Many of you will be aware that Python 2.6 was released a month ago (October 1st, 2008). This supports a lot of new syntax and functionality, but also deprecates some old modules (e.g. the sets module).

While Biopython 1.48 does mostly work with Python 2.6, we’ve been testing with Python 2.6 and have fixed a number of deprecations or breakages in our CVS repository. If using Biopython with Python 2.6 is important to you, please help out by testing the CVS code (which needs NumPy and not Numeric) and letting us know on the mailing list or bugzilla if we’ve missed anything.

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.

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 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers.

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.

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.org. My thanks to all code contributors who made this new release possible.

The BOSC 2008 Organizing Committee is pleased to announce that Julian Lombardi will be giving the keynote address this year. Dr. Lombardi is one of the original architects of the open-source, peer-to-peer OpenCroquet platform for creating and deploying deeply collaborative multi-user online applications and virtual worlds.

For further information about Dr. Lombardi, see the Wikipedia entry about him, his blog, and the OpenCroquet website.

We are pleased to announce the release of Biopython 1.45.

This release includes numerous code improvements and fixes, including in Bio.Seq, Bio.SeqIO, Bio.Entrez, Bio.PopGen, Bio.SwissProt, Bio.Cluster, Bio.SCOP, Bio.InterPro, Bio.GenBank, Bio.ExPASy, BioSQL, and the Biopython documentation. Too many to list them all here!

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.

–Michiel on behalf of the Biopython developers

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.org. My thanks to all code contributers who made this new release possible.