Author Archives: Naohisa Goto

BioRuby 1.4.3.0001 Released

We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs. “gem install bio” failed with Ruby 2.0 or later versions. lib/bio/db/gff.rb script encoding issue Bio::Blast::Default::Report parse error when subject sequence contains spaces. For … Continue reading

Posted in BioRuby, Code, Development, OBF, OBF Projects | Tagged | Leave a comment

BioRuby 1.4.3 released

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

Posted in BioRuby, Code, Development, OBF, OBF Projects | Tagged | Leave a comment

BioRuby 1.4.2 released

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.

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

BioRuby 1.4.1 released

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

BioRuby paper published

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

Posted in BioRuby, Code, Community, Development, Documentation, OBF, OBF Projects | Tagged | Leave a comment

BioRuby 1.4.0 released

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

Posted in BioRuby, Code, Development, OBF, OBF Projects | Tagged , | Leave a comment

BioRuby 1.3.1 released

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

Posted in BioRuby, Code, Community, Development, OBF Projects | Tagged | Leave a comment