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Bio-Linux Development Environment

Joe Wood. Bio-Linux Development Environment. 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.

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Bio-Linux Development Environment

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  1. Joe Wood Bio-Linux Development Environment

  2. Development on Bio-Linux • Programming Languages • Database management systems • Apache web server • Example – EGTDC Admin database • Bio-Linux and GRID

  3. Programming Languages • Perl/Bioperl • PHP • Python • Java • C/C++

  4. Perl • Practical Extraction and Report Language • Widely used in Bioinformatics • Open-source – perl modules • One-off tasks or larger applications

  5. 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);

  6. Databases • Relation Database Management System • Structured Query Language – SQL selectfirst_name,last_name from staff_names where first_name = 'Bob' • PostgreSQL • MySQL

  7. Apache Web Server • Web server installed in Bio-Linux • Web pages (HTML) • Web applications • Perl CGI, PHP, Databases

  8. 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

  9. EGTDC Admin database PHP HTML SQL Browser Database Web Server

  10. 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> .............................................

  11. Bio-Linux and Grid • Sharing of resources • Clusters • Condor job scheduler

  12. 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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