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