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.

Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15.  See the BOSC web site at /wiki/BOSC_2010 for details.  Submissions will only be accepted electronically at http://events.open-bio.org/BOSC2010/openconf.php. Graduate students, don’t forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award.

One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles , but they will now also accept filenames . This is a case of practicality beats purity (to quote the Zen of Python), and is particularly handy when doing very short scripts or working at the Python prompt.

A beta release for Biopython 1.54 is now available for download and testing. Since Biopython 1.53 was released at the end of last year, several new features and more documentation have been added, plus the usual bug fixes. For full details see the NEWS file.

The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer’s Google Summer of Code.  Our list of project ideas and mentors is linked from the O|B|F GSoC page. Student applications must be submitted to Google by April 9, 2010, see the official GSoC 2010 FAQ. That is less than three weeks away!