Category Archives: Blogroll

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

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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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 →

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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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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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Sanger FASTQ format and the Solexa/Illumina variants

Posted on December 17, 2009 by Peter

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ … Continue reading →

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