KNOB? KNOB KNOB

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1 KNOB Itoshi NIKAIDO

2 KNOB? KNOB KNOB

3 Bioinformatics?

4 データタイプがいっぱい

6 EMBOSS = 160 aaindexextract,abiview,acdc,acdpretty,acdtable,acdtrace,acdvalid,antigenic,backtranseq,ba nana,biosed,btwisted,cai,chaos,charge,checktrans,chips,cirdna,codcmp,coderet,compseq, cons,cpgplot,cpgreport,cusp,cutgextract,cutseq,dan,dbiblast,dbifasta,dbiflat,dbigcg,degap seq,descseq,diffseq,digest,distmat,dotmatcher,dotpath,dottup,dreg,einverted,embossdata, embossversion,emma,emowse,entret,epestfind,eprimer3,equicktandem,est2genome,etand em,extractfeat,extractseq,findkm,freak,fuzznuc,fuzzpro,fuzztran,garnier,geecee,getorf,hel ixturnhelix,hmoment,iep,infoalign,infoseq,isochore,lindna,listor,marscan,maskfeat,masks eq,matcher,megamerger,merger,msbar,mwcontam,mwfilter,needle,newcpgreport,newcpgs eek,newseq,noreturn,notseq,nthseq,octanol,oddcomp,palindrome,pasteseq,patmatdb,pat matmotifs,pepcoil,pepinfo,pepnet,pepstats,pepwheel,pepwindow,pepwindowall,plotcon,p lotorf,polydot,preg,prettyplot,prettyseq,primersearch,printsextract,profit,prophecy,proph et,prosextract,pscan,psiphi,rebaseextract,recoder,redata,remap,restover,restrict,revseq,se ealso,seqmatchall,seqret,seqretsplit,showalign,showdb,showfeat,showorf,showseq,shuffles eq,sigcleave,silent,sirna,sixpack,skipseq,splitter,stretcher,stssearch,supermatcher,syco,tco de,textsearch,tfextract,tfm,tfscan,tmap,tranalign,transeq,trimest,trimseq,twofeat,union,v ectorstrip,water,whichdb,wobble,wordcount,wordmatch,wossname,yank,

8 KNOB?

9 KNOPPIX for Bio

10 What s KNOB CD Linux Bioinformatics

11 One CD bootable CD OS Windows Windows

12 KNOB have... C/C++, Perl, Ruby, Python, FORTRAN, R, Lisp BioPerl, BioRuby, EMBOSS, NCBI-Tools (BLAST, epcr etc), boxshade, loki, Glimmer, ReadSeq, tree-puzzle, rasmol, pymol, Njplot, Bioconductor, SMA, ClustalW, FASTA2, FASTA3, G-language, fastlink, fastdnaml, Graphviz, gnuplot, HMMER...

13 Databases EMBOSS DDBJNEW, DDBJRELEASE, EMBL, REFSEQ, GenBANK, SpTrEMBL, PIR, REFSEQ Protein, SwissProt, SWall BioPerl/BioRuby KEGG, SwissProt, EMBL, GenBank, RefSeq WormBase, GMOD/GBrowse

14 Knoppix for Bio BioRuby/BioPerl/BioJava, EMBOSS NTFS Database Kernel /home Boot Loader Mini Root Internet cloop file Bio databases cloop = 700MB = 2GB GenomeNet KEGG NCBI GenBank EMBL

15 2005 KNOB KNOB bioinformatics Web service High throughput computing KNOB

16 KNOB G-language G-language!? colinux ClustalW orz...

17 KNOB on Windows

18 KNOB KAST

19 REST DAS (Distributed Annotation System) Genome Database Protein Database SOAP/WSDL DNA/Protein Database Metabolic Pathway

20 REST

21 EMBOSS $ seqret -sequence embl:xlrhodop Reads and writes (returns) sequences Output sequence [xlrhodop.fasta]: $ plotorf xlrhodop.fasta Plot potential open reading frames Graph type [x11]: png Created plotorf.1.png Request HTTP (REST) Search Server KNOB DNA Sequence

22 emboss.defalut

23 DAS (REST)

24 TIGR, USA RIKEN, Japan NCBI, USA Sanger, UK

25 Client/Server Interactions Request DAS client Protocol DAS server Server DAS Database Command Argument

26 Client/Server Interactions Response Head er XML DAS client HTTP/ OK Date: Sun, 12 Mar :13:51 GMT Server: Apache/1.3.6 (Unix) mod_perl/1.19 Last-Modified: Fri, 18 Feb :57:52 GMT Connection: close Content-Type: text/plain X-DAS-Version: DAS/1.5 X-DAS-Status: 200 X-DAS-Capabilities: error-segment/1.0; unknown-segment/1.0; unknown-feature/1.0;... <?xml version="1.0" standalone="no"?> <!DOCTYPE DASDSN SYSTEM " <DASDSN> <DSN> <SOURCE id="id1" version="version">source name 1</SOURCE> <MAPMASTER>URL</MAPMASTER> <DESCRIPTION>descriptive text 1</DESCRIPTION> </DSN> <DSN> <SOURCE id="id2" version="version">source name 2</SOURCE> <MAPMASTER>URL</MAPMASTER> <DESCRIPTION href="url">descriptive text 2</DESCRIPTION> </DSN>... </DASDSN> DAS server

27 BioRuby + BioRegistry #!/usr/bin/env ruby require bio reg = Bio::Registry.new serv = reg.get_database( genbank ) entry = serv.get_by_id( AA2CG ) puts entry

28 BioRuby + BioRegistry

29 stanza format

30 #!/usr/bin/env ruby require bio id = entry = Bio::PubMed.query(id) medline = Bio::MEDLINE.new(entry) reference = medline.reference puts reference.bibtex PubMed ID KNOB format HTTP Search Reference author = {Nikaido, I., Saito, C., Mizuno, Y., Meguro, M., Bono, H., Kadomura, M., Kono, T., Morris, G. A., Lyons, P. A., Oshimura, M., Hayashizaki, Y. and Okazaki, Y.}, title = {Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.}, journal = {Genome Res}, year = {2003}, volume = {13}, number = {6B}, pages = { }, }

31 SOAP/WSDL BLAST Search #!/usr/bin/perl use strict; use SOAP::Lite; my $seq; $seq.= $_ while <>; DNA sequence SOAP KNOB Result Server my $serv_ge = SOAP::Lite->service( ); my $serv_bl = SOAP::Lite->service( ); $serv_bl->proxy( timeout => 60*60*6); print $serv_bl->searchsimple( blastx, SWISS, $seq);

32 #!/usr/bin/env ruby KEGG API (BioRuby + SOAP) Enzyme num. SOAP Search Server Object require bio KNOB output serv = Bio::KEGG::API.new obj_list = [ eco:b0207, eco:b1300 ] fg_list = [ blue, #00ff00 ] bg_list = [ #ff0000, yellow ] p serv.color_pathway_by_objects( path:eco00053, obj_list, fg_list, bg_list)

33 output

34 Knoppix for Bio High thoughput Computing Editon CD

35 KNOB HTC Edition KNOB Knoppix for Bio - Bio Knoppix KNOB Condor Internet PVFS2 KNOB HTC Edition server CD serve r server node HUB server Condor, PVFS2 2005/5/20 IPAB 1 node 1 node 2 node N

36 Condor Condor Research Project Condor Pool Condor Project Homepage

37 PVFS2 (Parallel File System 2) node 1 node 2 node N The Parallel File System Project PVFS /5/20 IPAB 1

38 Knoppix Cluster Booting Sequence (1) Booting Head node (2) PXE Boot on Work nodes (3) PVFS Setup Wizard

40 fumikazu

41 3 KNOB bioinformatics Web service High throughput computing KNOB

42 KNOB 2.0 HTC

43 KNOB KNOB2.0 DVD edition!

44 Web service BioMoby Ensembl/Genome sequence DDBJ,

45 Biomoby

46 Taverna

47 HTC / InterProScan etc...

48 /

50 KNOB Project Hack Web service client

51 Project KNOB Download Mailing List Knob-friends ( ) Knob-friends@sourceforge.jp Knob-dev ( ) Knob-dev@sourceforge.jp Itoshi NIKAIDO

52 Web 2.0

53 Web 2.0

54 EMBOSS

57 Grasp the KNOB! grasp 1, (grip). 2,, (understand). [ 2 ]

KNOB Bio KNOPPIX

KNOPPIX for Bio 1CD Linux Itoshi NIKAIDO KNOB Bio KNOPPIX Knoppix for Bio KNOPPIX JP Itoshi NIKAIDO 2004/01/29 1.1.0 1.3.1 bio OS Mac OS X Xcode/fink Windows Cygwin Linux