Author Archives: Peter

OBF Annual Meeting 2011

Posted on October 28, 2011 by Peter

The annual Board of Directors Meeting of the Open Bioinformatics Foundation will take place on November 8, 2011. As in previous years, it will be held by conference call, estimated to be about 2 hrs long. 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 →

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

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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OBF and Google Summer of Code 2011

Posted on March 18, 2011 by Peter

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

Bioinformatics Open Source Conference (BOSC 2011) Call for Abstracts

Posted on March 4, 2011 by Peter

Call for talk and poster abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011), an ISMB 2011 SIG meeting to be held in Vienna, Austria, July 2011. Continue reading →

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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 →

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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 →

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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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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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