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. [Read More]

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. [Read More]

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). [Read More]

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 Old business Nov 2014 BoD meeting minutes New business Term expirations and Elections for the Board BOSC 2015: update from the 2015 chairs (Nomi, Peter) 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. [Read More]

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. [Read More]

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. [Read More]

(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. [Read More]

Announcing the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2015: Holly Bik 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. [Read More]

Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015. Dates: 10-11 July, 2015 Location: Dublin, Ireland Web site: /wiki/BOSC_2015 Email: bosc@open-bio.org BOSC announcements mailing list Twitter: @OBF_BOSC and @OBF_News Important Dates: March 24, 2015: Registration opens for ISMB and BOSC ( https://www.iscb.org/ismbeccb2015-registration) April 3, 2015: Deadline for submitting BOSC abstracts May 3, 2015: Notification of accepted talk abstracts emailed to authors July 8-9, 2015: BOSC Codefest 2015, Dublin July 10-11, 2015: BOSC 2015, Dublin July 10-14, 2015: ISMB/ECCB 2015, Dublin 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. [Read More]

Last year’s Google Summer of Code 2014 was very productive for the OBF 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. Google’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 organisations accepted for GSoC 2015. [Read More]