Development

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.

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

• Wibowo Arindrarto:
  SearchIO Implementation in Biopython
  mentored by Peter Cock
• Lenna Peterson:
  Diff My DNA: Development of a Genomic Variant Toolkit for Biopython
  mentored by Brad Chapman, Reece Hart, James Casbon
• Marjan Povolni:
  The worlds fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby
  mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
• Artem Tarasov:
  Fast parallelized GFF3/GTF parser in C++, with Ruby FFI bindings
  mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
• Clayton Wheeler:
  Multiple Alignment Format parser for BioRuby
  mentored by Francesco Strozzi and Raoul Bonnal

As in every year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF’s open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.

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).

Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.

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.

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.

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.

The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN:

• BioPerl-Run
• BioPerl-DB
• BioPerl-Network

Please report any bugs to our Redmine server.

Enjoy!

chris

BioPerl 1.6.9 is now available in CPAN.  In this release:

• Refactored Bio::Species/Bio::Tree
• New SeqIO modules (gbxml, msout, mbsout)
• Updates for perl 5.12
• Bio::Assembly support for SAM/BAM, Newbler, ace output
• Bio::DB::SeqFeature updates
• PAML updated to work with v. 4.4d
• lots of various bug fixes, around 50

Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way.  This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make.  In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet).    Please post if there are any problems.