Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI). A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module. Bio.SeqIO now includes read and write support for the SeqXML, a simple XML format offering basic annotation support. [Read More]

I’m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program. The accepted students, their projects, and their mentors (in alphabetical order): Justinas Vygintas Daugmaudis Michele dos Santos da Silva (2 students!) Mocapy++Biopython: from data to probabilistic models of biomolecules mentored by Thomas Hamelryck and Eric Talevich [Read More]

BioPerl 1.6.9 is now available in CPAN. In this release: Refactored Bio::Species/Bio::Tree New SeqIO modules (gbxml, msout, mbsout) Updates for perl 5.12 Bio::Assembly support for SAM/BAM, Newbler, ace output Bio::DB::SeqFeature updates PAML updated to work with v. 4.4d lots of various bug fixes, around 50 Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way. [Read More]

The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the downloads page on the Biopython website and from the Python Package Index. Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary. [Read More]

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. For more on GSoC, see GSoC 2011 FAQ. [Read More]

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. [Read More]

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. Redmine is a project management web application that has several nice features over other systems, including issue tracking, multiple project management, wikis, forums, and calendaring. [Read More]

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 abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. [Read More]