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.

Source distributions and Windows installers for Biopython 1.59 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 (which does not cover NumPy). Please note that this release will not work on Python 2.4 Most functionality is also working under Python 3.1 and 3.2 (including

The meeting was held conference call.

Agenda Old business 2010 BoD meeting minutes 2010 Financial Report Action items from the 2010 meeting New business BOSC BOSC 2011 (Nomi) - held with ISMB2011 in Vienna, Austria Money spent/made, attendee number, any other feedback BOSC 2012 - with ISMB 2012 in Long Beach, CA 2012 Organizing Committee chair Plans for the conference Google Summer of Code Org admin’s summary report (Rob Buels) Treasurer’s 2011

The annual Board of Directors Meeting of the Open Bioinformatics Foundation will take place on November 8, 2011. As in previous years, it will be held by conference call, estimated to be about 2 hrs long. The meeting will on Tuesday 8 November 2011, at 11am EST, 8am PST, 16:00 UTC/GMT, 17:00 CET, or Wednesday 9 November 1am JST. Note for translating into other time zones that by then both Europe and the US have gone off DST.

One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. I’ve just been updating the Biopython Tutorial (current version here, PDF) to include an example drawing this: Here’s a PDF version too. This example just parses the Arabidopsis thaliana GenBank files to get the chromosome lengths and the tRNA gene placements.