Obf

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. A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn’t notice any changes ;) In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. [Read More]

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. Although the unit tests are all fine, there is a small but real chance that we’ve accidentally broken things - which is why we’re doing this beta release. [Read More]

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. [Read More]

BioPerl has migrated to git and GitHub! We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz. If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID. Also, add the extra email (where ‘DEVNAME’ is your original Subversion account ID). [Read More]

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 Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby [Read More]

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: [Read More]

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. One obvious way to try to do this is to parse the file into an object representation (i. [Read More]

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. We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. [Read More]