The document discusses Kazuharu Arakawa's expertise in bioinformatics and systems biology. It provides an overview of his work using the G programming language and Bluebird database management system to analyze genomic data from databases like GenBank. Benchmark results show that the G language architecture can scale computation across multiple CPUs for genome analysis tasks.

1. n
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Kazuharu Arakawa
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Institute for Advanced Biosciences, Keio University
Graduate School of Media and Governance
Expertise: Bioinformatics, Systems Biology
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7. von Neumann

8. Bio*

9. Bio*

13. Bio*

14. Bio*

21. 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};
}

22. 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};
}

27. 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

28. $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};

31. 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

33. 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

35. ajax - asynchronous
javascript and xml

36. Adobe AIR
Flash/Flex, HTML/AJAX
Apple Dashboard
Windows Gadget
Slingshot (Rails)
etc...

38. FLASH QuickTime BDB
Ext-JS/YUI
Plug-in CSS JavaScript G-language
HTML Perl
RDB
CGI
Remote File Local File
HTTP Server
Client

49. Thank you.