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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>BioRuby</title>
<link href="bioruby.css" media="screen" rel="Stylesheet" type="text/css" />
</head>
<body>
<div id="content">
<div id="side">
<div class="title">News</div>
<ul>
<li>2015/07/10-11 <p><a href="http://www.open-bio.org/wiki/BOSC_2015">BOSC 2015</a> (<a href="https://github.com/georgeG/biogems.info/blob/master/doc/abstracts/BOSC_2015_abstract.pdf">Abstract</a>)</p></li>
<li>2015/07/01 <p><a href="http://bioruby.org/archive/bioruby-1.5.0.tar.gz">BioRuby 1.5.0</a> released (<a href="https://github.com/bioruby/bioruby/blob/1.5.0/ChangeLog">ChangeLog</a>)</p></li>
<li>2014/07/11-12 <p><a href="http://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a> (<a href="https://github.com/pjotrp/biogems.info/blob/master/doc/abstracts/BOSC2014_BioRuby_dev.md">Abstract</a>)</p></li>
<li>2013/07/19-20 <p><a href="http://www.open-bio.org/wiki/BOSC_2013">BOSC 2013</a> (<a href="http://www.open-bio.org/bosc2013/day1/BOSC2013_BioRuby_Update_-_Toshiaki_Katayama.pdf">PDF</a>)</p></li>
<li>2013/05/25 <p><a href="http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz">BioRuby 1.4.3.0001</a> released (<a href="https://github.com/bioruby/bioruby/blob/1.4.3.0001/ChangeLog">ChangeLog</a>)</p></li>
<li>2012/08/22 <p><a href="http://bioruby.org/archive/bioruby-1.4.3.tar.gz">BioRuby 1.4.3</a> released (<a href="https://github.com/bioruby/bioruby/blob/1.4.3/ChangeLog">ChangeLog</a>)</p></li>
<li>2012/07/13-14 <p><a href="http://www.open-bio.org/wiki/BOSC_2012">BOSC 2012</a> (<a href="http://www.slideshare.net/jandot/h-mishima-biogem-ruby-ucsc-api-and-bioruby">Slides</a>)</p></li>
<li>2011/08/26 <p><a href="http://bioruby.org/archive/bioruby-1.4.2.tar.gz">BioRuby 1.4.2</a> released (<a href="https://github.com/bioruby/bioruby/blob/1.4.2/ChangeLog">ChangeLog</a>)</p></li>
<li>2011/07/15-16 <p><a href="http://www.open-bio.org/wiki/BOSC_2011">BOSC 2011</a> (<a href="http://www.slideshare.net/bosc2011/raoul-bosc2011bio-ngs">Slides</a>)</p></li>
<li>2010/12/24 <p>BioRuby <a href="http://bioruby.open-bio.org/wiki/Plugins">plugin system</a> is released</li>
<li>2010/10/22 <p><a href="http://bioruby.org/archive/bioruby-1.4.1.tar.gz">BioRuby 1.4.1</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.4.1/ChangeLog">ChangeLog</a>)</p></li>
<li>2010/08/25 <p><a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq475">BioRuby paper</a> is published</li>
<li>2010/07/09-10 <p><a href="http://www.open-bio.org/wiki/BOSC_2010">BOSC 2010</a> (<a href="http://www.open-bio.org/w/images/3/36/15_BOSC2010.pdf">Slides</a>)</p></li>
<li>2009/12/29 <p><a href="http://bioruby.org/archive/bioruby-1.4.0.tar.gz">BioRuby 1.4.0</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog">ChangeLog</a>)</p></li>
<li>2009/09/03 <p><a href="http://bioruby.org/archive/bioruby-1.3.1.tar.gz">BioRuby 1.3.1</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.3.1/ChangeLog">ChangeLog</a>)</p></li>
<li>2009/03/15-21 <p><a href="http://hackathon2.dbcls.jp/">BioHackathon 2009</a></p></li>
<li>2009/02/24 <p><a href="http://bioruby.org/archive/bioruby-1.3.0.tar.gz">BioRuby 1.3.0</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.3.0/ChangeLog">ChangeLog</a>)</p></li>
<li><a href="http://bioruby.open-bio.org/wiki/History">... more ...</a></li>
</ul>
<div class="title">Links</div>
<ul>
<li><a href="http://www.ruby-lang.org/">Ruby</a><br />
+ <a href="https://rubygems.org/gems/bio">bio | RubyGems.org</a></li>
<li><a href="http://open-bio.jp/">Open-Bio.JP</a><br />
+ <a href="https://rubygems.org/gems/chemruby">ChemRuby</a></li>
<li><a href="http://open-bio.org/">O|B|F</a><br />
+ <a href="http://www.bioperl.org/">BioPerl</a><br />
+ <a href="http://www.biopython.org/">Biopython</a><br />
+ <a href="http://www.biojava.org/">BioJava</a><br />
+ <a href="http://www.biodas.org/">BioDAS</a><br />
+ <a href="http://www.biomoby.org/">BioMOBY</a></li>
<li>Misc<br />
+ <a href="http://biohaskell.org/">Biohaskell</a><br />
+ <a href="http://biocaml.org/">Biocaml</a><br />
+ <a href="http://biobike.org/">BioBIKE</a> <a href="http://www.biolisp.org/">(BioLisp)</a><br />
+ <a href="http://bioinformatics.org/">Bioinformatics.org</a></li>
</ul>
<br />
<a href="http://bioruby.org/"><img src="images/bioruby-link.gif" alt="bioruby.org" border="0" /></a>
</div><!-- side -->
<div id="title">
<p class="titletop">BioRuby</p>
<p class="titlesub">Open source bioinformatics library for Ruby</p>
</div><!-- title -->
<div id="main">
<div id="main_top">
<div class="section_title">Announcements</div>
<ul>
<li>BioRuby 1.5.0 is released on July 1, 2015. (<a href="http://bioruby.org/archive/bioruby-1.5.0.tar.gz">Download</a>) (<a href="https://github.com/bioruby/bioruby/blob/1.5.0/ChangeLog">ChangeLog</a>)
<li>At <a href="http://www.open-bio.org/wiki/BOSC_2015">the 16th Annual Bioinformatics Open Source Conference (BOSC 2015)</a> held in Dublin on July 10-11, George Githinji and Pjotr Prins will be presenting a talk entitled "The biogems community: Challenges in distributed software development in bioinformatics" (<a href="https://github.com/georgeG/biogems.info/blob/master/doc/abstracts/BOSC_2015_abstract.pdf">Abstract</a>).
<li><a href="http://gems.bioruby.org/">Biogem</a> is community developed plugins for the BioRuby. See the <a href="http://biogems.info/">complete list</a>, <a href="http://bioruby.open-bio.org/wiki/Plugins">generic information</a>, <a href="http://www.biogems.info/doc/README_rdoc.html">README</a>, <a href="http://www.biogems.info/howto.html">HOWTO</a> and <a href="http://www.biogems.info/doc/Tutorial_rdoc.html">Tutorial</a>.</li>
</ul>
<div class="section_title">Overview</div>
<ul>
<li>
BioRuby comes with a comprehensive set of free development tools and
libraries for bioinformatics and molecular biology, for the
Ruby programming language. BioRuby has components for sequence
analysis, pathway analysis, protein modelling and phylogenetic
analysis; it supports many widely used data formats and provides easy
access to databases, external programs and public web services,
including BLAST, KEGG, GenBank, MEDLINE and GO.
</li>
<li>
BioRuby comes with a
tutorial, documentation and an interactive environment, which can be
used in the shell, and in the web browser.
</li>
<li>
BioRuby is supported by the
<a href="http://www.open-bio.org/">Open Bioinformatics Foundation</a>
or O|B|F.
</li>
</ul>
<div class="section_title">Reference</div>
<p>
BioRuby: Bioinformatics software for the Ruby programming language<br/>
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama<br/>
<i>Bioinformatics</i> (2010) 26(20): 2617-2619. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq475">doi: 10.1093/bioinformatics/btq475</a>
</p>
</div>
<div id="main_left">
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-doc.png" alt="documentation" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Documentation</div>
<ul>
<li><a href="http://bioruby.open-bio.org/wiki/">Wiki page</a><br />
+ <a href="http://bioruby.open-bio.org/wiki/Tutorial">Tutorial</a><br />
+ <a href="http://bioruby.open-bio.org/wiki/SampleCodes">Sample codes</a><br /></li>
<li><a href="http://bioruby.org/rdoc/">API documentation</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-keynote.png" alt="presentations" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Presentations</div>
<ul>
<li><a href="http://www.open-bio.org/bosc2013/day1/BOSC2013_BioRuby_Update_-_Toshiaki_Katayama.pdf">BOSC 2013</a></li>
<li><a href="http://www.slideshare.net/jandot/h-mishima-biogem-ruby-ucsc-api-and-bioruby">BOSC 2012</a></li>
<li><a href="http://www.slideshare.net/ngotogenome/bioruby-bioinformatics-library">RubyKaigi 2011</a></li>
<li><a href="http://bioruby.org/archive/doc/">English slides</a></li>
<li><a href="http://bioruby.org/archive/doc/Japanese">Japanese slides</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-dev.png" alt="development" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Development</div>
<ul>
<li><a href="http://github.com/bioruby/bioruby">GitHub</a></li>
<li><a href="https://redmine.open-bio.org/projects/bioruby">Bug report</a></li>
<!--
<li><a href="http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=bioruby">BioRuby CVS repository</a> hosted by <a href="http://www.open-bio.org/wiki/SourceCode">(O|B|F)</a> is now deprecated.</li>
-->
</ul>
</div>
</td>
</tr>
</table>
</div>
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-shell.png" alt="bioruby shell" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">BioRuby shell</div>
<p>BioRuby comes with an <a href="http://bioruby.open-bio.org/wiki/BioRubyOnRails">interactive shell</a> also capable as a plugin for the <a href="http://rubyonrails.org/">Ruby on Rails</a></p>
</div>
</td>
</tr>
</table>
</div>
</div><!-- main_left -->
<div id="main_right">
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-download.png" alt="download" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Download</div>
<ul>
<li><a href="http://rubygems.org/gems/bio">RubyGems package</a></li>
<li><a href="http://bioruby.org/archive/">Source code archive</a></li>
<li><a href="http://gems.bioruby.org/">Plugins</a> (<a href="http://bioruby.open-bio.org/wiki/Plugins">usage</a>)</li>
<li><a href="http://bioruby.org/contrib/">Contributed codes</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-mail.png" alt="mailing list" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Mailng lists</div>
<ul>
<li><a href="http://lists.open-bio.org/mailman/listinfo/bioruby">English list</a></li>
<li><a href="http://lists.open-bio.org/mailman/listinfo/bioruby-ja">Japanese list</a></li>
<!-- <li><a href="http://lists.open-bio.org/mailman/listinfo/bioruby-cvs">CVS commit log</a></li> -->
</ul>
</div>
</td>
</tr>
</table>
</div>
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-link.png" alt="community" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Community</div>
<ul>
<li><a href="http://bioruby.open-bio.org/wiki/Contributors">Contributors</li>
<li><a href="http://bioruby.open-bio.org/wiki/Links#Blogs">Blogs</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>
<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-ipa.png" alt="IPA" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">IPA</div>
<p>Our project was supported by Information-technology Promotion Agency (<a href="http://www.ipa.go.jp/">IPA</a>) as an <a href="http://www.ipa.go.jp/jinzai/esp/">Exploratory Software Project</a> in 2005</p>
</div>
</td>
</tr>
</table>
</div>
</div><!-- main_right -->
</div><!-- main -->
</div><!-- content -->
</body>
</html>