Biopython 1.56 released
Posted on November 26, 2010
| peterc
The Biopython team is pleased to release Biopython 1.56, almost exactly three months after our last stable release ( Biopython 1.55).
The Bio.SeqIO module has been updated to support protein EMBL files (used for the patents database), IMGT files (a variant of the EMBL file format, with help from Uri Laserson), and UniProt XML files (thanks to Andrea Pierleoni). Also the SeqFeature object gained some new methods, and the Bio.Seq translation function can now be used with an arbitrary genetic code.
[Read More]Biopython dropping Python 2.4 Support?
Posted on November 18, 2010
| peterc
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 ElementTree XML parser and SQLite 3 support will be available.
[Read More]BioRuby 1.4.1 released
Posted on October 22, 2010
| NaohisaGoto
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.
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[Read More]Minutes:2010 ConfCall
Posted on October 5, 2010
| admin
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. Jason Stajich wants to resign in the near future, too.
[Read More]Biopython 1.55 released
Posted on August 31, 2010
| peterc
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]BioRuby paper published
Posted on August 27, 2010
| NaohisaGoto
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; doi: 10.1093/bioinformatics/btq475
Biopython 1.55 beta released
Posted on August 18, 2010
| peterc
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]Biopython 1.54 released
Posted on May 20, 2010
| andreas
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 moved to GitHub
Posted on May 14, 2010
| cjfields
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]O|B|F Google Summer of Code Accepted Students
Posted on May 2, 2010
| rbuels
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]
