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Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.  The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here:

Via CPAN:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/

Via the BioPerl website:

http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip

The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).

Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution.

Biopython 1.51 onward includes support for Sanger, Solexa and Illumina 1.3+ FASTQ files in Bio.SeqIO, which allows a lot of neat tricks very concisely. For example, the tutorial ( PDF) has examples finding and removing primer or adaptor sequences.

However, because the Bio.SeqIO interface revolves around SeqRecord objects there is often a speed penalty. For example for FASTQ files, the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing.

The release of Biopython 1.52 earlier this week marked the end of an era, it was our last release using CVS for source code control.

As of now, Biopython is using a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby project have been using github for some time, so we are in good company.

Our existing OBF hosted CVS repository will be maintained in the short to medium term as a backup, but will not be updated.

We are pleased to announce the release of BioRuby 1.3.1. This new release fixes many bugs existed in 1.3.0.

Here is a brief summary of changes.

• Refactoring of BioSQL support.
• Bio::PubMed bug fixes.
• Bio::NCBI::REST bug fixes.
• Bio::GCG::Msf bug fixes.
• Bio::Fasta::Report bug fixes and added support for multiple query sequences.
• Bio::Sim4::Report bug fixes.
• Added unit tests for Bio::GCG::Msf and Bio::Sim4::Report.
• License of BioRuby is clarified.

In addition, many changes have been made, mainly bug fixes. For more information, you can see ChangeLog.

We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by extending the functionality of existing modules, adding a set of application wrappers for popular alignment programs and fixing a number of minor bugs.

In particular, the SeqIO module can now write Genbank files that include features, and deal with FASTQ files created by Illumina 1.3+. Support for this format allows interconversion between FASTQ files using Solexa, Sanger and Ilumina variants using conventions agreed upon with the BioPerl and EMBOSS projects.

A beta release for Biopython 1.51 is now available for download and testing.

In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO’s support for the FASTQ format to include files created by Illumina 1.3+, and added a new set of application wrappers for alignment programs, and made numerous tweaks and bug fixes.

All the new features have been tested by the dev team but it’s possible there are cases that we haven’t been able to foresee and test, especially for the GenBank feature writer (as there as just so many possible odd fuzzy feature locations).

The BOSC 2009 schedule of speakers with links to abstracts has been posted at /wiki/BOSC_2009_Schedule.

Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC 2009.  For more information, see the BOSC 2009 web site at /wiki/BOSC_2009.

Abstract acceptances went out today–stay tuned for the schedule, which will be posted once the speakers have confirmed their invitations.

The early registration deadline for BOSC is Friday, May 15; don’t forget to take advantage of the discounted fee for early registrants at http://www.iscb.org/ismbeccb2009/registration.php.

As announced here, any last minute requests to postpone dropping support for Python 2.3 from the next release of Biopython must be posted to the main Biopython mailing list no later than Friday, May 8.