This is a reminder that the forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4. Looking back, we supported Python 2.3 for about six years - it was released July 2003, and Biopython 1.50 released in April 2009 was the last to support it. Similarly, Python 2.4 was released six years ago (November 2004). Dropping Python 2.4 support will allow use to assume standard library modules like the

We are pleased to announce the release of BioRuby 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added. Here is a brief summary of changes. PAML Codeml support is significantly improved: PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins.

Agenda Old business 2009 BoD meeting minutes New business BOSC BOSC 2010 (Kam) - held with ISMB2010 in Boston, MA, USA Money spent/made attendee number, any other feedback BOSC 2011 - with ISMB 2011 Vienna, Austria 2011 Organizing Committee chairs Plans for the conference Treasurer’s 2010 report (ChrisD) 2010 Financial report BoD membership and succession. Kam Dahlquist is resigning from the BoD.

The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable release ( Biopython 1.54) and the beta release earlier in August.

After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal.  The article is open access, so please take a look. BioRuby: Bioinformatics software for the Ruby programming language Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama Bioinformatics 2010;

We’ve just released a beta of Biopython 1.55 for user testing. Since Biopython 1.54 was released three months ago, we’ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we’ve had to update quite a lot of the older parts of the library.

The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes. This is the first stable release to feature the new Bio.Phylo module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and PhyloXML formats.

BioPerl has migrated to git and GitHub!

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro

In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores - and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as ‘B’). Hats off to Dr Torsten Seemann for raising awareness of this issue in his post on the seqanswers.com forum, referring to a presentation by Tobias Mann of Illumina which says: So, armed with this

This is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release). It is often useful to be able to extract a few records from a larger sequence file - for example, some sequences of interest from a full UniProt or GenBank dump.