Category Archives: Code

Biopython 1.61 released

Posted on February 5, 2013 by Peter

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online (PDF). Platforms/Deployment We currently support Python … Continue reading →

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BioRuby 1.4.3 released

Posted on August 21, 2012 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius. Here is a brief summary of changes. Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for … Continue reading →

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Travis-CI for Testing

Posted on July 30, 2012 by Peter

BioRuby, Biopython and BioPerl are now using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated. Continue reading →

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Biopython 1.60 released

Posted on June 25, 2012 by Peter

Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython … Continue reading →

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Cross-links in GenomeDiagram

Posted on March 2, 2012 by Peter

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 →

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Biopython 1.59 released

Posted on February 24, 2012 by Peter

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 →

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Chromosome Diagrams in Biopython

Posted on October 28, 2011 by Peter

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 →

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BioRuby 1.4.2 released

Posted on August 26, 2011 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.4.2. This new release fixes bugs existed in 1.4.1 and adds new features and improvement of performance. Here is a brief summary of changes.

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Biopython 1.58 released

Posted on August 18, 2011 by Peter

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 →

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Biopython 1.57 released

Posted on April 2, 2011 by Brad Chapman

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 →

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