Bioruby on Open Bioinformatics Foundation

BioRuby 1.5.1 released

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 07 Sep 2016 15:04:32 +0000

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.

For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available for download from the following links.

Tar.gz file: http://bioruby.org/archive/bioruby-1.5.1.tar.gz
Gem file: https://rubygems.org/gems/bio or http://bioruby.org/archive/gems/bio-1.5.1.gem

You can easily install by using RubyGems. First, check the version number by using search command:

% gem search --remote bio

and find “bio (1.5.1)” in the list. Then,

% sudo gem install bio

Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.

Because this release is a minor version up, only few changes picked from the git head are included.

Acknowledgments: Thanks to Dr. Mark Johnson about information of the NCBI website change.

BioRuby 1.5.0 released

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 02 Jul 2015 14:03:08 +0000

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. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available for download from the following links.

Tar.gz file: http://bioruby.org/archive/bioruby-1.5.0.tar.gz
Gem file: https://rubygems.org/gems/bio or http://bioruby.org/archive/gems/bio-1.5.0.gem

You can easily install by using RubyGems. First, check the version number by using search command:

% gem search --remote bio

and find “bio (1.5.0)” in the list. Then,

% sudo gem install bio

Note that BioRuby 1.5.X will be the final release version that supports Ruby 1.8.

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.

Hope you enjoy.

BioRuby 1.4.3.0001 Released

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 27 May 2013 12:44:57 +0000

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.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.3.0001.gem

We also put RubyGems pacakge at RubyGems.org and RubyForge.

You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.3.0001)” in the list. Then, % sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.

BioRuby 1.4.3 released

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 21 Aug 2012 16:47:56 +0000

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.to_re(“s”) typo.
Fixed: Bio::EMBL#os raises RuntimeError.
Fixed: bin/bioruby: Failed to save object with error message “can’t convert Symbol into String” on Ruby 1.9.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.3.tar.gz

Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.3.gem

We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:

% gem search –remote bio

and find “bio (1.4.3)” in the list. Then,

% sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.

Hope you enjoy.

BioRuby 1.4.2 released

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 26 Aug 2011 09:49:42 +0000

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.

Speed-up of Bio::RestrictionEnzyme::Analysis.cut: The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written by Tomoaki NISHIYAMA and Naohisa Goto.

New classes Bio::DDBJ::REST, REST interface for DDBJ Web API for Biology (WABI) web service in additon to SOAP. Currently, only selected APIs are implemented.

Bio::Blast with remote DDBJ server uses REST instead of SOAP because Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9. We can now use remote DDBJ BLAST server with Ruby 1.9.

The Tutorial.rd is updated by Pjotr Prins and Michael O’Keefe.

Many unit tests are added for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB and so on. Most of them are developed by Kazuhiro Hayashi during the Google Summer of Code 2010. New methods: Bio::Fastq#to_s, Bio::NCBI::REST::EFetch.nucleotide, Bio::NCBI::REST::EFetch.protein.

Bug fixes:

Bio::Blast: Failure of remote BLAST execution is fixed, due to the changes in GenomeNet and DDBJ.
Bio::Blast: When executing remote BLAST with “genomenet” server, options “-b” and “-v” are now correctly used to limit the number of hits to be reported.
Bio::SPTR (Bio::UniProt): Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines were not correctly parsed.
Bio::Reference#pubmed_url: Updated to follow recent NCBI changes.
Bio::Newick#reparse failure.
Bio::MEDLINE#reference: doi field should be filled.
Bio::Reference#endnote fails when url is not set.
Bio::FastaFormat#query passes nil to the given factory object.
BioRuby Shell: efetch(), getent(), and demo() fail.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.2.tar.gz

Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.2.gem

We also put RubyGems pacakge at RubyForge and RubyGems.org. You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.2)” in the list. Then, % sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches. In addition, thanks to NDBC / DBCLS BioHackathon2011 participants and organizers who try BioRuby during the BioHackathon2011.

Hope you enjoy.

BioRuby paper published

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 27 Aug 2010 00:13:15 +0000

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

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 29 Dec 2009 10:22:25 +0000

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. All of the three FASTQ format variants are supported. The code is written by Naohisa Goto, with the help of discussions in the open-bio-l mailing list. The prototype of Bio::Fastq class was first developed during the BioHackathon 2009 held in Okinawa.

DNA chromatogram support: Support for reading DNA chromatogram files are added. SCF and ABIF file formats are supported. The code is developed by Anthony Underwood.

MEME (motif-based sequence analysis tools) support: Support for running MAST (Motif Alignment & Search Tool, part of the MEME Suite, motif-based sequence analysis tools) and parsing its results are added, developed by Adam Kraut.

Improvement of KEGG parser classes: Some new methods are added to parse new fields added to some KEGG file formats. Unit tests for KEGG parsers are also added and improved. These are contributed by Kozo Nishida.

Many sample scripts are added: Many sample scripts showing demonstrations of usages of classes are added. They were originally primitive test codes written in the “if __FILE__ == $0” convention.

Unit tests can test installed BioRuby: Mechanism to load library and to find test data in the unit tests are changed, and target library path and test data path can be changed with environment variables.

Incompatible change: Bio::NCBI::REST needs email address: NCBI announced that all Entrez Utilities (E-utilities) requests must contain email and tool parameters, and requests without them will return error after June 2010. In BioRuby, to set default email address and tool name, following methods are added.

Bio::NCBI.default_email=(email)
Bio::NCBI.default_tool=(tool_name)

Note that no default email address is preset in BioRuby. Library users must set their own email address or implement to get user’s email address in some way (from input form, configuration file, etc).

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.0.tar.gz

Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.0.gem

We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search –remote bio and find “bio (1.4.0)” in the list. Then, % sudo gem install bio

Hope you enjoy.

Sanger FASTQ format and the Solexa/Illumina variants

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 17 Dec 2009 16:28:55 +0000

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:10.1093/nar/gkp1137

This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.

BioRuby 1.3.1 released

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Sep 2009 13:47:09 +0000

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. For more information, you can see ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.3.1.tar.gz

We also put RubyGems pacakge at RubyForge as always. You can easily install by using RubyGems. % sudo gem install bio

You can also obtain bioruby gem file from bioruby.org. http://bioruby.org/archive/gems/bio-1.3.1.gem

Hope you enjoy.