Lightweight DAS components in Perl

ProServer & Bio::Das::Lite Lightweight DAS components in Perl Roger Pettett Project Leader, Web Systems Wellcome Trust Sanger Institute

What is ProServer?

Standalone DAS 1.5+ Server

First server to support gene and protein DAS

Written in Perl

Using POE

Easily extensible

Supports a wide range of data sources

DBI, flat-file, GFF, Excel

Available on CPAN

ProServer Features

Simple to set up

Smallish memory footprint

We serve 2200+ sources in ~8-20Mb per process with ~2-4Mb shared

Easy to configure

.ini format file

Easy to extend

Lots of examples

ProServer Installation

wget http://www.sanger.ac.uk/proserver/ProServer-2.tar.gz

tar -xzvf ProServer-2.tar.gz

cd Bio-Das-ProServer

perl Makefile.PL

make test

[configure proserver.ini]

eg/proserver

ProServer Structure (1) Source Adaptor Data Server .ini file Transport

ProServer Structure (2) MySQL Transport Source Adaptor DB Server .ini file DB DB Oracle Transport DB DB

ProServer Configuration (1) [mysimplefile] adaptor = simple state = on transport = file filename = /path/to/genelist.txt baseurl = http://www.example.org/report?id= type = gene feature_query = field0 like "%s”

ProServer Configuration (2) [mysimpledb] adaptor = simpledb state = on transport = dbi dbhost = databasesrv1 dbport = 3306 dbname = simpledb dbuser = simplero dbpass = topsecret

ProServer Extensions (1)

Inherit and extend SourceAdaptor.pm

Edit capabilities

Implement for example, the build_features method to run a database SQL query or an API call and return the correct data structure.

ProServer Extensions (2) { ‘ label’ => ‘ Pelizaeus-Merzbacher disease’, 'id' => 10 , 'type' => ‘ decipher:known:ins ’, 'typecategory' => ’decipher', 'method' => ’decipher', 'start' => 102528707, 'end' => 103018423, 'note' => … , 'link' => …, ‘ linktxt’ => ‘Syndrome Report’, };

ProServer SourceHydra (1)

Clone sources with the same structure

One configuration section

For example: Ensembl DAS uploads

One hydra database

Many tables with the same schema

ProServer SourceHydra (2) [simplehydra] state = on adaptor = simpledb hydra = dbi transport = dbi basename = hydra dbname = hydra dbhost = databasesrv1 dbuser = hydraro password = topsecret

Things I’d like to do

ProServer

Apache plugins for ModPerl & CGI

Automatic registry updates

Live server statistics

Embedded graphics

Streamed responses

Yahoo Pipes-ish service proxy/aggregation

Bio::Das::Lite

A small DAS 1 client

Returns plain data structures

Few dependencies

LWP::Parallel::UserAgent for asynchronous I/O

SOAP::Lite for registry access

Available on CPAN

Bio::Das::Lite Synopsis use Bio:::Das::Lite my $singledsn = Bio::Das::Lite-> new(‘http://das.sanger.ac.uk/das/hgnc36’); my $features = $singledsn->features(‘X:1,1000000’); use Bio:::Das::Lite my $multidsn = Bio::Das::Lite->new({ ‘ dsn’ => [qw( http://das…das/hgnc36 http://das…/das/decipher)], }); my $multiseg = $bdl->features([qw(X:1,1000000 3:1,1000000 17:1,1000000)]);

Citing ProServer

ProServer: A simple, extensible Perl DAS server.

Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J, Pettett R

Bioinformatics. 2007;. PMID: 17237073 DOI: 10.1093/bioinformatics/btl650

Acknowledgements Rob Finn, Jim Stalker, David Jackson, Eugene Kulesha, Jody Clements, Tony Cox, Will Spooner, Andreas Kahari

More Information [email_address] Bug Reports & Feature Requests http://search.cpan.org/~rpettett/ Bio::Das::Lite http://www.sanger.ac.uk/proserver/ ProServer