EMBL-EBI Annual Scientific Report 2012

Alvis BrazmaPhD in Computer Science, Moscow StateUniversity, 1987. Postdoctoral research at NewMexico State University, US.At EMBL-EBI since 1997.Summary of progress 2012Ugis SarkansArrayExpress• Offered new ways of workingwith ArrayExpress data: Robjects, integration withGenomeSpace, visualisation inEnsembl for sequencing-baseddata;• Continued evolving theArrayExpress user interface toprovide a richer, moreconsistent service.Helen ParkinsonArrayExpress andExpression Atlas• Produced EMBL-EBI’s firstRDF endpoint for geneexpression data;• Released Zooma, an automatedannotation knowledgebasesupporting ArrayExpress, the EBIBioSamples Database and theExpression Atlas;• Welcomed the one millionthassay to ArrayExpress.Christoph SteinbeckMetabolights• Developed the MetaboLightsdatabase and archive, whichwas released in February 2012;• Assumed co-ordinationof COSMOS (EuropeanCommission co-ordinationaction) for metabolomicsstandards and data exchange.Henning HermjakobPRIDE• Achieved full production statusfor the ProteomeXchangeconsortium, co-ordinatinginternational data depositionstrategies for massspectrometry-based proteomicsdata;• Handled over 80 submissionsand more than 70 million newspectra;• Released format-specific libraries(Griss et al., 2012; Reisinger etal., 2012);• Released an updated depositiontool, PRIDE Converter (Côté etal., 2012);• Released data analysis support,PRIDE Inspector (Wang etal., 2012);• Implemented the capability todeposit large raw datasetsin PRIDE.2012 EMBL-EBI Annual Scientific Report21