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  1. 1. n o Kazuharu Arakawa 0 i Institute for Advanced Biosciences, Keio University Graduate School of Media and Governance Expertise: Bioinformatics, Systems Biology t g. c u d o r p
  2. 2. von Neumann
  3. 3. Bio*
  4. 4. Bio*
  5. 5. Bio*
  6. 6. Bio*
  7. 7. use Bio::SeqIO; $in = Bio::SeqIO->new(-file=>"ecoli.gbk", '-format'=>'GenBank'); $seq = $in->next_seq(); foreach $feat ($seq->all_SeqFeatures()){ next unless($feat->primary_tag eq ‘CDS’); print $feat->each_tag_value(“note”), “¥n”; } use G; $gb = load ecoli; foreach $cds ($gb->cds()){ say $gb->{$cds}->{note}; }
  8. 8. use Bio::SeqIO; $in = Bio::SeqIO->new(-file=>"ecoli.gbk", '-format'=>'GenBank'); $seq = $in->next_seq(); foreach $feat ($seq->all_SeqFeatures()){ next unless($feat->primary_tag eq ‘CDS’); print $feat->each_tag_value(“note”), “¥n”; } use Bio::DB::GenBank; use Bio::Seq; $gb = new Bio::DB::GenBank; $seq = $gb->get_Seq_by_acc(“NC_000913”); use G; $gb = load ecoli; # $gb = load(“genbank:NC_000913”); foreach $cds ($gb->cds()){ say $gb->{$cds}->{note}; }
  9. 9. Bluebird DBMS Before Bluebird… G-language GAE v.1 Virtual Memory Flatfile Database Odyssey Systems Prelude GenBank EMBL SWISS RAM file outfile Perl Interpreter stdin With Bluebird… Virtual Memory G-language GAE v.2 RDBMS PostgreSQL DBD DBI Flatfile Database Bluebird Odyssey Systems mySQL Skyline DBMS Oracle GenBank EMBL SWISS Sybase Informix file Perl Interpreter RAM stdin outfile
  10. 10. $db = db_load("gene", -driver=>"mysql", -database=>"mus_musculus_core_46_36g", -host=>"", -port=>3306, -primarykey=>"gene_id" ); say $db->{239967}->{status};
  11. 11. Infinity Internet Flatfile Database GenBank EMBL SWISS user G-language GAE v.2 core G server dynamic TCP/IP G client file Odyssey Systems Skyline stdin static CGI HTML apache browser Perl Interpreter Virtual Memory RDBMS PostgreSQL DBI DBD DBD DBI Bluebird Bluebird DBMS TCP/IP DBMS mySQL Oracle Sybase Informix RDBMS RAM PostgreSQL DB2 mySQL informix Oracle sybase outfile
  12. 12. benchmark kevin & samaguchi CPU: Pentium 4 Xeon Dual 2.8GHz + Hyper Threading Technology Memory: 4GB Server & CPU Speed kevin 1cpu 1.00 kevin 2cpu 1.63 kevin 1cpu + samaguchi 1 cpu 1.97 kevin 4cpu 2.30 kevin 2cpu + samaguchi 2cpu 3.22 2 kevin 4cpu + samaguchi 4cpu 4.61 computational time (s) e Genome Analysis Environment Simulation Environment
  13. 13. ajax - asynchronous javascript and xml
  14. 14. Adobe AIR Flash/Flex, HTML/AJAX Apple Dashboard Windows Gadget Slingshot (Rails) etc...
  15. 15. FLASH QuickTime BDB Ext-JS/YUI Plug-in CSS JavaScript G-language HTML Perl RDB CGI Remote File Local File HTTP Server Client
  16. 16. Thank you.