wiki/FASTQ_sequence_format">FASTQ</a> and <a href="http://bioperl.org/wiki/Qual_sequence_format">QUAL</a> files within our <a href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> interface. These formats are used for traditional Sanger capillary sequencing, and Roche 454 sequencing (Roche provide tools to convert from their binary SFF files) with PHRED quality scores. Solexa/Illumina sequencers produce a FASTQ variant where the quality scores are encoded differently, and this is also supported.</p> <p>As part of this work, the <a href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> has a new attribute holding a dictionary of per-letter-annotation (e.g. PHRED quality scores, Solexa quality scores, or for proteins secondary structure predictions), and the SeqRecord object can be sliced to give a new SeqRecord covering just part of the sequence, with the per-letter-annotation cropped to match.</p> <p>The code is in our <a href="http://biopython.org/wiki/CVS">CVS tree</a>, and <a href="http://github.com/biopython/biopython/tree/master">mirrored on github</a>, so those of you happy to install Biopython from source and help test it can grab the code now, and give it a go - feedback on the development <a href="http://biopython.org/wiki/Mailing_lists">mailing list</a> please. Alternatively, sit back and await the forthcoming Biopython 1.50 (beta) release, which should allow more widespread testing&hellip;</p> <p><em>Update:</em> This new functionality was included in <a href="http://news.open-bio.org/news/2009/04/biopython-release-150/" title="Biopython 1.50">Biopython 1.50</a>, including both Sanger standard FASTQ files and the original Solexa/Illumina FASTQ variant using Solexa scores. This did not cover the new FASTQ variant used on Solexa/Illumina 1.3+ but that is now supported in our development code, and will be included in Biopython 1.51. Peter, 2009/06/16</p>https://www.open-bio.org/2009/03/22/biopython-paper-published/Sun, 22 Mar 2009 18:45:51 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/22/biopython-paper-published/<p>An Application Note describing Biopython has recently been accepted for publication in the <a href="http://bioinformatics.oxfordjournals.org/">Oxford Journal <em>Bioinformatics</em></a>. An advance copy of the Open Access article is available online:</p> <blockquote> <p>P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M.J.L. de Hoon (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. <em>Bioinformatics</em>, <a href="http://dx.doi.org/10.1093/bioinformatics/btp163">doi:10.1093/bioinformatics/btp163</a></p> </blockquote>https://www.open-bio.org/2009/03/17/biopython-and-version-control-systems/Tue, 17 Mar 2009 14:52:02 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/17/biopython-and-version-control-systems/<p>Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of <a href="http://github.com/biopython/">Biopython on GitHub</a>, which is automatically updated from the OBF hosted <a href="http://www.biopython.org/wiki/CVS">Biopython CVS repository</a>. See our <a href="http://biopython.org/wiki/GitMigration">git migration wiki page</a> for details. If this is favorably received, then moving Biopython from CVS to git seems likely at some point this year.</p> <p>Originally, all the OBF hosted projects used <a href="http://www.nongnu.org/cvs/">CVS</a> for their source code repositories. At the start of 2008, <a href="http://www.bioperl.org">BioPerl</a> and <a href="http://www.biojava.org">BioJava</a> moved over to <a href="http://subversion.tigris.org/">Subversion (SVN)</a>, followed by <a href="http://www.biosql.org">BioSQL</a>. <a href="http://www.biopython.org">Biopython</a> was originally going to do the same, but this didn&rsquo;t actually happen. Having all the Bio* projects using the same version control system would have simplified server administration for the OBF, but using SVN wouldn&rsquo;t really have made that much difference to Biopython development. Discussion on the <a href="http://biopython.org/pipermail/biopython-dev/">Biopython development mailing list</a> has since shifted towards next-generation distributed version control systems like <a href="http://git-scm.com/">git</a> or <a href="http://bazaar-vcs.org/">Bazaar</a>.</p> <p>Quote from Linus Torvalds,</p> <blockquote> <p>The slogan of Subversion for a while was ‘CVS done right’, or something like that, and if you start with that kind of slogan, there&rsquo;s nowhere you can go. There is no way to do CVS right.</p> </blockquote> <p>In addition to creating the Linux kernel, Linus Torvalds more recently wrote <a href="http://git-scm.com/">git</a>, a prominent example of a distributed version control system. Rather than switching from CVS to SVN, the <a href="http://www.bioruby.org">BioRuby</a> project choose instead to use git, hosted on <a href="http://github.com">github</a> (see the <a href="http://github.com/bioruby/bioruby/tree/master">BioRuby repository</a>). Biopython is considering doing something similar - using a <em>distributed</em> version control system like git should make it easier for potential Biopython contributors to manage their own local copies of Biopython under version control.</p> <p>Peter, on behalf of the Biopython developers</p>https://www.open-bio.org/2009/03/10/google-summer-of-code-project-ideas-page/Tue, 10 Mar 2009 05:56:04 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/03/10/google-summer-of-code-project-ideas-page/<p>A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup:</p> <p><a href="http://open-bio.org/wiki/Google_Summer_Code_2009">http://open-bio.org/wiki/Google_Summer_Code_2009</a></p>https://www.open-bio.org/2009/02/24/bosc-2009-call-for-abstracts/Tue, 24 Feb 2009 22:09:24 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/24/bosc-2009-call-for-abstracts/<p>Please forward as appropriate and forgive multiple postings.</p> <p>Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009</p> <p>An ISMB 2009 Special Interest Group (SIG) Date: June 27-28, 2009 Location: Stockholm, Sweden URL: <a href="https://www.open-bio.org/wiki/BOSC_2009">/wiki/BOSC_2009</a> Abstract submission via EasyChair: <a href="https://www.easychair.org/login.cgi?conf=bosc2009">https://www.easychair.org/login.cgi?conf=bosc2009</a></p> <p>Important Dates Monday, April 13: Abstract deadline May 1, 2009: Notification of accepted abstracts May 15, 2009: Early Registration Discount Cut-off date June 27-28, 2009: BOSC 2009</p> <p>The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.</p> <p>Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.</p> <p>This year’s conference will mark the 10th anniversary of BOSC. To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead: Open Source Solutions to Grand Challenges in Bioinformatics.” We are inviting abstracts for two different types of talks:</p> <p>1. Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.</p> <p>2. Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.</p> <p>In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session. This year’s topics include: Topics Design Patterns in Bioinformatics Regulatory Genomics Multicore and GPGPU computing Data &amp; Analysis Management (shared session with DAM SIG) Computational Grids Visualization There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.</p> <p>To contact the organizing committee, e-mail <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">bosc at open-bio.org.</a></p> <p>To sign up for BOSC-related announcements, subscribe to the Bosc-announce list ( <a href="http://lists.open-bio.org/mailman/listinfo/bosc-announce">http://lists.open-bio.org/mailman/listinfo/bosc-announce</a>).</p> <p>BOSC 2009 Organizing Committee Kam D. Dahlquist (Chair) Lonnie R. Welch (Co-chair) Hilmar Lapp Jens Lichtenberg Frank Drews Andrew Dalke Jim Procter Seán I. O&rsquo; Donoghue Anton Nekrutenko Steffen Moeller</p>https://www.open-bio.org/2009/02/13/google-summer-of-code-call-for-bio-volunteers/Fri, 13 Feb 2009 21:01:36 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/13/google-summer-of-code-call-for-bio-volunteers/<p>Google is committed to run the <a href="http://code.google.com/soc/2008">Summer of Code program</a> again this year. It will be for the 5th time.</p> <p>In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project. Projects (or umbrella organizations) wishing to participate in the program apply during the organization application period (March 9-13 in 2009). Those accepted into the program provide project ideas and supply mentors that guide the work on those. Students apply to a project within the program with specific project ideas, based on those suggested or based on their own idea, get ranked by the mentors of the project, and those accepted into the program get paired up with mentors. Projects are chiefly about programming, the coding period is 3 months (Jun-Aug), and there is no travel required by either student or mentor. The program is global; other than the US trade restrictions that Google is under, there are no restrictions as to where student or mentor reside. The main motivations behind the program are to recruit new contributors to open-source projects, and to produce more open-source code. See the <a href="http://code.google.com/opensource/gsoc/2009/faqs.html">program FAQs</a> for more information.</p> <p>I&rsquo;ve had the honor of being part of the program for the last two years, administering <a href="http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2007">NESCent&rsquo;s participation as an organization in 2007</a> and <a href="http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2008">2008</a> and in 2007 mentoring a student. I have to say I find it the most awesome open-source program since sliced bread (or the invention of BLAST if that means more to you). Despite that and sadly enough, there has been a dearth of participating bioinformatics projects (though some notable ones, such as CytoScape have participated).</p> <p>There have been two Bio* Summer of Code projects under the NESCent umbrella, <a href="http://biojava.org/wiki/BioJava:PhyloSOC07">one in 2007</a> and <a href="http://bioperl.org/wiki/PhyloXML_support_in_BioPerl">one in 2008</a>. I would be willing to volunteer to take the lead on and administer a full-blown participation of O|B|F as a Bio* umbrella organization, provided 1) at least one Bio* person volunteers to serve as backup administrator, and 2) enough Bio* contributors volunteer to serve as prospective mentors. (Note that if we apply as an organization, there is no guarantee that we would be accepted. In fact, in the past up to 2/3 of applying organizations have been rejected.)</p> <p>Mentoring involves participating in creating the page of project ideas (I&rsquo;d provide template and guidance), corresponding with applicants who have questions, participating in student application ranking, and for primary mentors (those directly assigned to a student) based on empirical evidence at least 5hrs/week of time spent with the student to help him/her get over obstacles or avoid wrong paths.</p> <p>I think almost all mentors would concur that the experience was very gratifying, but as a mentor you will be spending a non-negligible amount of time with the student. I think it is the student-mentor pairing and interaction, not the stipend, that in the end makes the participation for students uniquely productive in terms of learning, and different from simply contributing to the project of choice (which they could always do).</p> <p>For a personal impression for how the program is from a mentor perspective, I&rsquo;ll let Chris Fields speak who was the mentor for the 2008 phyloXML in BioPerl project. From a student&rsquo;s perspective, I&rsquo;ll leave it to the 2007 Biojava student Bohyun Lee (blee34-at-mail.gatech.edu) and the 2008 BioPerl student Mira Han (mirhan-at-indiana.edu) to comment (if they are still on the list).</p> <p>So if you think this is a good idea for Bio* to be part of, if you would like to help in some way, if you can see yourself as a mentor, or if you are a lurking would-be student, please let yourself be heard. Email either to the developer list of your Bio* project or to me.</p>https://www.open-bio.org/2009/02/11/hello-twitter-world/Wed, 11 Feb 2009 21:27:09 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/02/11/hello-twitter-world/<p>O|B|F News feed is now available in <a href="http://twitter.com/">Twitter</a>! You are welcome to <a href="http://twitter.com/obf_news">follow us</a>.</p> <p>Cheers, The O|B|F Admins.</p>https://www.open-bio.org/2009/01/07/kam-dahlquist-elected-to-board-of-directors/Wed, 07 Jan 2009 16:51:01 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2009/01/07/kam-dahlquist-elected-to-board-of-directors/<p>The <a href="https://www.open-bio.org/wiki/Minutes:2008_ConfCall#Minutes" title="2008 BoD meeting minutes">minutes of the November 2008 O|B|F Board of Directors meeting</a> have been posted. The most important result of that meeting is that <a href="http://myweb.lmu.edu/kdahlqui/">Kam Dahlquist</a> was elected to the Board, bringing the number of <a href="https://www.open-bio.org/wiki/Board">Board members</a> back to four. Please join us in extending a warm welcome to Kam!</p> <p>We aim to elect additional Directors this year, please contact the <a href="https://www.open-bio.org/wiki/Board#Nominating_Committee">Nominating Committee</a> if you are interested in serving, or if you know people who might be. Suggestions of people we should tap to serve are also welcome and appreciated.</p> <p>Among the other topics discussed the more important ones were the preparations for BOSC 2009, the hosting offer from the Ohio Supercomputer Center (OSC), and possibilities for obtaining 501(c)3 tax exempt status. See the minutes for details.</p>https://www.open-bio.org/2008/11/18/obf-conference-call-board-meeting/Tue, 18 Nov 2008 19:46:32 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/18/obf-conference-call-board-meeting/<p>The OBF Conference call is scheduled for 12:30PM to 2PM PST on Wednesday Nov 19, 2008.  Members of the <a href="https://www.open-bio.org/">Open Bioinformatics Foundation</a> and those interested in the decisions are invited to listen in and participate.  A brief agenda is available <a href="https://www.open-bio.org/wiki/Minutes:2008_ConfCall">here</a>.</p> <p>Please email Hilmar Lapp at hlapp _AT_ gmx.net for call in number and codes if you wish to participate or listen to the discussion.  Those official members should have gotten an email via the  OBF members email list.</p>https://www.open-bio.org/2008/11/08/obf-board-meeting/Sat, 08 Nov 2008 13:30:54 +0000board@open-bio.org (Open Bioinformatics Foundation)https://www.open-bio.org/2008/11/08/obf-board-meeting/<p>The OBF board meeting will be held via conference call on Nov 19, from 12:30PM to 2PM PST.  Agenda items and information about participating is available on the <a href="http://open-bio.org/wiki/Minutes:2008_ConfCall">agenda webpage</a>. We anticipate this call primarily to manage administrative tasks for the foundation. We welcome input on including more members in the OBF leadership and helping set the direction for the foundation.</p>