[BioRuby] BioRuby 1.4.0 is released

[Naohisa GOTO]

Hi all,

We are pleased to announce the release of BioRuby 1.4.0.

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

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

You can also obtain bioruby gem file from bioruby.org.
  http://bioruby.org/archive/gems/bio-1.4.0.gem

Here is a brief summary of changes.

= 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 Aliginment & Search Tool,
part of the MEME Suite, motif-based sequence analysis tools)
and parsing its results are added. The code is 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.

= 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.


In addition, many changes have been made, including incompatible
changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog
in the release archive or at:

http://github.com/bioruby/bioruby/blob/1.4.0/RELEASE_NOTES.rdoc
http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog

Hope you enjoy.


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