Biopython

Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of Biopython on GitHub, which is automatically updated from the OBF hosted Biopython CVS repository. See our git migration wiki page for details. If this is favorably received, then moving Biopython from CVS to git seems likely at some point this year. Originally, all the OBF hosted projects used CVS for their source code repositories. At the start of 2008, BioPerl and BioJava moved over to Subversion (SVN), followed by BioSQL. [Read More]

We are pleased to announce the release of Biopython 1.49. There have been some significant changes since Biopython 1.48 was released a few months ago, which is why we initially released a beta for wider testing. Thank you to all those who tried this and reported the minor problems uncovered. As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library). [Read More]

We are pleased to announce a beta release of Biopython 1.49. There are been some significant changes since Biopython 1.48 was released two months ago, which is why we are initially releasing a beta for wider testing. As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library). As in the previous releases, Biopython 1.49 beta supports Python 2.3, 2. [Read More]

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. [Read More]

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]

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]

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]

We are pleased to announce the release of Biopython 1.43. This release includes a brand-new set of parsers in Bio.SeqIO by Peter Cock for reading biological sequence files in various formats, an updated Blast XML parser in Bio.Blast.NCBIXML, a new UniGene flat-file parser by Sean Davis, and numerous improvements and bug fixes in Bio.PDB, Bio.SwissProt, Bio.Nexus, BioSQL, and others. Believe it or not, even the documentation was updated. Source distributions and Windows installers are available from the Biopython website at http://biopython. [Read More]