Phyloinformatics Summer of Code supports OBF Travel Fellowship Program

The Open Bioinformatics Foundation is pleased to announce a gift of USD 18,125 from the Phyloinformatics Summer of Code toward the OBF travel fellowship program. The program, announced earlier this year on March 1, 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 Bioinformatics Open Source Conference (BOSC), OBF’s flagship event.

The funds for this gift are a legacy of the seven years during which the National Evolutionary Synthesis Center (NESCent) served as a mentoring organization in the Google Summer of Code™. Over the years, NESCent’s program, the Phyloinformatics Summer of Code, 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.

Todd Vision, former Associate Director of Informatics at NESCent, says “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.”

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.”

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.

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 served as the Outreach Coordinator for BOSC 2015, the theme of which was Increasing Diversity.

About OBF: The Open Bioinformatics Foundation (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 Software in the Public Interest, Inc., a 501(c)(3) fiscal sponsorship organization.

About NESCent: The National Evolutionary Synthesis Center (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 Triangle Center for Evolutionary Medicine (TriCEM).

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BOSC CodeFest 2016

The Bioinformatics Open Source Conference (BOSC) 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’ll get together this summer, July 8-9, in Orlando, Florida.

Abstracts for BOSC 2016 talks and posters are due this Friday, April 1st. We want to hear about your research and encourage everyone to submit an abstract. We love talks from newcomers to BOSC as well as established projects: no idea is too big or small. We also offer Travel Fellowships for speakers if money would be a barrier to attending.

Prior to BOSC, we organize a free two day collaborative working session called Codefest. We’ll establish friendships and collaborations while helping new members find fun work and extending existing projects. It’s a time to learn, teach, develop and grow. This year we’re kindly hosted by the FamiLAB workspace in Orlando. So in addition to getting to work with fellow OpenBio members, you’ll have the chance to learn about the Orlando maker community.

We hope you’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.

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BOSC 2016 Keynote Speakers

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2016:

Jennifer Gardy

Jennifer Gardy

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 – “genomic epidemiology”, which uses a pathogen’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.

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’s documentary series The Nature of Things, has hosted CBC’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.

Dr. Gardy’s keynote topic is “The open-source outbreak: can data prevent the next pandemic?”

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.

Homepage: Jennifer Gardy, Twitter: @JenniferGardy

Steven Salzberg

Steven Salzberg

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’s leading DNA sequencing centers at the time.

Salzberg’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’s software is free and open source, and their systems have been downloaded hundreds of thousands of times.

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.

Dr. Salzberg will speak about “Open source, open access, and open data: why science moves faster in an open world”.

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.

Homepage: Steven Salzberg, Twitter: @StevenSalzberg1

The BOSC 2016 call for abstracts is currently open, and BOSC/ISMB 2016 registration will open next week. We hope to see you in Florida!

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BOSC 2016 Call for Abstracts

Call for Abstracts for the 17th Annual Bioinformatics Open Source Conference (BOSC 2016), a Special Interest Group (SIG) of ISMB 2016.

[BOSC Logo]

Important Dates:

[ISMB 2016 logo]
  • Call for one-page abstracts opens: March 1, 2016
  • Abstract submission deadline: April 1, 2016extended to Monday 4 April 2016
  • Travel fellowship application deadline: April 15, 2016
  • Authors notified: May 6, 2016
  • Codefest 2016: July 6-7, 2016, Orlando, FL (confirming venue)
  • BOSC 2016: July 8-9, 2016, Orlando, FL
  • ISMB 2016: July 8-12, 2016, Orlando, FL

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.

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 OBF Travel Fellowship announcement for more information.

Session topics include:

  • Open Science and Reproducible Research
  • Standards and Interoperability
  • Data Science
  • Visualization
  • Translational Bioinformatics
  • Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in helping to sponsor BOSC 2016, please contact us! Sponsors in 2015 included Google, GigaScience, Curoverse and Bina – we thank them for their support.

BOSC 2016 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko

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OBF Travel Fellowship Program

We are very pleased to announce our new Open Bioinformatics Foundation (OBF) Travel Fellowship program. 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 Bioinformatics Open Source Conference (BOSC).

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 BOSC 2015 report, 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. OBF’s bylaws have included a nondiscrimination clause from the outset. OBF’s major member projects have not only always welcomed new participants to their communities, but embraced passing on leadership to people who hadn’t been part of the “inner circle” from the beginning.

However, being on the “inside” 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 low diversity observed for open-source project communities in general.

We’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 BOSC 2015 panel discussion. When asked for a show of hands of who was there for the first time, nearly half of the attendees’ hands went up! We believe firmly that with enough dedicated and sustained attention, our community can include everyone who shares our mission. We also believe that eventually more diversity at our community events will trickle down to increasing the diversity of participants in our member projects.

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 calling on donors and BOSC sponsors. You can earmark your contribution to be used specifically for funding this program – simply email the Board if the donation form does not leave enough space.

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.

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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 and/or tweet to @OBF_News.

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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.

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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:

% 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 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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