bio-linux development environment joe wood. development on bio-linux ● programming languages ●...
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Bio-Linux Development Environment
Joe Wood
Development on Bio-Linux● Programming Languages● Database management systems● Apache web server● Example – EGTDC Admin database● Bio-Linux and GRID
Programming Languages● Perl/Bioperl● PHP● Python● Java● C/C++
Perl● Practical Extraction and Report Language● Widely used in Bioinformatics● Open-source – perl modules● One-off tasks or larger applications
Bioperl● Bioinformatics modules● Installed on Bio-Linux
use Bio::Perl;
$seq_object = get_sequence('swissprot',"ROA1_HUMAN");
$blast_result = blast_sequence($seq_object);
write_blast(">roa1.blast",$blast_report);
Databases● Relation Database Management System● Structured Query Language – SQLselect first_name,last_name
from staff_names
where first_name = 'Bob'
● PostgreSQL● MySQL
Apache Web Server● Web server installed in Bio-Linux● Web pages (HTML)● Web applications● Perl CGI, PHP, Databases
EGTDC Admin Database● Web application developed on Bio-Linux● PostgreSQL Database● PHP web front-end● EG Awardees and projects, Bio-Linux
clones,GeneSpring Installs, Courses and Course attendees
EGTDC Admin database
Database Web Server Browser
SQL PHP HTML
Example of PHP code // generate and execute a query
$query = "SELECT distinct category ".
"FROM query_defs";
$result = pg_exec($connection, $query) or die("Error in query:
$query. " . pg_last_error($connection));
$rows = pg_numrows($result);
// if records present
if ($rows > 0){
?><TABLE><? // iterate through resultset
for ($i=0; $i<$rows; $i++){
$row = pg_fetch_row($result, $i);
?>
<FORM ACTION="<?php echo $_SERVER['PHP_SELF'] ?>" METHOD="POST" >
<TR ALIGN=LEFT VALIGN=TOP> .............................................
Bio-Linux and Grid● Sharing of resources● Clusters● Condor job scheduler
Bio-Linux Clustering● Bio-Linux – Condor integrated● Condor currently in testing● BLAST searches have been run across
multiple machines● Site cluster ~1 year● Interconnect Bio-Linux clones – cluster
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