Tag Archives: BioRuby

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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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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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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BioRuby 1.4.0 released

Posted on December 29, 2009 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements. PhyloXML support: Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, … 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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BioRuby 1.3.1 released

Posted on September 2, 2009 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.3.1. This new release fixes many bugs existed in 1.3.0. Here is a brief summary of changes. Refactoring of BioSQL support. Bio::PubMed bug fixes. Bio::NCBI::REST bug fixes. Bio::GCG::Msf bug fixes. Bio::Fasta::Report … Continue reading →

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BioRuby 1.3.0 is released

Posted on February 25, 2009 by obfadmin

Hi all, We are pleased to announce the release of BioRuby 1.3.0. The archive is available at: http://bioruby.org/archive/bioruby-1.3.0.tar.gz Web page: http://bioruby.org/ http://bioruby.open-bio.org/ API documentation: http://bioruby.org/rdoc/ Bug report: http://rubyforge.org/projects/bioruby/ (Updating of http://bioruby.rubyforge.org/ is still in progress. Please wait for a moment.) … Continue reading →

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