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.

Cross-links in GenomeDiagram

I’ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in Biopython 1.59. You can now control the start and end points of individual tracks, and you can add cross-links between regions of … Continue reading

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

Biopython 1.59 released

Source distributions and Windows installers for Biopython 1.59 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Continue reading

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

Chromosome Diagrams in Biopython

One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. I’ve just been updating the Biopython Tutorial (current version here, PDF) to include an example drawing this: Here’s a PDF … Continue reading

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

Biopython 1.58 released

Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI). A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of … Continue reading

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

Biopython 1.57 released

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 … Continue reading

Posted in Biopython, Code, Development, OBF, OBF Projects | Tagged , , | Leave a comment

OBF and Google Summer of Code 2011

Google announced today the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for the 2011 Google Summer of Code! Continue reading

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

Introduction of OpenID logins for OBF wikis

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

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

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?

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

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