To date, Biopython releases have relied on the original numerical python library, Numeric (used in python with “import Numeric”). In the next release we will at last be moving to its successor, NumPy (used in python with “import numpy”). This transition is already under way in the Biopython source code repository. For further details, or to voice your opinion or enthusiasm, please join the Biopython Mailing List(s). Finally, for anyone interested in the background story, the SciPy project has a page describing the history of the numerical python libraries. [Read More]

We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete). The following additional file formats are now supported in Bio.SeqIO and Bio.AlignIO: reading and writing “tab” format (simple tab separated) writing “nexus” files reading “pir” files (NBRF/PIR) basic support for writing “genbank” files (GenBank plain text) This release also fixes some problems reading Clustal alignments (introduced in Biopython 1. [Read More]

This is a belated news entry announcing the second BioSQL v1.0 (code-named Tokyo) release, v1.0.1, which was made on August 2, 2008. It is available from the BioSQL downloads page. This version of the schema should be fully backwards compatible with the v1.0.0 schema for nearly all software and queries. The only change is relaxing a column width constraint. Migration scripts are for those who want to simply upgrade their existing database. [Read More]

We are pleased to announce the release of Biopython 1.47. This release includes a new Bio.AlignIO module, updates to Bio.Blast, parsers for NCBI’s Entrez E-Utilities, numerous other code improvements and fixes, and an extended and updated documentation. In particular if you use Biopython to access NCBI’s E-Utilities, we encourage you to download and install this release to ensure full compliance with NCBI’s access rules. Source distributions and Windows installers are available from the Biopython website at http://biopython. [Read More]

After a long wait and several earlier attempts, version 1.0.0 (code-named Tokyo, see below) of BioSQL has finally been released. The release can be downloaded at http://biosql.org/DIST/ as .tar.gz, .tar.bz, and Zip (which also has Windows-style end-of-line characters) archives. The full release announcement can be found in the BioSQL mailing list archives, and in the distribution itself. [Read More]

Our application to hold BOSC as a two-day SIG (Special Interest Group) meeting in conjunction with ISMB has been accepted for this year. BOSC will take place July 18 and 19 in Toronto, Canada. [Read More]

We are pleased to announce the release of Biopython 1.44. This release includes lots of code improvements and fixes in the Blast interface and parsers, sequence input/output, the SwissProt parser, the clustering routines, as well as a brand new module for population genetics. For reasons of compatibility, some radical changes were necessary in some parts of the code; please let us know if you find some functionality missing. Source distributions and Windows installers are available from the Biopython website at http://biopython. [Read More]

Venue: Cafe Prückl, Vienna Date: 7/21/2007, 5.30pm Attending: Jason Stajich (OBF President), Hilmar Lapp (OBF Parliamentarian), Darin London, Kam Dahlquist BOSC Had 94 attendees registered specifically for BOSC as of July 9th Do we have an audience? Is there a niche that BOSC continues to fill? The numbers seem to speak a clear voice. Show-and-tell was received positively, but didn’t play as big a role anymore Want to continue running the conference Venue: Seems much favorable to associate with an existing major event One model could be to associate with different events on an alternating basis, such as IMSB every other year and a different conference every other year Need a new Organizing Committee, several people volunteered to help organizing Committee should decide on sessions, timetable, outreach venues Session chairs who are also charged to identify the most desirable speakers Should have budget to reimburse travel for key speakers who otherwise wouldn’t be able to come Need to look into venue and procedure for publishing the talks Include a hackathon? [Read More]