Category Archives: Documentation

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

Introduction of OpenID logins for OBF wikis

Posted on March 17, 2011 by Chris Fields

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

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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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

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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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 →

Posted in BioJava, BioPerl, Biopython, BioRuby, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects | Tagged , , , , , | Leave a comment

Interleaving paired FASTQ files with Biopython

Posted on December 14, 2009 by Peter

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ).

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BioPerl core 1.6.1 PPM available

Posted on October 10, 2009 by Chris Fields

BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be … Continue reading →

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BioPerl 1.6.1 released

Posted on September 29, 2009 by Chris Fields

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally … Continue reading →

Posted in BioPerl, Community, Development, Documentation, General, OBF, OBF Projects | Tagged , | 1 Comment