Apply for OBF Membership online

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 online form.

Membership in the OBF is free, and is open to anyone who has attended BOSC or can otherwise demonstrate commitment to OBF’s goals. 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.

If you have any questions about OBF or OBF membership, you can contact us at board@open-bio.org and/or tweet to @OBF_BOSC.

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Biopython 1.66 released

Source distributions and Windows installers for Biopython 1.66 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

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.

Further work on the Bio.KEGG and Bio.Graphics modules now allows drawing KGML pathways with transparency.

The Bio.SeqIO "abi" parser now decodes almost all the documented fields used by the ABIF instruments – including the individual color channels.

Bio.PDB now has a QCPSuperimposer module using the Quaternion Characteristic Polynomial algorithm for superimposing structures. This is a fast alternative to the existing SVDSuperimposer code using singular value decomposition.

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. Bio.Entrez.parse(...) now supports NCBI XML files using XSD schemas, which will be downloaded and cached like NCBI DTD files.

A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand were parsed into CompoundLocations was fixed: complement(join(...)) as used by NCBI worked, but join(complement(...),complement(...),...) 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.

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.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

  • Alan Medlar (first contribution)
  • Anthony Mathelier (first contribution)
  • Antony Lee (first contribution)
  • Anuj Sharma (first contribution)
  • Ben Fulton (first contribution)
  • Bertrand Néron (first contribution)
  • Brandon Invergo
  • Carlos Pena
  • Christian Brueffer
  • Connor T. Skennerton (first contribution)
  • David Arenillas (first contribution)
  • David Nicholson (first contribution)
  • Emmanuel Noutahi (first contribution)
  • Eric Rasche (first contribution)
  • Fabio Madeira (first contribution)
  • Franco Caramia (first contribution)
  • Gert Hulselmans (first contribution)
  • Gleb Kuznetsov (first contribution)
  • João Rodrigues
  • John Bradley (first contribution)
  • Kai Blin
  • Kian Ho (first contribution)
  • Kozo Nishida (first contribution)
  • Kuan-Yi Li (first contribution)
  • Leighton Pritchard
  • Lucas Sinclair
  • Michiel de Hoon
  • Peter Cock
  • Saket Choudhary
  • Sunhwan Jo (first contribution)
  • Tarcisio Fedrizzi (first contribution)
  • Tiago Antao
  • Vincent Davis

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.

Posted in Biopython, Blogroll, Code, Community, Development, OBF, OBF Projects | Tagged , , , , , | 25 Comments

BioRuby 1.5.0 released

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.

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Here is a brief summary of changes.

  • Ruby 2.0.0, 2.1, 2.2 support.
  • Some features are removed because of remote service discontinuance or difficulty of code maintenance.
  • Refactoring of code.
  • Bio::SPTR is renamed as Bio::UniProtKB.
  • Bug fixes.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available for download from the following links.

You can easily install by using RubyGems. First, check the
version number by using search command: www.bestessaywritingservice.co.uk

% gem search --remote bio

and find “bio (1.5.0)” in the list. Then,

% sudo gem install bio

Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.

Acknowledgments: Thanks to all persons reporting issues and/or
submitting patches.

Hope you enjoy.

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BOSC 2015 Panel – increasing diversity

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 we announced the theme of the BOSC 2015 panel would be “Open Source, Open Door: increasing diversity in the bioinformatics open source community”. Our complete list of panellists is:

  • Panel chair Mónica Muñoz-Torres (@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). 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.
  • Holly Bik (@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.
  • Michael R. Crusoe (@biocrusoe) is the lead for the k-h-mer project at C. Titus Brown’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’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.
  • Aleksandra Pawlik (@aleksandrana) 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.
  • Jason Williams (@JasonWilliamsNY) 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’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.

In addition the BOSC 2015 co-chairs Nomi Harris and Peter Cock 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.S. Today is the deadline for discounted early registration, and the deadline to submit a late breaking lightning talk or poster abstract. See BOSC 2015 for more details.

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Public OBF Board of Directors Meeting

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 World Clock). The developing agenda for the meeting is posted, as are the dial-in details.

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 masterpapers.com 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’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.

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’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.

I look forward to the Board meeting, and to seeing many of you in July at the 2015 BOSC in Dublin.

Hilmar Lapp, President, OBF Board of Directors

Update: Karen Cranston was elected to the board at the 12 May Public OBF Board Meeting.

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Open Source, Open Door: increasing diversity in the bioinformatics open source community

The Bioinformatics Open Source Conference (BOSC) 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.

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’t white, older people, people from outside North America and Europe, and non-programmers.

During a Birds of a Feather (BoF) session held at BOSC 2014, 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.

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, we welcomed Dr. Sarah Hird as our new Outreach Coordinator. Sarah is currently a UC Davis Chancellor’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 promoting diversity in STEM.  “I am personally and professionally interested in how we can make “the Academy” a more representative sample of the world around us,” she says.

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 code of conduct published on the ISMB/ECCB 2015 website. 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.

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.

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 Monica Munoz-Torres and will include panellists Holly Bik and Jason Williams (see bios below).

  • 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).
  • 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.
  • Jason Williams (Twitter: @JasonWilliamsNY) 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.

We are looking for two more panellists, and have some ideas – but your suggestions are welcome! Please email the BOSC committee or just tweet panellist ideas at @OBF_BOSC.

Finally, please spread the word about BOSC! The deadline for submitting abstracts for regular-length talks is tomorrow (Friday, April 3 – update: extended to Tuesday, April 7 due to Easter/Passover weekend), but there will also be opportunities for last-minute lightning talks and posters.

 

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GSoC project Sambamba published in scientific journal

(This is a repost of a BLOG on Google Open Source news about Google’s open source student programs and software releases)

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.

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.

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!

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.

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

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