Obf-Projects

We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs.

• “gem install bio” failed with Ruby 2.0 or later versions.
• lib/bio/db/gff.rb script encoding issue
• Bio::Blast::Default::Report parse error when subject sequence contains spaces.

For more information, see RELEASE_NOTES.rdoc and ChangeLog.

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

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.

The Open Bioinformatics Foundation (OBF) will be holding a public Board of Directors meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT).

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).

Our aging server which has run for 5+ years the OBF sites has finally reached end of its lifespan. We are currently migrating sites to AWS volumes and sites for a temporary period while we decide about how to continue to support these services in the future.  There will be some downtime while the all-volunteer OBF admin team makes time to fix this.

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!?)

I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a Software in the Public Interest (SPI) associated project, rather than its own not-for-profit incorporation.

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

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius.

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.

Earlier this year BioRuby and then Biopython and BioPerl started using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated:

• 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.

Source distributions and Windows installers for Biopython 1.60 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 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.

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.