[BioRuby] BioRuby 1.3.0 is released

[Toshiaki Katayama]

Goto-san,

Thank you for your wonderful works on this release.

Just note that we've updated the BioRuby web sites:

> Web page:
>  http://bioruby.org/

This site is our project top page as in the past.

>  http://bioruby.open-bio.org/


This remains as our mirror site.

The new site design had actually been at the mirror site
for one year and we finally bring it to the main site
(beautiful icons are courtesy of Okamoto-san).


Additionally, I have edited the structure of our Wiki site at

http://bioruby.open-bio.org/wiki/

extensively to clarify the contents in it. I've also added a new
page for BioRuby on Rails.

Regards,
Toshiaki Katayama

On 2009/02/25, at 1:39, Naohisa Goto wrote:

> 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
>
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