n
                                                               o
    Kazuharu Arakawa
0




                            ...
von Neumann
Bio*
Bio*
Bio*
Bio*
use Bio::SeqIO;

$in = Bio::SeqIO->new(-file=>"ecoli.gbk", '-format'=>'GenBank');
$seq = $in->next_seq();

foreach $feat (...
use Bio::SeqIO;

$in = Bio::SeqIO->new(-file=>"ecoli.gbk", '-format'=>'GenBank');
$seq = $in->next_seq();

foreach $feat (...
Bluebird DBMS

      Before Bluebird…
                                                                G-language GAE v.1

...
$db = db_load("gene",
                    -driver=>"mysql",
                    -database=>"mus_musculus_core_46_36g",
   ...
Infinity                                           Internet
                                                               ...
benchmark                     kevin & samaguchi


                                                           CPU: Pentium ...
ajax - asynchronous
 javascript and xml
Adobe AIR

            Flash/Flex, HTML/AJAX




            Apple Dashboard
            Windows Gadget
             Sling...
FLASH         QuickTime                                        BDB
                                  Ext-JS/YUI


        ...
Thank you.
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OB9-G-language-Arakawa

  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=>"ensembldb.ensembl.org", -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.
  1. ¿Le ha llamado la atención una diapositiva en particular?

    Recortar diapositivas es una manera útil de recopilar información importante para consultarla más tarde.

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