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 – SQL select 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 DatabaseWeb 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 ($rows > 0){ ?> <? // iterate through resultset for ($i=0; $i<$rows; $i++){ $row = pg_fetch_row($result, $i); ?> " METHOD="POST" >

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