Category Archives: Biopython

The Biopython Project is an international distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world.

Introduction of OpenID logins for OBF wikis

Posted on March 17, 2011 by Chris Fields

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login … Continue reading →

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Documentation, OBDA / BioSQL, OBF, OBF Projects, Website | Leave a comment

OBF Redmine server now available

Posted on March 17, 2011 by Chris Fields

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 … Continue reading →

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Code, Community, Development, OBDA / BioSQL, OBF, OBF Projects | Leave a comment

Biopython 1.56 released

Posted on November 26, 2010 by Peter

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 … Continue reading →

Posted in Biopython, Code, Development, OBDA / BioSQL, OBF Projects | Tagged , , | 1 Comment

Biopython dropping Python 2.4 Support?

Posted on November 18, 2010 by Peter

The forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4. If you would be negatively affected us dropping support for Python 2.4, please let us know as soon as possible. Continue reading →

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Biopython 1.55 released

Posted on August 31, 2010 by Peter

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 … Continue reading →

Posted in Biopython, Code, Development, OBF, OBF Projects | Tagged | 1 Comment

Biopython 1.55 beta released

Posted on August 18, 2010 by Peter

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 … Continue reading →

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Biopython 1.54 released

Posted on May 20, 2010 by davidw

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 … Continue reading →

Posted in Biopython, Code, Community, Development, General, Google Summer of Code, OBF, OBF Projects | Tagged , | Leave a comment

O|B|F Google Summer of Code Accepted Students

Posted on May 2, 2010 by Robert Buels

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment … Continue reading →

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Development, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | Leave a comment

Illumina FASTQ files – Read Segment Quality Control Indicator

Posted on April 30, 2010 by Peter

In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores – and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as ‘B’). … Continue reading →

Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF, OBF Projects | Tagged , | Leave a comment

Partial sequence files with Biopython

Posted on April 27, 2010 by Peter

This is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release). It is often useful to be able to extract … Continue reading →

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