Category Archives: Development

BioRuby 1.4.1 released

Posted on October 22, 2010 by Naohisa Goto

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.

Posted in BioRuby, Code, Development, OBF, OBF Projects | 1 Comment

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 →

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BioRuby paper published

Posted on August 26, 2010 by Naohisa Goto

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 … Continue reading →

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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 →

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BioPerl has moved to GitHub

Posted on May 14, 2010 by Chris Fields

BioPerl has migrated to git and GitHub!  We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz. If you are a current BioPerl developer (had a previous account for direct access … Continue reading →

Posted in BioPerl, Blogroll, Code, Community, Development, Documentation, General, OBF, OBF Projects | 1 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 →

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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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Making Biopython SeqIO and AlignIO easier

Posted on April 5, 2010 by Peter

One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also … Continue reading →

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