Development

The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the downloads page on the Biopython website and from the Python Package Index.

Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the ability to run the BLAST tools and save the output as ASN.1 format, and then convert this to any other supported BLAST ouput format (plain text, tabular, XML, or HTML) with the blast_formatter tool. The wrappers were also updated to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer’s Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2011 FAQ.

The OBF now has a sparkly new Redmine instance running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly).  Bugs and user names (along with email contacts) from our old Bugzilla v2 server have been migrated over, though some links need to be fixed.

Redmine is a project management web application that has several nice features over other systems, including issue tracking, multiple project management, wikis, forums, and calendaring.

The Biopython team is pleased to release Biopython 1.56, almost exactly three months after our last stable release ( Biopython 1.55).

The Bio.SeqIO module has been updated to support protein EMBL files (used for the patents database), IMGT files (a variant of the EMBL file format, with help from Uri Laserson), and UniProt XML files (thanks to Andrea Pierleoni). Also the SeqFeature object gained some new methods, and the Bio.Seq translation function can now be used with an arbitrary genetic code.

This is a reminder that the forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4.

Looking back, we supported Python 2.3 for about six years - it was released July 2003, and Biopython 1.50 released in April 2009 was the last to support it. Similarly, Python 2.4 was released six years ago (November 2004).

Dropping Python 2.4 support will allow use to assume standard library modules like the ElementTree XML parser and SQLite 3 support will be available. There are also several new language features in Python 2.5+ which will be useful, and it should make supporting Python 3 a little easier as well.

We are pleased to announce the release of BioRuby 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added.

Here is a brief summary of changes.

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The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable release ( Biopython 1.54) and the beta release earlier in August.

A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn’t notice any changes ;)

In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation.

After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal.  The article is open access, so please take a look.

BioRuby: Bioinformatics software for the Ruby programming language Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama Bioinformatics 2010; doi: 10.1093/bioinformatics/btq475

We’ve just released a beta of Biopython 1.55 for user testing.

Since Biopython 1.54 was released three months ago, we’ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we’ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we’ve accidentally broken things - which is why we’re doing this beta release.

The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes.

This is the first stable release to feature the new Bio.Phylo module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and PhyloXML formats. The module is the result of Eric Talevich’s Google Summer of Code project which was supported by The National Evolutionary Synthesis Center (NESCent).