I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a Software in the Public Interest (SPI) associated project, rather than its own not-for-profit incorporation. An electronic vote of O|B|F members on whether or not to provisionally approve the invitation from SPI closed yesterday at 19:00 UTC.

Agenda Old business 2011 December BoD meeting minutes New business Approval of changes to O|B|F Bylaws Minutes Venue: held by WebEx conference with audio bridge through phone (donated by BioTeam), scheduled for Sep 11, 2012, 11.30am EDT (15:30 UTC) Attending: Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Jason Stajich, Peter Cock Guests: Scott Markel Minutes: Hilmar

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius. Here is a brief summary of changes. Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element. Many failures and errors running on JRuby and Rubinius are resolved. Strange behavior related with “circular require” is fixed.

Earlier this year BioRuby and then Biopython and BioPerl started using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated: BioRuby Biopython BioPerl The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems.

Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 and PyPy 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported.

BioJava 3.0.4 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ . - This is mainly a bug fix release addressing issues with the protein structure and disorder modules - One new feature: SCOP data can now be accessed from either the original SCOP site in the UK (v. 1.75) or from Berkeley (v. 1.75A) .

Hello all, I’m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 5 very capable students to work on OBF projects this summer as part of the Google Summer of Code (GSoC) program.

Applications due 19:00 UTC, April 6, 2012. /wiki/Google_Summer_of_Code The Open Bioinformatics Foundation (OBF) Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world.

Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for Google Summer of Code 2012! Google Summer of Code (GSoC) is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer.

Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012.

I’ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in Biopython 1.59. You can now control the start and end points of individual tracks, and you can add cross-links between regions of different tracks, as shown here: This example attempts a simplified reproduction of Figure 6 in Proux et al. (2002), and shows three related phage genomes one above the other.