We are pleased to announce the release of BioRuby 1.5.1.
In this new release, NCBI Entrez web client classes, Bio::NCBI::REST and Bio::PubMed, are changed to use HTTPS instead of HTTP, to prepare NCBI website transitioning to HTTPS.
[Read More]BioRuby 1.5.0 released
We are pleased to announce the release of BioRuby 1.5.0. This new release includes support of recent Ruby versions (Ruby 2.0.0, 2.1 and 2.2), improvement of codes, and bug fixes.
Here is a brief summary of changes.
Ruby 2.0.0, 2.1, 2.2 support. Some features are removed because of remote service discontinuance or difficulty of code maintenance. Refactoring of code. Bio::SPTR is renamed as Bio::UniProtKB. Bug fixes. In addition, many changes have been made, including incompatible changes.
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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 more information, see RELEASE_NOTES.rdoc and ChangeLog.
[Read More]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 storing a graphics element. Many failures and errors running on JRuby and Rubinius are resolved. Strange behavior related with “circular require” is fixed. Fixed: Genomenet remote BLAST does not work. Fixed: Bio::NucleicAcid.
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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.
[Read More]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 Bonnal, Jan Aerts and Toshiaki Katayama Bioinformatics 2010; doi: 10.1093/bioinformatics/btq475
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, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with the National Evolutionary Synthesis Center (NESCent).
FASTQ file format support: Support for reading and writing FASTQ file format is added.
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Sanger FASTQ format and the Solexa/Illumina variants
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 variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10.
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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 bug fixes and added support for multiple query sequences. Bio::Sim4::Report bug fixes. Added unit tests for Bio::GCG::Msf and Bio::Sim4::Report. License of BioRuby is clarified. In addition, many changes have been made, mainly bug fixes.
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