BioRuby 2005 Toshiaki Katayama Human Genome Center,University of Tokyo, Japan Toshiaki Katayama Human Genome Center,University.

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Presentation transcript:

BioRuby 2005 Toshiaki Katayama Human Genome Center,University of Tokyo, Japan Toshiaki Katayama Human Genome Center,University of Tokyo, Japan Bioinformatics Open Source Conference, June , Detroit

What's BioRuby? BioPerl for the Ruby programmer

BioRuby updates BioRuby released Sim4, BLAT, Spidey parsers are added Unit tests is being added by Moses Hohman KEGG GLYCAN database is supported KEGG API 4.0 released (tested with BioRuby) APIs for LIGAND, GLYCAN, REACTION databases Colored PATHWAY in HTML format is available BioRuby released Sim4, BLAT, Spidey parsers are added Unit tests is being added by Moses Hohman KEGG GLYCAN database is supported KEGG API 4.0 released (tested with BioRuby) APIs for LIGAND, GLYCAN, REACTION databases Colored PATHWAY in HTML format is available

What's coming next? BioRuby will be released soon Bug fixes We will not continue to support Ruby 1.6 RubyGems for easy installation % gem install bioruby ChemRuby project started Nobuya Tanaka (KEGG lab.) Financial support for developping docs/tests and integration of Bio and Chem -Ruby BioRuby will be released soon Bug fixes We will not continue to support Ruby 1.6 RubyGems for easy installation % gem install bioruby ChemRuby project started Nobuya Tanaka (KEGG lab.) Financial support for developping docs/tests and integration of Bio and Chem -Ruby Ruby1.8 inside!

Exploratory Software Project 1 year financial support from IPA Infotech Promoting Agency, Japan "BioRuby + ChemRuby" 4 core developers documentations, unit tests develop new features integration of these projects 1 year financial support from IPA Infotech Promoting Agency, Japan "BioRuby + ChemRuby" 4 core developers documentations, unit tests develop new features integration of these projects Bio(Chem)RubyHackathon every month!?

Bio + Chem informatics RefSeq PDBPubMedPubChem GenPept EMBL UniProt GenBank Sequence DBs GENES ENZYME PATHWAY COM POUND 3D structures Gene expressions UCSC Literatures Ensembl KEGG DAS Bio::DAS (REST CGI) Bio::DAS (REST CGI) Bio::Flat(BDB) Bio::Fetch(HTTP) Bio::SQL(RDB) Bio::Flat(BDB) Bio::Fetch(HTTP) Bio::SQL(RDB) Bio::KEGG::API (SOAP/WSDL) Bio::KEGG::API (SOAP/WSDL) Bio::GenBank, Bio::EMBL etc. Bio::GenBank, Bio::EMBL etc. E-Utils (CGI) E-Utils (CGI) Bio::Pathway Softwares Bio::Sequence Bio::Reference Bio::BLAST, Bio::HMMER etc. Bio::BLAST, Bio::HMMER etc. HMMER TINKER Various format Compound DBs LIGAND OBDA

in KEGG lab, korg = "bsu" serv = Bio::KEGG::API.new list = serv.list_pathways(korg) list.each do |path| pathway = path.entry_id fg_list = Array.new bg_list = Array.new genes = serv.get_genes_by_pathway(pathway) genes.each do |gene| fg_list << "#000000" bg_list << exp2rgb(gene) || "#cccccc" end url = serv.color_pathway_by_objects(pathway, genes, fg_list, bg_list) serv.save_image(url) end korg = "bsu" serv = Bio::KEGG::API.new list = serv.list_pathways(korg) list.each do |path| pathway = path.entry_id fg_list = Array.new bg_list = Array.new genes = serv.get_genes_by_pathway(pathway) genes.each do |gene| fg_list << "#000000" bg_list << exp2rgb(gene) || "#cccccc" end url = serv.color_pathway_by_objects(pathway, genes, fg_list, bg_list) serv.save_image(url) end BioRuby + KEGG API Katayama ： developing KEGG API, KEGG DAS etc. Tanaka ： developing algorithms for structure search etc. ChemRuby Connect seamlessly..

Open Bio Japan Promoting Open Bio* in Japan Tutorials, documentations, mailing lists Japanese bioinfo developer's meeting G-language, KNOB, BioRuby etc... ( Promoting Open Bio* in Japan Tutorials, documentations, mailing lists Japanese bioinfo developer's meeting G-language, KNOB, BioRuby etc... (

More info? Toshiaki Katayama Mitsuteru Nakao Naohisa Goto Nobuya Tanaka Toshiaki Katayama Mitsuteru Nakao Naohisa Goto Nobuya Tanaka BioPerlBioRuby ChemRuby