BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010. The BOSC 2010 web site can be accessed here: /wiki/BOSC_2010. The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community. [Read More]

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: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10. [Read More]

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. There have been some additions to our core objects - the Seq (and related UnknownSeq) objects gained upper and lower methods (like the string methods of the same name but alphabet aware) plus a new ungap method. [Read More]

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. The dial-in number is +1-518-825-1400, participant code 279610. [Read More]

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

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 & Sysadmin report (JasonS and ChrisD) Domain names currently registered, upcoming expirations, newly purchased names Proposal to purchase new hardware - 2009 hardware purchase proposal Proposal to purchase box for upstream SPAM filtering System Administration status & coverage report (who, what, issues, future) Consider possibility of moving code mirroring to public (code. [Read More]

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! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). [Read More]

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. [Read More]