KNOB Bio KNOPPIX

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1 KNOPPIX for Bio 1CD Linux Itoshi NIKAIDO

2 KNOB Bio KNOPPIX

3 Knoppix for Bio KNOPPIX JP Itoshi NIKAIDO 2004/01/

4 bio

6 OS Mac OS X Xcode/fink Windows Cygwin Linux

7 Bio Bio

8 bio DNA Sequence auto sequencer mrna expression Microarray Protein-Protein Interaction Yeast/Mammalian 2 hybrid DNA-Protein Interaction ChIP onchip

9 データタイプがいっぱい

10 EMBOSS = 160 aaindexextract,abiview,acdc,acdpretty,acdtable,acdtrace,acdvalid,antigenic,backtrans eq,banana,biosed,btwisted,cai,chaos,charge,checktrans,chips,cirdna,codcmp,coderet,c ompseq,cons,cpgplot,cpgreport,cusp,cutgextract,cutseq,dan,dbiblast,dbifasta,dbiflat,d bigcg,degapseq,descseq,diffseq,digest,distmat,dotmatcher,dotpath,dottup,dreg,einvert ed,embossdata,embossversion,emma,emowse,entret,epestfind,eprimer3,equicktandem, est2genome,etandem,extractfeat,extractseq,findkm,freak,fuzznuc,fuzzpro,fuzztran, garnier,geecee,getorf,helixturnhelix,hmoment,iep,infoalign,infoseq,isochore,lindna,list or,marscan,maskfeat,maskseq,matcher,megamerger,merger,msbar,mwcontam,mwfilter, needle,newcpgreport,newcpgseek,newseq,noreturn,notseq,nthseq,octanol,oddcomp,pa lindrome,pasteseq,patmatdb,patmatmotifs,pepcoil,pepinfo,pepnet,pepstats,pepwheel,p epwindow,pepwindowall,plotcon,plotorf,polydot,preg,prettyplot,prettyseq,primersearc h,printsextract,profit,prophecy,prophet,prosextract,pscan,psiphi,rebaseextract,recode r,redata,remap,restover,restrict,revseq,seealso,seqmatchall,seqret,seqretsplit,showalig n,showdb,showfeat,showorf,showseq,shuffleseq,sigcleave,silent,sirna,sixpack,skipseq,s plitter,stretcher,stssearch,supermatcher,syco,tcode,textsearch,tfextract,tfm,tfscan,t map,tranalign,transeq,trimest,trimseq,twofeat,union,vectorstrip,water,whichdb,wobbl e,wordcount,wordmatch,wossname,yank,

ed,embossdata,embossversion,emma,emowse,entret,epestfind,eprimer3,equicktandem, est2genome,etandem,extractfeat,extractseq,findkm,freak,fuzznuc,fuzzpro,fuzztran,

12 Perl Hacker GD.pm, CGI.pm UNIX/Linux/Mac OS X BioPerl Subject: Rubyist BioRuby Windows (or Mac) orz...

13 Knoppix for Bio CD

14 Knoppix for Bio CD

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

16 KNOB have... C/C++, Perl, Ruby, Python, Fortrun, 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...

17 Knoppix for Bio CD

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

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 KNOB HTTP (REST) Search Server 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 Server DAS Database Command Argument DAS server

26 Client/Server Interactions Response Header 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 Server 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 #!/usr/bin/perl use strict; use SOAP::Lite; my $seq; $seq.= $_ while <>; BLAST Search Server DNA sequence SOAP Result KNOB my $serv_ge = SOAP::Lite->service(' GetEntry.wsdl'); 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 require 'bio' KNOB output Object 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

35 KNOB HTC BioMoby

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

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

39 KNOB Kernel BioRuby/BioPerl/BioJava, EMBOSS /master /source Boot Loader Mini Root cloop file cloop = 700MB = 2GB

40 KNOB BioRuby/BioPerl/BioJava, EMBOSS Kernel Boot Loader Mini Root chroot HDD /master /source./configure; make; make install apt-get install cloop file Internet cloop = 700MB = 2GB apt server

41 KNOB Kernel Boot Loader BioRuby/BioPerl/BioJava, EMBOSS HDD /master /source Mini Root cloop file cloop = 700MB = 2GB

42 KNOB Kernel BioRuby/BioPerl/BioJava, EMBOSS Boot Loader CD image HDD /master /source Mini Root cloop file cloop = 700MB = 2GB

43 KNOPPIX Root Shell $ mkdir -p /mnt/sda1/source/v3.7 $ mkdir -p /mnt/sda1/master/ $ cp -a /KNOPPIX/* /mnt/sda1/source/v3.7 $ cp -p /cdrom/* /mnt/sda1/master $ chroot /mnt/sda1/source/v3.7 $ mount -t proc /proc proc $ apt-get install hoge $ wget $ tar zxvf hoge.tar.gz; cd hoge; $./configure; make; make install; $ umount /proc $ mkisofs -R -L -V "KNOB 1.3.0" -hide-rr-moved -v /mnt/sda1/source/v3.7 create_compressed_fs > /mnt/sda1/master/knoppix/knoppix $ cd /mnt/sda1/master $ mkisofs -v -R -J -no-emul-boot -boot-load-size 4 -boot-info-table -b boot/isolinux/ isolinux.bin -c boot/isolinux/boot.cat -hide-rr-moved -o /mnt/sda1/master/ knob1.3.0.iso /mnt/sda1/master

KNOB? KNOB KNOB

KNOB Itoshi NIKAIDO itoshi@saitama-med.ac.jp KNOB? KNOB KNOB Bioinformatics? データタイプがいっぱい EMBOSS = 160 aaindexextract,abiview,acdc,acdpretty,acdtable,acdtrace,acdvalid,antigenic,backtranseq,ba nana,biosed,btwisted,cai,chaos,charge,checktrans,chips,cirdna,codcmp,coderet,compseq,