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. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code (GSoC). [Read More]

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. For more on GSoC, see the GSoC 2012 FAQ. [Read More]

Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012. Dates: July 13-14, 2012 Location: Long Beach, California Web site: /wiki/BOSC_2012 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 13, 2012: Deadline for submitting abstracts May 7, 2012: Notification of accepted talk abstracts emailed to authors July 11-12, 2012: Codefest 2012 programming session July 13-14, 2012: BOSC 2012 July 15-17, 2012: ISMB 2012 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. [Read More]

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. Different classes of genes have been given different colors, while the strength of the red shaded cross-links indicates the percentage identity of the linked genes. [Read More]

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 modules using NumPy), and under PyPy (excluding our NumPy dependencies). [Read More]

The meeting was held conference call. Agenda Old business 2010 Financial Report 2011 BoD meeting minutes New business Treasurer’s 2011 report: File:2011-OBF-Treasurers-Report v1.pdf (Chris Dagdigian) Elections: Hilmar Lapp, running for office of President Nomi Harris, running for office of Parliamentarian Peter Cock, running for BoD member-at-large Alternative procedure(s) for elections (Jason Stajich) Minutes Venue: held by conference call, scheduled for Dec 13, 11am EST (16:00 UTC) (originally scheduled for 12pm EST, by mistake started 1 hour earlier) [Read More]

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 report: File:2011-OBF-Treasurers-Report v1.pdf (Chris Dagdigian) BoD membership and succession. [Read More]

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. [Read More]

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. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. [Read More]