New BioJava Logo Design Competition

 Posted on June 14, 2016  |  andreas

BioJava is organizing a design competition to come up with a new logo. Anybody can participate: The logo should look modern and be better than the current one (yellow circle) The logo should be able to be rendered as a favicon, as well as large (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok. Logos shall not look similar in any way to the trademarked Java programming language logo. [Read More]

Biopython 1.67 released

 Posted on June 8, 2016  |  peterc

This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure. Source distributions and Windows installers for Biopython 1.67 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI). This release of Biopython supports Python 2. [Read More]

Welcome to our Google Summer of Code 2016 students

 Posted on April 25, 2016  |  kblin

The Open Bioinformatics Foundation is participating in the Google Summer of Code 2016 program, and last Friday the selected students were announced. Congratulations to all of you, and welcome. I also want to use this opportunity to thank all students who applied. Resources are limited and your proposals did not make it easy to select our finalists. We wish you all the best for your future endeavours, and hope to be able to work with you in future. [Read More]

BOSC CodeFest 2016

 Posted on March 28, 2016  |  brad

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. [Read More]

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]

GSoC project Sambamba published in scientific journal

 Posted on April 1, 2015  |  pjotrp

(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]

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]

Biopython 1.65 released

 Posted on December 17, 2014  |  peterc

Dear Biopythoneers, Source distributions and Windows installers for Biopython 1.65 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 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2. The most visible change is that the Biopython sequence objects now use string comparison, rather than Python’s object comparison. [Read More]

Biopython 1.64 released

 Posted on May 29, 2014  |  tiago

Source distributions and Windows installers for Biopython 1.64 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 and 2.7, 3.3 and also the new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython 2.7b2. The new experimental module Bio.CodonAlign facilitates building codon alignment and further analysis upon it. This work is from the Google Summer of Code (GSoC) project by Zheng Ruan. [Read More]