[BioRuby] BioRuby 1.3.0 is released

[Naohisa Goto]

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.)

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-1.3.0.gem

Here is a brief summary of changes.

  * Support for GenBank/EMBL formatted sequence output with
    improvements of Bio::Sequence.
  * BioSQL support is completely rewritten by using ActiveRecord. 
  * Bio::Blast bug fixes and improvements.
  * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements.
  * Bio::Locations improvements.
  * New classes and modules.
    * Bio::Hinv
    * Bio::NCBI::REST
    * Bio::PAML::Codeml
    * Bio::TogoWS::REST

In addition, many changes have been made, including incompatible changes.
For more information, you can see summary of changes at
http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc

and ChangeLog at

http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog

In ChangeLog, the release date is described as 20 Feb 2009, which
indicates frozen date of the archive. I'm sorry I took much time
for the final check of the archive contents.

Hope you enjoy.


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