ProServer

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ProServer BioDasLiteLightweight DAS
components in Perl
Roger Pettett Project Leader, Web
Systems Wellcome Trust Sanger Institute
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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

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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

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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

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ProServer Structure (1)
Server
.ini file
Source Adaptor
Transport
Data
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ProServer Structure (2)
Server
.ini file
Source Adaptor
MySQL Transport
Oracle Transport
DB
DB
DB
DB
DB
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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
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ProServer Configuration (2)
mysimpledb adaptor simpledb state
on transport dbi dbhost databasesrv1 dbport
3306 dbname simpledb dbuser
simplero dbpass topsecret
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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.

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ProServer Extensions (2)
label gt Pelizaeus-Merzbacher
disease, 'id' gt 10, 'type'
gt decipherknownins, 'typecategory' gt
decipher', 'method' gt decipher', 'start
' gt 102528707, 'end' gt
103018423, 'note' gt , 'link'
gt , linktxt gt Syndrome Report,
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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

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ProServer SourceHydra (2)
simplehydra state on adaptor
simpledbhydra dbi transport dbi basename
hydra dbname hydra dbhost databasesrv1 dbuser
hydraro password topsecret
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Things Id 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

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BioDasLite

• A small DAS 1 client
• Returns plain data structures
• Few dependencies
• LWPParallelUserAgent for asynchronous I/O
• SOAPLite for registry access
• Available on CPAN

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BioDasLite Synopsis
use BioDasLite my singledsn
BioDasLite-gt new(http//das.sanger.ac.uk/da
s/hgnc36) my features singledsn-gtfeatures(X
1,1000000)
use BioDasLite my multidsn
BioDasLite-gtnew( dsn gt
qw(http//dasdas/hgnc36
http//das/das/decipher), ) my multiseg
bdl-gtfeatures(qw(X1,1000000 31,1000000
171,1000000))
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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

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Acknowledgements

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

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