GMOD

PSU Presentation

This Wiki page is an edited version of Chinmay’s presentation.

1 Sanger Pathogen Sequencing Unit (PSU)
2 Technical - Connections
3 Technical - Code Generation
4 Technical - Transactions
5 Problems 1, 2, & 3
6 Demo – Sample Problem

Sanger Pathogen Sequencing Unit (PSU)

GeneDB is the organism data and annotation database for the Pathogen Sequencing Unit (PSU) at the Sanger Institute, UK
Contains 37 organisms, which is expected to grow to 62
Artemis is an annotation/DNA graphical interface
PSU is currently migrating to chado schema
We’ve implemented a common interface with the two leading open source frameworks: Hibernate and iBatis

Technical - Connections

Connections for the Hibernate engine are configured in the Spring configuration file

<bean id="dataSource" class="org.apache.commons.dbcp.BasicDataSource">
               <property name="driverClassName" value="org.postgresql.Driver" />
               <property name="url" value="jdbc:postgresql://holly.sanger.ac.uk:5432/chado" />
               <property name="username" value="DELIBERATELY_BOGUS_NAME"/>
               <property name="password" value="WIBBLE" />
</bean>

Uses a connection pool
Connection to the database is specified graphically, so the iBatis configuration file has variables for the location:

<property name="JDBC.Driver" value="org.postgresql.Driver"/>
 
<property name="JDBC.ConnectionURL” value="jdbc:postgresql://${chado}"/>
 
<property name="JDBC.Username" value="${username}"/>
 
<property name="JDBC.Password" value="${password}"/>

provide database location, username & password
select from scrollable list of feature with residues (organisms in separate Postgres schemas) what to open in Artemis

Technical - Code Generation

The shared interface and hibernate implementation were originally generated
There’s no explicit code generation (although the Spring and Hibernate runtimes may use them behinds the scenes)

Technical - Transactions

Transactions are fully supported

Problems 1, 2, & 3

Creating a gene

genes[0] = new Feature(ORG, GENE, "xfile", false, false, now, now);
 
genes[0].setSeqLen(1029);
sequenceDao.persist(genes[0]);
 
FeatureLoc loc = new FeatureLoc(SOURCE_FEATURE, genes[0], 13691, false, 14720, false, (short)1, 0, 0 ,0);
 
sequenceDao.persist(loc);
 
addFeatureProp(genes[0], "description", "A test gene for GMOD meeting");
 
addSynonymsToFeature(genes[0], "mulder", "scully");
 
createExon("exon1", genes[0], 13691, 13767, now, 0);
 
createExon("exon2", genes[0], 14687, 14720, now, 1);

Retrieve a gene

Feature f = sequenceDao.getFeatureByUniqueName("xfile");
displayGene(f);

Update a gene

genes[0].setUniqueName("x-file");
 
sequenceDao.merge(genes[0]);

private Feature createExon(String name, Feature gene, int min, int max, Timestamp now, int rank) {
 
        Feature exon = new Feature(ORG, EXON, name, false, false, now, now);
        exon.setSeqLen(max-min);
        sequenceDao.persist(exon);
 
        FeatureLoc loc = new FeatureLoc(SOURCE_FEATURE, exon, min, false, max, false,
                                      (short)1, 0, 0 ,0);
        sequenceDao.persist(loc);
 
        return exon;
 
}

Demo – Sample Problem

Simple web page to demonstrate displaying a basic feature

<st:section name="Naming" id="gene_naming" collapsed="false" collapsible="false"
hideIfEmpty="true">
   <dl>
            <dt><b>symbol:</b></dt>
            <dd>${feature.uniqueName}</dd>
  </dl>
  <db:synonym name="synonym" var="name" collection="${feature.featureSynonyms}">
    <br /><b>Synonym:</b> <db:list-string collection="${name}" />
  </db:synonym>
  <dt><b>Type:</b></dt>
  <dd>${feature.cvTerm.name}</dd>
 
<st:section name="Exons" collapsed="false" collapsible="true" hideIfEmpty="true">
            <display:table name="exons" uid="tmp" pagesize="30" class="simple" cellspacing="0"
cellpadding="4">
                 <display:column property="uniqueName" title="Exon"/>
                 <display:column property="featureLocsForSrcFeatureId.fmin" title="Start"/>
                 <display:column property="featureLocsForSrcFeatureId.fmax" title="end"/>
            </display:table>
</st:section>
 
<st:section name="cds" collapsible="true">
            <b>${feature.residues}</b>
</st:section>

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Last updated at 21:16 on 9 October 2012.
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