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.

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

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.

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.

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

• Dates: July 8-9, 2016
• Location: Orlando, FL
• Web site: /wiki/BOSC_2016
• Email: bosc@open-bio.org
• BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce
• Twitter: @OBF_BOSC and @OBF_News

Important Dates:

• Call for one-page abstracts opens: March 1, 2016
• Abstract submission deadline: April 1, 2016 - extended 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.

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.

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.

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.

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.

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.

Agenda

Venue: to be held by conference call on May 12, 2015, 1pm EDT (17:00 UTC, 18:00 BST, 19:00 CEST, 10am PDT) 
Dial-in Information: +1-857-216-2939 PIN: 62534 http://www.uberconference.com/hlapp

1. Old business
   • Nov 2014 BoD meeting minutes
2. New business
   1. Term expirations and Elections for the Board
   2. BOSC 2015: update from the 2015 chairs (Nomi, Peter)
   3. Update on ISCB “Community of Special Interest” (COSI) (Peter)

Minutes

Etherpad for notes: https://etherpad.mozilla.org/OBF-BoD-Meeting-May2015

Attending:

• Directors: Present: Chris Fields (via phone), Hilmar, Chris Dag., Nomi Harris, Peter Cock.
• Guests: Karen Cranston (Board candidate)

Minutes:

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.