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1 2005 IPA Ruby ::: BioRuby + ChemRuby ::: <k@bioruby.org> + BioRuby:, + ChemRuby:

http://bioruby.org/ O B F (http://open-bio.

2 O B F ( BioPerl, BioPython, BioJava,.. (

3 Ewan Birney BioPerl BioRuby BioRuby BioRuby ChemRuby

4 (TB)

5 / 1 /

6 DNA(, ) DB EMBL UniProt RefSeq GenBank GenPept GENES ENZYME LIGAND COM POUND PubChe m UCSC Ensembl KEGG DAS, DB PubMed PATHWAY PDB TINKER HMMER

7 ( ) I/O ( ) ( )

8 BOSC2005 Bio + Chem Bio Chem

9 * * * * * * BioRuby

(GenBank, UniProt,...) (PDB,...) HEADER LIGASE 15-DEC-04 1VQ3 TITLE CRYSTAL STRUCTURE OF PHOSPHORIBOSYLFORMYLGLYCINAMIDINE TITLE 2 SYNTHASE, PURS SUBUNIT (EC 6.3.5.3) (TM1244) FROM TITLE 3 THERMOTOGA MARITIMA AT 1.

214 1.00 29.86 ATOM 5 CB HIS A -3 70.492 29.234 5.702 1.00 33.52 XML (DAS, KGML,...) <?xml version="1.0" standalone="yes"?> <!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.

10 (GenBank, UniProt,...) (PDB,...) HEADER LIGASE 15-DEC-04 1VQ3 TITLE CRYSTAL STRUCTURE OF PHOSPHORIBOSYLFORMYLGLYCINAMIDINE TITLE 2 SYNTHASE, PURS SUBUNIT (EC ) (TM1244) FROM TITLE 3 THERMOTOGA MARITIMA AT 1.90 A RESOLUTION : ATOM 1 N HIS A ATOM 2 CA HIS A ATOM 3 C HIS A ATOM 4 O HIS A ATOM 5 CB HIS A XML (DAS, KGML,...) <?xml version="1.0" standalone="yes"?> <!DOCTYPE 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> <METHOD id="enzyme">enzyme</method> <START> </START> <END> </END> (ArrayExpress,...) Affymetrix:CompositeSequence:HG_U95Av2:AFFX-HUMGAPDH/M33197_5_at AFFX-HUMGAPDH/M33197_5_at IPB M33197 ENSG Affymetrix:CompositeSequence:HG_U95Av2:AFFX-HUMGAPDH/M33197_M_at AFFX-HUMGAPDH/M33197_M_at IPB M33197 ENSG Affymetrix:CompositeSequence:HG_U95Av2:AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_3_at IPB M33197 ENSG

11 BioRuby >> (TB) (>700DB) Perl BioPerl NAR DB issue Perl Ruby The 2005 update includes 719 databases

12 * * * * * * * ChemRuby

13 (SMILES, InChI,...) CC1C(C(CC(O1)OC2C(C(C(OC2OC3=C4C=C5C=C3OC6=C(C=C(C=C6)C(C(C (=O)NC(C(=O)NC5C(=O)NC7C8=CC(=C(C=C8)O)C9=C(C=C(C=C9C(NC (=O)C(C(C1=CC(=C(O4)C=C1)Cl)O)NC7=O)C(=O)O)O)O)CC(=O)N)NC(=O) C(CC(C)C)NC)O)Cl)CO)O)O)(C)N)O (MDL, Tinker,...) ISISHOST D XML (CML, CDXML,...) <?xml version="1.0" encoding="utf-8"?> <!DOCTYPE CDXML SYSTEM " > <CDXML CreationProgram="ChemDraw 7.0" Name="hypericin.mol" BoundingBox=" " V P O O O O 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...

14 DB

15 ChemRuby DB ChemRuby kcf, sdf, rdf, rxn, mol, msi, g98, cdx EPS OpenBabel (sf.net) - (tinker) (subcomp),

16 Innovation & Business Architecture Inc. BioRuby ChemRuby

17 RefSeq PDB PubMed PubChe m GenPept EMBL UniProt GenBank DNA(, ) DB GENES ENZYME PATHWAY COM POUND UCSC Ensembl KEGG DAS Bio::DAS (REST CGI) Bio::Flat(BDB) Bio::Fetch(HTTP) Bio::SQL(RDB) Bio::KEGG::API (SOAP/WSDL) Bio::GenBank, Bio::EMBL etc. E-Utils (CGI) Bio::Pathway Bio::Sequence Bio::Reference Bio::BLAST, Bio::HMMER etc. HMMER TINKER, DB LIGAND Bio Chem

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

18 KEGG DB KEGG API (SOAP ), 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_l serv.save_image(url) end

19 Ruby CGI SOAP

21 Ruby BioPerl 20 C YARV 49

22 7 BioRuby Ruby1.8 BioRuby API UnitTest OpenBio 2 BioRuby 1.0 ChemRuby 1.0

23 BioRuby/ChemRuby

24 BioRuby/ChemRuby 1. API RDoc

25 BioRuby/ChemRuby 1. API RDoc

26 BioRuby/ChemRuby 1. API RDoc

27 BioRuby/ChemRuby 1. API RDoc BioRuby + ChemRuby

28 BioRuby/ChemRuby 1. API RDoc BioRuby + ChemRuby 5. Test::Unit 6. -

29 BioRuby/ChemRuby 1. API RDoc BioRuby + ChemRuby 5. Test::Unit 6. -

32 Thank you, Pjotr!

33 RDoc

34 README.DEV LGPL Test::Unit autoload

35 BioPerl BioRuby

38 BOSC2005 Bioinformatics Open Source Coference BioPerl 2005/06/23

39 Ruby

40 DNA

41 BioRuby/ChemRuby

44 autoload ruby -r bio -e 0 30 % repeat 10 { time ruby -r bio -e 0 } : 0.74s user 0.16s system total (9/10): 0.01s user 0.01s system total

45 bioruby -- irb DB

46 Bio::KEGG::KGML Bio::KEGG::EXPRESSION Bio::ColorScheme

49 Innovation & Business Architecture Inc. BioRuby ChemRuby

50 ChemRuby

51 (MDL, Tinker,...) ISISHOST D V P O O O O M END (SMILES, InChI,...) XML (CML, CDXML,...) <?xml version="1.0" encoding="utf-8"?> <!DOCTYPE CDXML SYSTEM " > <CDXML CreationProgram="ChemDraw 7.0" Name="hypericin.mol" BoundingBox=" " CC1C(C(CC(O1)OC2C(C(C(OC2OC3=C4C=C5C=C3OC6=C(C=C(C=C6)C(C(C (=O)NC(C(=O)NC5C(=O)NC7C8=CC(=C(C=C8)O)C9=C(C=C(C=C9C(NC (=O)C(C(C1=CC(=C(O4)C=C1)Cl)O)NC7=O)C(=O)O)O)O)CC(=O)N)NC(=O) C(CC(C)C)NC)O)Cl)CO)O)O)(C)N)O (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...

52 LogP Graph

54 NP 10 CPU Boost Graph Library VF

55 Adjacency Matrix

56 Adjacency Matrix

57 Finding Match Matrix

58 Match Matrix

59 int numofbits(int bits) { int num = 0; int mask = 1; for( ; mask!= 0 ; mask = mask << 1 ){ if( bits & mask ) num++ ; } return num; } int numofbits(long bits) { bits = (bits & 0x ) + (bits >> 1 & 0x ); bits = (bits & 0x ) + (bits >> 2 & 0x ); bits = (bits & 0x0f0f0f0f) + (bits >> 4 & 0x0f0f0f0f); bits = (bits & 0x00ff00ff) + (bits >> 8 & 0x00ff00ff); return (bits & 0x0000ffff) + (bits >>16 & 0x0000ffff); }

62 API

65 Test::Unit 51.6%

66 Test::Unit ruby install.rb test

70 KEGG API

71 KEGG API v , , ,408 58,125 56,986 28,529 24,815 24, , ,866 1,348,470 2,688,317 SOAP::Lite/Perl/0.60 SOAP4R/1.5.3-ruby1.8.2 Axis/1.2RC2 SOAP4R/1.5.2 SOAPpy/ Axis/1.2RC1 SOAP::Lite/Perl/0.55 Axis/1.1 SOAPpy/ SOAP4R/1.5.3-ruby1.8.2-http-acc Axis/1.2RC3 Axis/1.2beta

72 KEGG API v , , ,802 71,742 29,953 24, ,343 1,422,207 1,536,014 1,840,929 SOAP4R/1.5.2 SOAP4R/1.5.3-ruby1.8.2 SOAP::Lite/Perl/0.60 SOAPpy/ SOAP::Lite/Perl/0.55 SOAPpy/ Axis/1.2.1 Axis/1.2alpha Axis/1.2RC2 SOAPpy/0.11.3

73 11-12 KAST 1, Test::Unit, YARV 2 BioRuby, ChemRuby 1.0 SciRuby, )

74 BioRuby ChemRuby

75 01_cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C _bsu_BG _cpd_C00074

未踏成果報告会-fix.key

未踏成果報告会-fix.key BioRuby/ChemRuby http://www.tmd.ac.jp/artsci/biol/textbook/celltop.htm 350 280 210 140 2000 / 1 / 27 70 0 1995 96 97 98 99 2000 01 02 03 04 05 RefSeq PDB PubMed PubChem GenPept EMBL UniProt GenBank