The updated Biopython Tutorial and Cookbook is online (PDF).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ‘beta’ installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows.

Please note we are phasing out support for Python 2.5. We will continue support for at least one further release (Biopython 1.62). This could be extended given feedback from our users. Focusing on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier.

Features

GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows an octagonal shape, like the existing BOX sigil but with the corners cut off. JAGGY shows a box with jagged edges at the start and end, intended for things like NNNNN regions in draft genomes. Finally BIGARROW is like the existing ARROW sigil but is drawn straddling the axis. This is useful for drawing vertically compact figures where you do not have overlapping genes.

New module Bio.Graphics.ColorSpiral can generate colors along a spiral path through HSV color space. This can be used to make arbitrary ‘rainbow’ scales, for example to color features or cross-links on a GenomeDiagram figure.

The Bio.SeqIO module now supports reading sequences from PDB files in two different ways. The “pdb-atom” format determines the sequence as it appears in the structure based on the atom coordinate section of the file (via Bio.PDB,
so NumPy is currently required for this). Alternatively, you can use the “pdb-seqres” format to read the complete protein sequence as it is listed in the PDB header, if available.

The Bio.SeqUtils module how has a seq1 function to turn a sequence using three letter amino acid codes into one using the more common one letter codes. This acts as the inverse of the existing seq3 function.

The multiple-sequence-alignment object used by Bio.AlignIO etc now supports an annotation dictionary. Additional support for per-column annotation is planned, with addition and splicing to work like that for the SeqRecord per-letter annotation.

The Bio.Motif module has been updated and reorganized. To allow for a clean deprecation of the old code, the new motif code is stored in a new module Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif.

Experimental Code – SearchIO

This release also includes Bow’s Google Summer of Code work writing a unified parsing framework for NCBI BLAST (assorted formats including tabular and XML), HMMER, BLAT, and other sequence searching tools. This is currently available with the new BiopythonExperimentalWarning to indicate that this is still somewhat experimental. We’re bundling it with the main release to get more public feedback, but with the big warning that the API is likely to change. In fact, even the current name of Bio.SearchIO may change since unless you are familiar with BioPerl its purpose isn’t immediately clear.

Contributors

• Brandon Invergo
• Bryan Lunt (first contribution)
• Christian Brueffer (first contribution)
• David Cain
• Eric Talevich
• Grace Yeo (first contribution)
• Jeffrey Chang
• Jingping Li (first contribution)
• Kai Blin (first contribution)
• Leighton Pritchard
• Lenna Peterson
• Lucas Sinclair (first contribution)
• Michiel de Hoon
• Nick Semenkovich (first contribution)
• Peter Cock
• Robert Ernst (first contribution)
• Tiago Antao
• Wibowo ‘Bow’ Arindrarto

The meeting will be held online or over conference call. We will post details about how to dial in or connect closer to the date (here).

On the agenda Richard Holland and Chris Fields are running for election to the Board, and some other items primarily up for discussion, including how to keep our membership roll up-to-date and increasing with the least barriers. We will post a more detailed agenda in advance of the meeting (here).

OBF members should have already received notice of this meeting via the OBF member’s mailing list.

Nearly all projects use public source code repositories such as github or sourceforge so no problems with access to the code should be limiting. Mailing lists are still using the old server but will be moved to the AWS site in the next few days and we are working to have little downtime for the lists.  Mediawiki sites are moving in stages and so far Bioperl, Biopython, and the OBF wikis have been migrated.  This news site has also been migrated to AWS and this is the 1st post from it (will it work!?)

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. We had a participation of 39 out of 105 eligible, or 37%, which is far above the quorum of 10%. The tally is 38 for provisionally accepting and 1 against. The tally can be seen (and audited) here:
https://vote.heliosvoting.org/helios/e/OBFjoiningSPI

The SPI Board vote on resolution 2012-09-28.jb.1 (“Open Bioinformatics Foundation as associated project”) resulted in 8 yes, 0 no, 0 abstain. Given the result of our election, I accepted the invitation right away.

Thanks to everyone who voted. On behalf of the Board, I am thrilled about the turnout!

This terminates O|B|F’s status as its own corporation, which over the years has been more trouble than gain. As an SPI-associated project, we can now accept donations that are 501(c)3 tax-exempt in the US, aside from other benefits. In the coming weeks and months we will be articulating what kind of objectives, platforms, and activities we can or should pursue, given our new status. I’ll communicate separately about that once it gets off the ground.

Finally, please join me in thanking Josh Berkus (SPI & PostgreSQL) for shepherding our joining SPI all the way through. And please also join me in saying hi to the SPI community – as I have done earlier I’d like to encourage everyone to consider joining the SPI as well. It’s a friendly community, and I like to think we can enrich it.

This is a historic day for our organization. Have a drink tonight

Cheers,

-hilmar

Note: This post is based on an email sent yesterday to the OBF member’s mailing list.

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.
• Fixed: Genomenet remote BLAST does not work.
• Fixed: Bio::NucleicAcid.to_re(“s”) typo.
• Fixed: Bio::EMBL#os raises RuntimeError.
• Fixed: bin/bioruby: Failed to save object with error message “can’t convert Symbol into String” on Ruby 1.9.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.3.tar.gz
Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.3.gem

We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:
% gem search –remote bio
and find “bio (1.4.3)” in the list. Then,
% sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.

Hope you enjoy.

• BioRuby
• Biopython
• BioPerl

The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems.

Travis-CI gives us continuous testing, but for the moment only covers one operating system (currently 32 bit Ubuntu Linux using Virtual Machines). This automated testing is therefore complementary to our existing OBF BuildBot server which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.

However, Travis-CI are working on a new feature – automatic testing of pull requests, currently only available on a donation basis – which the OBF was happy to support.

What this means is that when a contributor has some code ready for integration, they can issue a GitHub pull request, and then Travis-CI will automatically run the unit tests with those proposed changes. This is something that currently the core-developers would normally do manually as part of evaluating proposed changes, so having this happen automatically should be a big help.

We’re excited about making more use of Travis-CI for other OBF projects. Thus far we’ve been really impressed with Travis-CI.

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.

Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy). We are now encouraging early adopters to help beta testing on these platforms, and have included a ‘beta’ installer for Python 3.2 under 32-bit Windows.

Features

New module Bio.bgzf supports reading and writing BGZF files (Blocked GNU Zip Format), a variant of GZIP with efficient random access, most commonly used as part of the BAM file format and in tabix. This uses Python’s zlib library internally, and provides a simple interface like Python’s gzip library. Using this the Bio.SeqIO indexing functions now support BGZF compressed sequence files. See this blog post for more background on BGZF and SeqIO.

The GenBank/EMBL parser will now give a warning on unrecognized feature locations and continue parsing (leaving the feature’s location as None). Previously it would abort with an exception, which was often unhelpful.

The Bio.PDB.MMCIFParser is now compiled by default (but is still not available under Jython, PyPy or Python 3).

The SFF parser in Bio.SeqIO now decodes Roche 454 ‘universal accession number’ 14 character read names, which encode the timestamp of the run, the region the read came from, and the location of the well.

In the Phylo module, the “draw” function for plotting tree objects has become much more flexible, with improved support for matplotlib conventions and new parameters for specifying branch and taxon labels. Writing in the PhyloXML format has been updated to more closely match the output of other programs. A wrapper for the program RAxML has been added under Bio.Phylo.Applications, alongside the existing wrapper for PhyML.

Additionally there have been other minor bug fixes and more unit tests.

Contributors

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

• Brandon Invergo
• Eric Talevich
• Jeff Hussmann (first contribution)
• John Comeau (first contribution)
• Kamil Slowikowski (first contribution)
• Kevin Jacobs
• Lenna Peterson (first contribution)
• Matt Fenwick (first contribution)
• Peter Cock
• Paul T. Bathen
• Wibowo Arindrarto

- 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) .

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.

For the accepted students: congratulations! You have risen to the top of a very competitive application process. Now it’s time to “put your money where your mouth is”, as the saying goes. Let’s get out there and write some great code this summer!

Best regards,

Robert Buels
OBF GSoC 2012 Organization Administrator

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.

The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from sequence search I/O in Biopython to lightweight sequence objects and lazy parsing in BioPerl, a next-generation BioRuby interface to Ensembl to developing cloud-optimized versions of BioJava modules. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also particularly welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 26 through Friday, April 6th, 2012.

INQUIRIES:

We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details.

2012 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs

Rob Buels
OBF GSoC 2012 Admin