Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer’s Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer.
Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login system will be disabled and OpenID will be the default path for new accounts so users to make wiki changes. This currently appears to have cut the incidence of spam significantly.
The OBF now has a sparkly new Redmine instance running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly). Bugs and user names (along with email contacts) from our old Bugzilla v2 server have been migrated over, though some links need to be fixed.
Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( BOSC 2011), an ISMB 2011 Special Interest Group (SIG). Dates: July 15-16, 2011 Location: Vienna, Austria Web site: /wiki/BOSC_2011 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted
On behalf of the BOSC 2010 Organizing Committee, I am pleased to announce that the BOSC 2010 Proceedings has been published today in BMC Bioinformatics. Special thanks go to the abstract and proceedings reviewers who helped make this possible.
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
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;