Open Bio* O B F -- Open Bio Foundation BioRuby BioPerl BioPython BioJava BioDAS BioMOBY BioPipe EMBOSS Ensembl OmniGene GMOD GBrowse Apollo OBDA BioCa

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1 BioRuby 京大化研バイオインフォマティクスセンター 2003/1/28 infobiologist 第二回研究会 ۆ 伝研

2 Open Bio* O B F -- Open Bio Foundation BioRuby BioPerl BioPython BioJava BioDAS BioMOBY BioPipe EMBOSS Ensembl OmniGene GMOD GBrowse Apollo OBDA BioCaml BioLisp BioCyc BioConductor BioPathways BioBlog BioLinux :

3 BioHackathon 2002/01 Arizona, 2002/02 Cape Town 2003/02 Singapore Will be annual event? Hackathon 1 week intensive hacking BOSC (ISMB) for open discussion

4 Schedule hack hack hack

5 Hacking Room

6 Hacking Matrix

7 Hacking Sofa

8 BioRuby hackathon results BioFetch BioSQL EMBL/GenBank/SwissProt in MySQL/PostgreSQL BioRegistry ~/.bioinformatics/seqdatabase.ini /etc/bioinformatics/seqdatabase.ini

rb BioSQL EMBL/GenBank/SwissProt in MySQL/PostgreSQL

9 OBDA Open Bio* Open Bio* Sequence Database Access BioRegistry (Stanza) BioFlat (Simple index, BDB) BioFetch (CGI/HTTP) BioSQL (MySQL, PostgreSQL, Oracle) XEMBL (SOAP based) BioCORBA (BSANE compliant)

BioFetch (CGI/HTTP) BioSQL (MySQL, PostgreSQL, Oracle)

10 BioFlat % bioflat --makeindex mydatabase gbvrl*.seq % bioflat mydatabase ENTRY_ID

11 BioFetch WWW (HTTP) CGI EBI dbfetch BioRuby biofetch.rb format=default format=fasta ( ) style=html style=raw db=genbank db=prosite db=pathway... id= ID

12 biofetch.bioruby.org/

13 BioSQL GenBank/EMBL/SwissProt BioPerl sequence MySQL or PostgreSQL or Oracle RDBMS BioPerl BioJava

14 BioRegistry (Stanza ) ~/.bioinformatics/seqdatabase.ini /etc/bioinformatics/seqdatabase.ini [swissprot] protocol=biosql location=db.bioruby.org dbname=biosql driver=mysql biodbname=sp DB name [genbank] [swissprot] etc. Protocol Location [embl] protocol=biofetch location= biodbname=embl : biosql, index-berkeleydb, index-flat, biofetch, bsane-corba, xembl

org dbname=biosql driver=mysql biodbname=sp DB name [genbank] [swissprot] etc.

15 OBDA #!/usr/bin/env ruby require 'bio' reg = Bio::Registry.new # # OBDA HTTP MySQL # db # fetch db = reg.db("swissprot") entry = db.fetch("tetw_butfi")

16 Nature 417: (2002)

17 Table mountain

18 Sunset

19 BioRuby Bio::Sequence, Bio::Location, Bio::Feature Bio::DB Bio::Blast, Bio::Fasta Blast/Fasta Bio::PubMed, Bio::Reference BibTeX Bio::Registry, Bio::SQL, Bio::Fetch, Bio::FlatFile OBDA Bio::Pathway, Bio::Relation

20 FASTA BioRuby #!/usr/bin/ruby require 'bio' flatfile = Bio::FastaFormat.open('filename') flatfile.each do entry puts entry.entry_id puts entry.seq puts entry end

21 FASTA BioPerl #!/usr/bin/perl use Bio::SeqIO; my $seqio = new Bio::SeqIO(-format => 'fasta', -file => 'filename'); While ( my $entry = $seqio->next_seq ) { print $entry->display_id, "\n"; print $entry->seq, "\n"; print ">", $entry->desc, "\n", $entry->seq, "\n"; }

22 FASTA BioPython #!/usr/bin/python from Bio import Fasta iter = Fasta.Iterator(open('filename'), Fasta.RecordParser()) while 1: entry = iter.next() if not(entry): break print entry.title print entry.sequence print entry

23 #!/usr/bin/env ruby # hello world for bioinformatician require 'bio' gene = Bio::Seq::NA.new("catgaattattgtagannntgataaagacttgac") prot = gene.translate Ë "HELL*XW*RLD" puts plot.split('x').join(' ').capitalize.gsub(/\*/, 'o') << '!' Ë ["HELL*", "W*RLD"] Ë "HELL* W*RLD" Ë "Hell* w*rld" Ë "Hello world" Ë Hello world!

24 Blast/Fasta/Hmmer BioRuby GenomeNet EMBOSS BioRuby Jemboss, Bio-EMBOSS

25 Blast BioRuby Blast local #!/usr/bin/ruby require 'bio' blast = Bio::Blast.local('blastp', 'hoge.pep') flatfile = Bio::FastaFormat.open('queryfile') flatfile.each do seq result = blast.query(seq) result.each do hit puts hit.query_id, hit.target_id, hit.evalue if hit.evalue < 0.05 end end

26 BioPerl Blast local (SearchIO ) #!/usr/bin/perl use Bio::SeqIO; use Bio::Tools::Run::StandAloneBlast; use Bio::Tools::BPlite; = ('program' => 'blastp', 'database' => 'hoge.pep'); my $factory = Bio::Tools::Run::StandAloneBlast->new(@params); my $input = Bio::SeqIO->new(-format => 'fasta', -file => "queryfile"); while ( my $seq = $input->next_seq ) { $result = $factory->blastall($seq); while ( my $hit = $result->nextsbjct ) { while ( my $hsp = $hit->nexthsp ) { print $result->query, $hit->name, $hsp->p, "\n" if $hsp->p < 0.05; last; } } }

27 BioPython Blast local #!/usr/bin/python from Bio import Fasta from Bio.Blast import NCBIStandalone iterator = Fasta.Iterator(open("queryfile"), Fasta.RecordParser()) while 1: query = iterator.next() if not(query): break open("query.fst", "w").write(str(query)) out, error = NCBIStandalone.blastall("blastall", "blastp", "hoge.pep", "query.fst") parser = NCBIStandalone.BlastParser() result = parser.parse(out) for alignment in result.alignment: for hsp in alignment.hsps: if hsp.expect < 0.05: print query.title, alignment.title, hsp.expect

28 PubMed PubMed #!/usr/bin/env ruby require 'bio' entries = Bio::PubMed.search(ARGV.join(" ")) puts entries % pmsearch.rb genome bioinformatics Medline

29 PubMed ID BiBTeX #!/usr/bin/env ruby require 'bio' ARGV.each do pmid entry = Bio::PubMed.query(pmid) reference = Bio::MEDLINE.new(entry).reference puts reference.bibtex end % pm2bibtex.rb BiBTeX

30 /bb [^b]{2}/ to be or not to be GenBank GenBank Location bio/location.rb location <aside>why oh why doesn't Perl have a nice garbage collector. And when Perl 6 comes and Parrot does have one, will Perl 5 be "ported" to Parrot?</aside> said Ewan Ruby :-)

31 Open Bio* Open Bio* Info q--p

32 bioruby.org/

33 q--p BioRuby URL, PMID, ISBN

34 q--p BioRuby PubMed HTML cron MySQL HTML

35 GMOD/GBrowse w/ KEGG Stein Ensemble, DAS gmod.bioruby.org/

36 BRGB GenBank, RefSeq MySQL GD PNG SVG A0

37 kumamushi.net/

38 1mm MPa (6000 ) 90% 30MPa 300MPa 100 tun : DNA

39 くまむし観察装置

43 9

44 BioRuby BioSQL, GFF, DAS GMOD/GBrowse KEGG API SOAP(DAS, XEMBL, ), CORBA EMBOSS, ClustalW, MAFFT PATHWAY, SSDB, KO, GO, InterPro BioFetch Entrez E-utils PDB

45 BioRuby.org ftp://bioruby.org/ cvs.bioruby.org presentation by T. Katayama

BioRuby Ruby Bioinfomatics Blast BioPerl, BioJava, BIoPython Ruby

BioRuby, BioRuby Ruby Bioinfomatics Blast BioPerl, BioJava, BIoPython Ruby Open Bio* O B F -- Open Bio Foundation BioRuby Ensembl BioCaml BioPerl OmniGene BioLisp BioPython GMOD BioConductor BioJava Apollo