I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.

We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code control.

The official 2009 Board of Directors meeting is taking place today, Monday Dec 14, at 4pm EST (21:00 UTC) via teleconference. If you are an O|B|F member, you will have received the announcement and dial-in information earlier. O|B|F Board of Director meetings are public - anyone interested in O|B|F business can participate, which is one reason we are holding the meeting over teleconference.

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions &

Agenda Old business 2008 BoD meeting minutes New business BOSC BOSC 2009 (Kam) Money spent/made attendee number, any other feedback BOSC 2010 - held with ISMB2010 in Boston, MA, USA Treasurer’s 2009 report (ChrisD) 2009 Financial report BoD membership and succession. Nomination of Nomi Harris for election to the BoD Need plan to elect new BoD members and rotate officers. OBF Hardware &

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.

BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.

Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network They can also be downloaded from the BioPerl website: http://bioperl.org/DIST/RC/ This is the first run where we’ve switched to a regular Module::Build installation, so expect some initial bumps!

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code.

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.

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.