[BioRuby] BioRuby 1.4.2 released

[Naohisa Goto]

Hi, all,

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.

Tar.gz file: http://bioruby.org/archive/bioruby-1.4.2.tar.gz
Gem file:  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

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.

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.

-- 
Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp