BioRuby project update
Toshiaki Katayama <k@bioruby.org>
Human Genome Center
University of TokyoJapanThe 8th annual Bioinformatics Open Source Conference - 2007/7/19-20 @ Vienna

Introduction• BioRuby - bioinformatics library for Ruby language• Object oriented scripting language• Originally made in Japan• Getting popular by "Ruby on Rails" web development framework

History• 1993 Ruby language is born
• 1996 BioPerl project started• 1999 BioPython, BioJava projects started• 2000 BioRuby project started• 2002 BioHackathon #1, #2• 2003 BioHackathon #3• 2006 BioRuby 1.0 released• 2006 Phyloinformatics Hackathon #1 (at NESCent)• 2007 BioRuby 1.1 released

Functionality• As a library• Bioinformatics analysis (2000-2007)• Sequences, Pathways, References etc.
• Databases, Applications, and Web services• Chemoinformatics analysis combined with ChemRuby (2005)• Phyloinfomatics analysis (2006)• As an application• Interactive shell (2006)• Web application development with Ruby on Rails (2007)

Strength• Up-to-date support for the KEGG database• Pathways, Organisms, Genes, Compounds, Enzymes, Drugs etc.
http://www.genome.jp/kegg/• Web services (SOAP/WSDL library is bundled with Ruby)• DDBJ XML, EBI web service, KEGG API etc.
http://xml.nig.ac.jp/
http://www.ebi.ac.uk/Tools/webservices/
http://www.genome.jp/kegg/soap/• Web applications (Ruby on Rails made development easy)• MPI bioinformatics toolkit, KEGG on Rails etc.
http://toolkit.tuebingen.mpg.de/
http://dev.kegg.jp/• Very easy to install (less than few miniutes, no '--force' required :-)BioRuby 1.1• Released today! (2007/7/19)• http://bioruby.org/• http://bioruby.org/archive/bioruby-1.1.0.tar.gz• http://rubyforge.org/projects/bioruby/• http://rubyforge.org/frs/download.php/22958/bio-1.1.0.gem

What's new?
• License is changed to Ruby's• Distributed under the same terms as Ruby
• Phyloinfomatics modules• Bio::Tree, Newick, NEXUS etc.
• BioRuby plugin generator for Ruby on Rails• bioruby --rails

New modules• Bio::Tree - Phylogenetic tree class by Naohisa Goto
• Bio::Newick - Newick tree format parser/formatter by Daniel Amelang• Bio::NEXUS - NEXUS tree format parser/formatter by Christian M Zmasek• Bio::Phylip - Phylip alignment/matrix parser by Naohisa Goto
• Bio::GCG::Msf - MSF alignment parser by Naohisa Goto
• Bio::Ensembl - Ensembl Genome Browser client by Mitsuteru Nakao• Bio::PTS1 - Peroxisomal targeting signal predictor by Mitsuteru Nakao• Bio::Iprscan - InterPro scan parser by Mitsuteru Nakao• Bio::SOFT - NCBI GEO SOFT parser by Trevor Wennblom• Bio::Lasergene - DNAStar Lasergene sequence parser by Trevor Wennblom• Bio::RestrictionEnzyme - REBASE based utilities by Trevor Wennblom• Bio::Map - Linkage maps and markers by Jan Aerts• Bio::Muscle, Bio::Probcons, Bio::Tcoffee by Jeffrey BlakesleeEnhancements• Bio::Command to provide transparenet HTTP proxy access• Bio::KEGG::* - followed recent changes• Bio::Alignment - added support for Phylip, Molphy, GCG MSF formats• New methods• Bio::SOAPWSDL, Bio::BLAT, Bio::MAFFT, Bio::ClustalW, Bio::PROSITE,Bio::KEGG::KGML, Bio::Sequence::NA• Bio::AminoAcids support for Pyrrolysine, Selenocysteine etc.
• BioRuby shell plugins• soap, blast, psort, codon, seq• Bio.shell methods

Bug fixes• Bio::PDB by Mikael Borg
• Bio::DAS by Dave Thorne• Bio::SQL by Raoul Jean Pierre Bonnal• Bio::GFF3 by Hien Le• Bio::Blast::Fastacmd by Shuji Shigenobu• Bio::Fasta by Fredrik Johansson• Bio::FlatFile by Naohisa GotoPhyloinformatics Hackathon• NESCent (Dec 2006)• Objectives• Phylogenetic tree - Bio::Tree• Phyloinformatics formats - NEXUS, Newick etc.
• Interface for interactive analysis - BioRuby on Rails

Installation• Installing Ruby (few minutes)

http://www.ruby-lang.org/% ./configure% sudo make install• Installing RubyGems (few seconds)

http://rubyforge.org/projects/rubygems/% sudo ruby setup.rb• Installing Ruby on Rails (few minutes)

http://rubyforge.org/projects/rsruby/% sudo gem install rails -y• Installing BioRuby (few seconds)

http://bioruby.org/% sudo gem install bioruby• Installing RSRuby (few seconds)

http://rubyforge.org/projects/rsruby/% export R_HOME="/Library/Frameworks/R.framework/Resources"% sudo gem install rsruby -- --with-R-dir=$R_HOMEor% ruby setup.rb config -- --with-R-dir=$R_HOME% ruby setup.rb setup% sudo ruby setup.rb install

Bundledin Mac OS X
Leopard!

Future plans• Integration with Ruby on Rails• Data models• Web service• Visualization• Documentation• Publication

http://bioruby.org/