未踏成果報告会-fix.key

Size: px

Start display at page:

Download "未踏成果報告会-fix.key"

えつまごみぶち
6 years ago
Views:

1 BioRuby/ChemRuby

3 / 1 /

7 RefSeq PDB PubMed PubChem GenPept EMBL UniProt GenBank DNA(, ) DB GENES ENZYME PATHWAY CM PUND UCSC Ensembl KEGG DAS Bio::DAS (REST CGI) Bio::Flat(BDB) Bio::Fetch(HTTP) Bio::SQL(RDB) Bio::KEGG::API (SAP/WSDL) Bio::GenBank, Bio::EMBL etc. E-Utils (CGI) Bio::Pathway Bio::Sequence Bio::Reference Bio::BLAST, Bio::HMMER etc. HMMER TINKER, DB LIGAND

(GenBank, UniProt,...) (PDB,...) HEADER LIGASE 15-DEC-04 1VQ3 TITLE CRYSTAL STRUCTURE F PHSPHRIBSYLFRMYLGLYCINAMIDINE TITLE 2 SYNTHASE, PURS SUBUNIT (EC 6.3.5.3) (TM1244) FRM TITLE 3 THERMTGA MARITIMA AT 1.

9 (GenBank, UniProt,...) (PDB,...) HEADER LIGASE 15-DEC-04 1VQ3 TITLE CRYSTAL STRUCTURE F PHSPHRIBSYLFRMYLGLYCINAMIDINE TITLE 2 SYNTHASE, PURS SUBUNIT (EC ) (TM1244) FRM TITLE 3 THERMTGA MARITIMA AT 1.90 A RESLUTIN : ATM 1 N HIS A ATM 2 CA HIS A ATM 3 C HIS A ATM 4 HIS A ATM 5 CB HIS A XML (DAS, KGML,...) <?xml version="1.0" standalone="yes"?> <!DCTYPE DASGFF SYSTEM " <DASGFF> <GFF version="1.01" href=" features?segment=eco%3a %2c "> <SEGMENT id="eco" start=" " stop=" " version="1.0"> <FEATURE id="ec: /7199" label=" "> <TYPE id="enzyme:kegg" category="enzyme">enzyme:kegg</type> <METHD id="enzyme">enzyme</methd> <START> </START> <END> </END> (ArrayExpress,...) Affymetrix:CompositeSequence:HG_U95Av2:AFFX-HUMGAPDH/M33197_5_at HUMGAPDH/M33197_5_at IPB M33197 ENSG Affymetrix:CompositeSequence:HG_U95Av2:AFFX-HUMGAPDH/M33197_M_at HUMGAPDH/M33197_M_at IPB M33197 ENSG Affymetrix:CompositeSequence:HG_U95Av2:AFFX-HUMGAPDH/M33197_3_at HUMGAPDH/M33197_3_at IPB M33197 ENSG AFFX AFFX AFFX

10 (SMILES, InChI,...) CC1C(C(CC(1)C2C(C(C(C2C3=C4C=C5C=C3C6=C(C=C(C=C6)C(C(C (=)NC(C(=)NC5C(=)NC7C8=CC(=C(C=C8))C9=C(C=C(C=C9C(NC(=)C (C(C1=CC(=C(4)C=C1)Cl))NC7=)C(=))))CC(=)N)NC(=)C(CC(C)C) NC))Cl)C)))(C)N) (MDL, Tinker,...) ISISHST D XML (CML, CDXML,...) <?xml version="1.0" encoding="utf-8"?> <!DCTYPE CDXML SYSTEM " xml/cdxml.dtd" > <CDXML CreationProgram="ChemDraw 7.0" Name="hypericin.mol" BoundingBox=" " V P M END (CDX,...) : 0d6a jCD : e : d e ChemDraw : 0f e2e hypericin.cd : ff ffff ffff ff x : ff ff ff ffff ff : 00ff ff ff ffff ff ff...

KEGG DB KEGG API (SAP ), KEGG DAS ( ) ChemRuby + subcomp Connect seamlessly.. BioRuby + KEGG API # 106 # # process KEGG Expression data here... serv = Bio::KEGG::API.new list = serv.

12 KEGG DB KEGG API (SAP ), KEGG DAS ( ) ChemRuby + subcomp Connect seamlessly.. BioRuby + KEGG API # 106 # # process KEGG Expression data here... serv = Bio::KEGG::API.new list = serv.list_pathways(org) 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 << hash[gene] "#cccccc" end url = serv.color_pathway_by_objects(pathway, genes, fg_list, serv.save_image(url) end

14 Google BioRuby BioPython DB 57,800 DB 185,000 BioJava 243,000 BioPerl DB 962,000

15 >> Perl BioPerl Perl Ruby

16 ChemRuby kcf, sdf, rdf, rxn, mol, msi, g98, cdx PDF, PNG, JPEG penbabel (sf.net) - (tinker) (subcomp),

18 Java SAP/WSDL % java -classpath axis.jar:jaxrpc.jar:commons-logging.jar:commons-discovery.jar: saaj.jar:wsdl4j.jar:. org.apache.axis.wsdl.wsdl2java -p keggapi % javac -classpath axis.jar:jaxrpc.jar:wsdl4j.jar:. keggapi/kegglocator.java % jar cvf keggapi.jar keggapi/* import keggapi.*; class GetGenesByPathway { public static void main(string[] args) throws Exception { KEGGLocator locator = new KEGGLocator(); KEGGPortType serv = locator.getkeggport(); String query = args[0]; String[] results = serv.get_genes_by_pathway(query); for (int i = 0; i < results.length; i++) { System.out.println(results[i]); } } }

19 Ruby SAP/WSDL #!/usr/bin/env ruby require 'soap/wsdldriver' wsdl = " serv = SAP::WSDLDriverFactory.new(wsdl).create_driver serv.generate_explicit_type = true puts serv.get_enzymes_by_pathway(argv.shift)

28 BioPerl BioRuby

33 BioRuby % bioruby kumage Loading config (session/config)... done Loading object (session/object)... done Loading history (session/history)... done... B i o R u b y i n t h e s h e l l... Version : BioRuby / Ruby bioruby> kuma = seq("gb:af237819") bioruby> kuma.translate

34 BioRuby on Rails

35 % repeat 10 { time ruby -r bio -e 0 } : 0.74s user 0.16s system total (9/10): 0.01s user 0.01s system total

38 RMagick PNG, JPEG require chem mol = Chem.open_mol( ATP ) mol.save( ATP.pdf ) P P P N N N N N

39 Rast!?

40 N N N P P P N N Before After

41 N N N N N N N N S N N S N N N Machine Learning ChemRuby

43 Bioinformatics pen Source Conference BioPerl 2005/06/23

45 BioRuby/ChemRuby

49 : GUI : CUI } BioRuby/ChemRuby Ruby :,,, Test::Unit, SAP

52 Hits Month

54 tun K K K

giw2005-bioruby-bof.key

giw2005-bioruby-bof.key 2005 IPA Ruby ::: BioRuby + ChemRuby ::: http://bioruby.org/ + BioRuby:, + ChemRuby: http://bioruby.org/ O B F (http://open-bio.org) BioPerl, BioPython, BioJava,.. (http://open-bio.jp)