Agenda Venue: to be held by conference call on Dec 12, 2013, 12pm EDT (17:00 UTC) Dial-in Number: 1-605-475-5950 (US Midwest) Participant Access Code: 279610 Old business Apr 2013 BoD meeting minutes New business Board elections (by secret electronic ballot): Hilmar Lapp, running for a 2nd term as President Peter Cock, running for office of Secretary Nomi Harris, running for a 2nd term on the Board, as at-large member To the extent available, review of 2013 financials (Hilmar) BOSC 2014: update from and vote of confidence for the 2014 chairs (Nomi, Peter) Does OBF and/or BOSC want to be listed as an ISCB “Community of Special Interest” (COSI) along side other SIGs and communities? [Read More]

Agenda Venue: to be held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC) Dial-in Number: 1-605-475-5950 (Midwest) Participant Access Code: 279610 Old business Nov 2012 BoD meeting minutes Treasurer’s 2012 report (Chris Dagdigian) New business Administration of O|B|F’s 2013 Google Summer of Code participation (Pjotr Prins) Minutes Venue: held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC) Attending: Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Chris Fields, Peter Cock; Jason Stajich joined for the last 15 minutes. [Read More]

Source distributions and Windows installers for Biopython 1.63 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI). The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5). This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3. The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. [Read More]

Note: I’m reposting here the original announcement from Florent Angly on the BioPerl mail list. Dear all, Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats. [Read More]

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website. This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5). This release of Biopython supports Python 2. [Read More]

UPDATE: As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio to CPAN this past March. Unfortunately that release (v1.7) appears to have version collisions with this one (v.1.6.910); therefore I’m packaging a new point release ( v1.6.920) that removes Bio::Biblio to prevent this. That has now been uploaded to CPAN and should be available shortly. [Read More]

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI). Python support This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported. We still fully support Python 2. [Read More]

Hello from Berlin, where the pre-BOSC informal CodeFest 2013 meeting is already underway. We’re looking forward to seeing even more of you on Friday and Saturday for BOSC 2013. BOSC 2013 will be the 14th annual Bioinformatics Open Source Conference, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. [Read More]

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online ( PDF). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). [Read More]