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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. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

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. Note there are some minor differences in the GenBank annotation we’ve used and the genes shown in the original figure.

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). We are now encouraging early adopters to help beta testing on these platforms.

The meeting was held conference call.

Agenda

1. Old business

   • 2010 Financial Report

   • 2011 BoD meeting minutes

2. New business

   1. Treasurer’s 2011 report: File:2011-OBF-Treasurers-Report v1.pdf (Chris Dagdigian)
   2. Elections:
      • Hilmar Lapp, running for office of President
      • Nomi Harris, running for office of Parliamentarian
      • Peter Cock, running for BoD member-at-large
   3. 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)

Agenda

1. Old business

   • 2010 BoD meeting minutes

   • 2010 Financial Report

2. Action items from the 2010 meeting

3. New business

   1. 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
   2. Google Summer of Code
      • Org admin’s summary report (Rob Buels)
   3. Treasurer’s 2011 report: File:2011-OBF-Treasurers-Report v1.pdf (Chris Dagdigian)
   4. BoD membership and succession.
      • Nominations: Peter Cock
      • Plan to elect new BoD members and rotate officers.
   5. Additional topics proposed by community
      • How to become an affiliate project? (Alan R Williams)
      • BioSmalltalk as an OBF member project? (Hernán Morales)
      • CloudBiolinux as an OBF member project? (Pjotr Prins, Brad Chapman)
      • OBF Europe and Asia (Steffen Möller), branch organisations for tax free donations from the public or industry. Possibly in conjunction with Debian’s Software in the Public Interest setup.
      • OBF holding copyright as a community organization using the Apache model for licensing (Jean Peccoud)

Minutes from the meeting

Venue: held by conference call, scheduled for Nov 8, 2011, 11am EST (16:00 UTC).

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. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. Here the figure just uses a different color for each chromosome, but you can color each feature individually.

We are pleased to announce the release of BioRuby 1.4.2. This new release fixes bugs existed in 1.4.1 and adds new features and improvement of performance.

Here is a brief summary of changes.

Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module.

Bio.SeqIO now includes read and write support for the SeqXML, a simple XML format offering basic annotation support. See Schmitt et al (2011) in Briefings in Bioinformatics.

I’m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program.

The accepted students, their projects, and their mentors (in alphabetical order):

Justinas Vygintas Daugmaudis Michele dos Santos da Silva (2 students!) Mocapy++Biopython: from data to probabilistic models of biomolecules mentored by Thomas Hamelryck and Eric Talevich