Obf

Note: I’m reposting here the original announcement from Florent Angly on the BioPerl mail list.

Dear all,

Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats.

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website.

This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5).

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI).

Python support

This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported.

We still fully support Python 2.5, 2.6, and 2.7. Support under Jython is available for versions 2.5 and 2.7 and under PyPy for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.

Hello from Berlin, where the pre-BOSC informal CodeFest 2013 meeting is already underway. We’re looking forward to seeing even more of you on Friday and Saturday for BOSC 2013.

BOSC 2013 will be the 14th annual Bioinformatics Open Source Conference, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the ISMB/ECCB 2013 is in Berlin, Germany.

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.