1. MOLGENIS and the eXtensible Genotype And Phenotype database project (xgap) Morris A. Swertz et al DAM & BOSC sigs Stockholm, June 27 2009 EBI Biobanking platform

3. MOLGENIS, why and how biologist biologist biological challenges inbreed 100 10.000 1,000,000 100,000 10,000 10 10,000,00 QTL profiles network correlate genome strains individuals markers expressions preprocess probes microarrays 100 hybridize 100,000 genotype genotypes norm exprs. map

4. MOLGENIS, why and how biologist biologist biological challenges suitable infrastructure inbreed 100 10.000 1,000,000 100,000 10,000 10 10,000,00 QTL profiles network correlate genome strains individuals markers expressions preprocess probes microarrays 100 hybridize 100,000 genotype genotypes norm exprs. map bioinformatician softw engineers €

5. MOLGENIS, why and how biologist biologist Reinventing wheels, Wasting time Hard to integrate biological challenges suitable infrastructure bioinformatician softw engineers inbreed 100 100.000 10,000,000 1000 10,000 10 1000 genotype individuals mass peaks genotypes QTL profiles strains network SNP arrays correlate LC/MS genome map preprocess aligned peaks €

6. Alternative strategy http://www.molgenis.org Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243 http://www.molgenis.org

7. MOLGENIS, why and how Platform and generators Little language <!-- entity organization --> <entity name= &quot;Experiment&quot; label= &quot;Experiment&quot; > <field name= &quot;ExperimentID&quot; key= &quot;1“ r eadonly= &quot;true&quot; label= &quot;ExperimentID(autonum)&quot;/> <field name= &quot;Medium&quot; type= &quot;xref&quot; xref_field= &quot;Medium.name&quot; /> /> <field name= &quot;Protocol&quot; label= &quot;Experiment Protocol&quot; /> <field name= &quot;Temperature&quot; type= &quot;int&quot; Blueprint model <!-- entity organization --> <entity name= &quot;Experiment&quot; label= &quot;Experiment&quot; > <field name= &quot;ExperimentID&quot; key= &quot;1“ r eadonly= &quot;true&quot; label= &quot; ExperimentID(autonum )&quot;/> <field name= &quot;Medium&quot; type= &quot;xref&quot; xref_field= &quot;Medium.name&quot; /> /> <field name= &quot;Protocol&quot; label= &quot;Experiment Protocol&quot; /> <field name= &quot;Temperature&quot; type= &quot;int&quot; + bioinformatician softw engineer inbreed 100 10.000 1,000,000 100,000 10,000 10 10,000,00 QTL profiles network correlate genome strains individuals markers expressions preprocess probes microarrays 100 hybridize 100,000 genotype genotypes norm exprs. 10.000 map biologist biologist http://www.molgenis.org Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243

8. Upgrade to new research Platform and generators Little language <!-- entity organization --> <entity name= &quot;Experiment&quot; label= &quot;Experiment&quot; > <field name= &quot;ExperimentID&quot; key= &quot;1“ r eadonly= &quot;true&quot; label= &quot;ExperimentID(autonum)&quot;/> <field name= &quot;Medium&quot; type= &quot;xref&quot; xref_field= &quot;Medium.name&quot; /> /> <field name= &quot;Protocol&quot; label= &quot;Experiment Protocol&quot; /> <field name= &quot;Temperature&quot; type= &quot;int&quot; Blueprint model <!-- entity organization --> <entity name= &quot;Experiment&quot; label= &quot;Experiment&quot; > <field name= &quot;ExperimentID&quot; key= &quot;1“ r eadonly= &quot;true&quot; label= &quot;ExperimentID(autonum)&quot;/> <field name= &quot;Medium&quot; type= &quot;xref&quot; xref_field= &quot;Medium.name&quot; /> /> <field name= &quot;Protocol&quot; label= &quot;Experiment Protocol&quot; /> <field name= &quot;Temperature&quot; type= &quot;int&quot; + bioinformatician softw engineer biologist biologist New Biology New Biology http://www.molgenis.org Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243 inbreed 100 100.000 10,000,000 1000 10,000 10 1000 genotype individuals mass peaks genotypes QTL profiles strains network SNP arrays correlate LC/MS genome map preprocess aligned peaks

9. Upgrade to new software tools Platform and software generators Little language <!-- entity organization --> <entity name= &quot;Experiment&quot; label= &quot;Experiment&quot; > <field name= &quot;ExperimentID&quot; key= &quot;1“ r eadonly= &quot;true&quot; label= &quot;ExperimentID(autonum)&quot;/> <field name= &quot;Medium&quot; type= &quot;xref&quot; xref_field= &quot;Medium.name&quot; /> /> <field name= &quot;Protocol&quot; label= &quot;Experiment Protocol&quot; /> <field name= &quot;Temperature&quot; type= &quot;int&quot; Blueprint model <!-- entity organization --> <entity name= &quot;Experiment&quot; label= &quot;Experiment&quot; > <field name= &quot;ExperimentID&quot; key= &quot;1“ r eadonly= &quot;true&quot; label= &quot;ExperimentID(autonum)&quot;/> <field name= &quot;Medium&quot; type= &quot;xref&quot; xref_field= &quot;Medium.name&quot; /> /> <field name= &quot;Protocol&quot; label= &quot;Experiment Protocol&quot; /> <field name= &quot;Temperature&quot; type= &quot;int&quot; + bioinformatician softw engineer biologist biologist inbreed 100 100.000 10,000,000 1000 10,000 10 1000 genotype individuals mass peaks genotypes QTL profiles strains network SNP arrays correlate LC/MS genome map preprocess aligned peaks http://www.molgenis.org Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243

10. Demo

11. Step 1: model* m.a.swertz@rug.nl / individuals expressions probes *Can also extract automatically from an existing database

12. m.a.swertz@rug.nl /

13. Step 2: generate Download and customize... Model file XML Generate APIs in Java, R, Web services and HTTP MyScript Plugins FormGen MenuGen TreeGen PluginGen MatrixGen JTypeGen JDBCMapGen JListGen JReadCsvGen HSQLGen JDatabaseGen MySQLGen    RMatrixGen WSGen RListGen data infrastructure user interaction infrastructure Communication infrastructure

15. eXtensible Genotype And Phenotype database for QTL and GWAS experiments

18. First objective m.a.swertz@rug.nl / researcher researcher annotations Raw and processed data database my GaP

21. 1. Model / DATA (matrix) TRAIT SUBJECT DATA ELEMENT TRAIT  SUBJECT

25. UML: XGAP extends FuGE m.a.swertz@rug.nl / Uniform core to ease sharing of data and tools Various traits for new research Various subjects for new research ? ?

26. 2. Mode, run MOLGENIS

27. Connect to R statistics Workflow ready web-services UML documentation of your model Edit & trace your data Import/export to Excel plugin your own scripts (R/QTL) Tech keywords: object oriented data models, multi-platform java, tomcat/glassfish web server, mysql/postgresql database, Eclipse/Netbeans IDE, Java API, WSDL/SOAP API, R-project API, MVC, freemarker templates and css for custom layout, open source.

28. Proof of the pudding

29. Ongoing work

30. Next step: add processing Sheets thanks to Joeri van der Velde and Danny Arends Generalize for all MOLGENIS instances: (1) Extend MOLGENIS model for tool integration <tool name=“rqtl”> <input name=“data” entity=“data”/> … </tool> (2) Integrate workflow definition and execution Extending on Taverna/Galaxy model & APIs…