Biopython 1.66 released

 Posted on October 21, 2015  |  peterc

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]

BOSC 2015 Panel - increasing diversity

 Posted on June 5, 2015  |  peterc

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]

Public OBF Board of Directors Meeting

 Posted on May 1, 2015  |  hilmar

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]

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

 Posted on April 2, 2015  |  nlharris

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]

BOSC 2015 Keynote Speakers

 Posted on March 26, 2015  |  peterc

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]

BOSC 2015 call for Abstracts

 Posted on March 5, 2015  |  peterc

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]

Sadly OBF not accepted for GSoC 2015

 Posted on March 3, 2015  |  peterc

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]

OBF Google Summer of Code 2014 Wrap-up

 Posted on February 23, 2015  |  hilmar

GoogleSummer_2014logo In 2014, OBF had six students in the Google Summer of Code 2014™ (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).

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 Bioinformatics Open-Source Conference (BOSC).  In part this was also motivated by " paying it forward", a concept central to growing healthy open-source communities, after the larger domain-agnostic language projects such as SciRuby and PSF 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.

[Read More]

BOSC welcomes Sarah Hird as Outreach Coordinator

 Posted on January 5, 2015  |  nlharris

The BOSC 2015 Organizing Committee is pleased to welcome Sarah Hird as our new Outreach Coordinator. BOSC is eager to increase the participation of individuals and groups that have been historically underrepresented at our conferences, and Sarah will be spearheading this effort. 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. [Read More]

BOSC 2015 will be in Dublin with ISMB/ECCB 2015

 Posted on September 18, 2014  |  peterc

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’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).. Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. [Read More]