[BioRuby] BioRuby 1.4.1 released

Naohisa Goto ngoto at gen-info.osaka-u.ac.jp
Fri Oct 22 06:44:05 UTC 2010

We are pleased to announce the release of BioRuby 1.4.1.
This new release fixes bugs existed in 1.4.0 and new features are added.

Here is a brief summary of changes.

PAML Codeml support is significantly improved:
PAML Codeml result parser is completely rewritten and is significantly
improved. The code is developed by Pjotr Prins.

KEGG PATHWAY and KEGG MODULE parsers are added: 
The code is developed by Kozo Nishida and Toshiaki Katayama.

Bio::KEGG::GENES and Bio::KEGG::GENOME bug fixes and
new methods: Some of them are due to the file format changes.

Test codes are added and improved:
They are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince,
and Naohisa Goto.

Bug fixes in Bio::Tree: some methods did not work correctly.

Platform-dependent bug when calling external programs: Detection of
platform is improved not to call fork(2) on platforms that do not
support it (e.g. JRuby).

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-1.4.1.tar.gz

Gem file is also available at:  http://bioruby.org/archive/gems/bio-1.4.1.gem

We also put RubyGems package at 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 (1.4.1)” in the list. Then,
% sudo gem install bio

Finally, we are sorry that many new features are waiting to be merged
to BioRuby, including  HMMER3 support. These will be included in the
next major release version.

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

More information about the BioRuby mailing list