EMBL-EBI Annual Scientific Report 2012

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dGenes, genomes and variationSummary of progress 2012Paul FlicekEnsembl and 1000Genomes• Issued four major releases ofEnsembl, featuring significantupdates to our key resourcesfor human and model organismgenomics;• Managed and made availabledata from the 1000 GenomesProject, which finalised andpublished its phase 1 analysis;• Welcomed the mountain gorillagenome and four others toEnsembl;• Began processing Blueprint andother reference epigenomic data,which complements referencehuman variation data in 1000Genomes;• Launched first version of the dataportal for the International MousePhenotyping Consortium;• Formed new Variation Team;• Provided evidence for cohesin’srole in tissue specific transcriptionalregulation.Paul KerseyEnsembl Genomes• Launched PhytoPath, a newportal for plant pathogen data;• Offered metabolic data for over4000 bacterial genomes throughthe Microme portal;• Developed a new integrativeportal for plant genomics data aspart of the transPLANT project;• Contributed to significantpublications on the butterfly andwheat genomes;• Provided the first integratedgenome browser resource for thebarley genome;• Commenced participation in newprojects to assemble, annotateand disseminate the genomesof wheat, barley and the bitingmidge;• Issued four public releases ofEnsembl Genomes.12 2012 EMBL-EBI Annual Scientific Report
Summary of progress 2012Sarah HunterMetagenomics• Formally launched the EBIMetagenomics portal to thepublic;• Added new softwareanalysis tools to pipeline formetagenomics data analysis.Guy CochraneEuropean NucleotideArchive• Enabled the capture, processingand presentation of majornew raw read, read alignment,assembly and annotationdatasets;• Led community discussions onthe use of lossless and lossycompression in sequence datamanagement;Justin PaschallEGA and DGVa• Formed new Variation Team;• Began development of theEuropean Variation Archive(EVA), a unified interface forDGVa and EGA;• Oversaw the substantial growthof EGA and DGVa following newELIXIR partnerships formed withSpain and Finland.• Released version 1 of the CRAMsequence-data-compressiontoolkit;• Built, tested and deployed theENA advanced search service,supporting rich and granularinteractive and programmaticdiscovery of ENA data;• Enhanced the Webin datasubmission tool;• Deployed new submission anddata presentation services forgenome assembly information;• Developed training courses andonline training materials anddelivered training workshops.2012 EMBL-EBI Annual Scientific Report13
Page 1 and 2: EMBL-European Bioinformatics Instit
Page 3: Table of contentsIntroduction & ove
Page 6 and 7: EMBL-EBI 2012It was a year of trans
Page 8 and 9: New service developments• Underst
Page 10 and 11: Organisation ofEMBL-EBI Leadership
Page 12 and 13: dGenes, genomes and variationThe Eu
Page 16 and 17: European Nucleotide ArchiveOur team
Page 18 and 19: Vertebrate genomicsThe Vertebrate G
Page 20 and 21: Nonvertebrate genomicsWe provide to
Page 22 and 23: gMolecular atlasLife scientists are
Page 24 and 25: Functional genomicsThe Functional G
Page 26 and 27: Functional genomics productionOur t
Page 28 and 29: Functional genomics developmentOur
Page 30 and 31: PProteins and protein familiesUniPr
Page 32 and 33: UniProt contentOne of the central a
Page 34 and 35: UniProt developmentOur team provide
Page 36 and 37: InterProOur team co-ordinates the I
Page 38 and 39: sMolecular and cellular structureUn
Page 40 and 41: Protein Data Bank in EuropeThe majo
Page 42 and 43: PDBe content and integrationOur goa
Page 44 and 45: PDBe databases and servicesOur team
Page 46 and 47: yMolecular systemsThe genes and gen
Page 48 and 49: Proteomics servicesThe Proteomics S
Page 50 and 51: Chemical biologyThe importance of s
Page 52 and 53: ChEMBLThe ChEMBL team develops and
Page 54 and 55: Cheminformatics and metabolismOur t
Page 56 and 57: cCross-domain toolsand resourcesSci
Page 58 and 59: Literature servicesScientific liter
Page 60 and 61: Research2012 has seen the further t
Page 62 and 63: Bertone groupPluripotency, reprogra
Page 64 and 65:
Birney groupNucleotide dataDNA sequ
Page 66 and 67:
Enright groupFunctional genomics an
Page 68 and 69:
Goldman groupEvolutionary tools for
Page 70 and 71:
Le Novère groupComputational syste
Page 72 and 73:
Luscombe groupGenomics and regulato
Page 74 and 75:
Marioni groupComputational and evol
Page 76 and 77:
Rebholz groupPhenotypes and multili
Page 78 and 79:
Saez-Rodriguez groupSystems biomedi
Page 80 and 81:
Thornton groupProteins: structure,
Page 82 and 83:
The EMBL International PhDProgramme
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SupportOur support teams provide fo
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T TrainingAs part of EMBL-EBI’s m
Page 88 and 89:
IIndustry programmeSince 1996 the I
Page 90 and 91:
NExternal relationsAs a European In
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sExternal servicesOur team manages
Page 94 and 95:
SSystems and networkingOur team man
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q AdministrationThe EMBL-EBI Admini
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Funding and resource allocationDesp
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Growth of core resourcesIn 2012 the
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CollaborationsEMBL-EBI is a highly
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Staff growthOur organisational stru
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Scientific advisory commiteesEMBL S
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The International Nucleotide Sequen
Page 110 and 111:
EMDataBank Advisory Committee• Jo
Page 112 and 113:
Major database collaborationsARRAYE
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THE GENE ONTOLOGY CONSORTIUM• Agb
Page 116 and 117:
REACTOME• New York University Med
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Publications in 2012In 2012, EMBL-E
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Doreleijers, J. F., Vranken W. F.,
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Kruger, F. A., Rostom R. and Overin
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Sahakyan, Aleksandr B., Cavalli And
Page 128:
EMBL - European Bioinformatics Inst
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EMBL-EBI Annual Scientific Report 2012

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