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).

As in the previous releases, Biopython 1.49 supports Python 2.3, 2.4 and 2.5 but should now also work fine on Python 2.6. Please note that we intend to drop support for Python 2.3 in a couple of releases time (see previous news article).

We also have some new functionality, starting with the basic sequence object (the Seq class) which now has more methods. This encourages a more object orientated coding style, and makes basic biological operations like transcription and translation more accessible and discoverable.

Our BioSQL interface can now optionally fetch the NCBI taxonomy on demand when loading sequences (via Bio.Entrez) allowing you to populate the taxon/taxon_name tables gradually. Also, BioSQL should now work with the psycopg2 driver for PostgreSQL (as well as the older psycopg driver), and the handling of feature locations has also been improved.

We’ve also updated the Biopython Tutorial and Cookbook (also available in PDF).

Finally, our old parsing infrastructure (Martel and Bio.Mindy) is now considered to be deprecated, meaning mxTextTools is no longer required to use Biopython. This should not affect any of the typically used parsers (e.g. Bio.SeqIO and Bio.AlignIO).

Given there have been more changes than in recent Biopython releases, please do check your old scripts still work fine, and let us know on the mailing list or file a bug if there is anything wrong.

Source distributions and Windows installers are available from the Biopython website: biopython.org

Thanks!

-Peter on behalf of the Biopython developers

The OBF Conference call is scheduled for 12:30PM to 2PM PST on Wednesday Nov 19, 2008.  Members of the Open Bioinformatics Foundation and those interested in the decisions are invited to listen in and participate.  A brief agenda is available here.

Please email Hilmar Lapp at hlapp _AT_ gmx.net for call in number and codes if you wish to participate or listen to the discussion.  Those official members should have gotten an email via the  OBF members email list.

The OBF board meeting will be held via conference call on Nov 19, from 12:30PM to 2PM PST.  Agenda items and information about participating is available on the agenda webpage. We anticipate this call primarily to manage administrative tasks for the foundation. We welcome input on including more members in the OBF leadership and helping set the direction for the foundation.

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, 2.4 and 2.5 but should now also work fine on Python 2.6. Please note that we intend to drop support for Python 2.3 in a couple of releases time (see previous news article).

We also have some new functionality, starting with the basic sequence object (the Seq class) which now has more methods. This encourages a more object orientated coding style, and makes basic biological operations like transcription and translation more accessible and discoverable.

Our BioSQL interface can now optionally fetch the NCBI taxonomy on demand when loading sequences (via Bio.Entrez) allowing you to populate the taxon/taxon_name tables gradually. Also, BioSQL should now work with the psycopg2 driver for PostgreSQL (as well as the older psycopg driver).

Finally, our old parsing infrastructure (Martel and Bio.Mindy) is now considered to be deprecated, meaning mxTextTools is no longer required to use Biopython. This should not affect any of the typically used parsers (e.g. Bio.SeqIO and Bio.AlignIO).

So, if you are feeling brave and know the risks, please try out Biopython 1.49 beta, and let us know on the mailing lists if it works, or more importantly if something doesn’t.

We’d also like feedback on the updated Biopython Tutorial and Cookbook (also available in PDF).

Source distributions and Windows installers are available from the Biopython website: biopython.org

Thanks!

-Peter on behalf of the Biopython developers

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.

The next release of Biopython should support Python 2.3 to 2.6 inclusive

However, the bad news is that we are considering dropping support for Python 2.3 after only a couple more releases - please get in touch via the mailing list ASAP if this will cause you problems.

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.

The SeqRecord and Alignment objects have a new method to get the object as a string in a given file format (handled via Bio.SeqIO and Bio.AlignIO).

Bio.PubMed and the online code in Bio.GenBank are now considered obsolete, and we intend to deprecate them after the next release. For accessing PubMed and GenBank, please use Bio.Entrez instead. Martel and Bio.Mindy are now considered to be obsolete, and are likely to be deprecated and removed in a future release, at which point we will drop the optional dependency on mxTextTools. Bio.Fasta is also considered to be obsolete, please use Bio.SeqIO instead. We do intend to deprecate this module eventually, however, for several years this was the primary FASTA parsing module in Biopython and is likely to be in use in many existing scripts.

In addition a number of other modules have been deprecated, including: Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics - see the DEPRECATED file for full details.

Source distributions and Windows installers are available from the Biopython website: biopython.org

My thanks to all bug reporters, code contributors and others who made this new release possible.

–Peter on behalf of the Biopython developers

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.

In addition, the script load_ncbi_taxonomy.pl has been fixed to no longer require the taxon primary key and the NCBI taxon ID to be identical. The Bio* language bindings should not be affected by this change.

For full details, see Hilmar’s official announcement on the BioSQL mailing list

BOSC 2008 will be in Toronto, CANADA this summer July 18 & 19, 2008. There will also be a panel discussion on developing open-source software during ISMB during the lunch break on Tuesday July 22.

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.

–Michiel on behalf of the Biopython developers