Introduction to EMBL-EBI.

Transcription

1 Introduction to EMBL-EBI

2 What is EMBL-EBI? Part of EMBL Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia 2

3 What is EMBL-EBI Heidelberg Hamburg Hinxton Basic research in molecular biology Administration EMBO Structural biology Grenoble Bioinformatics Monterotondo 1500 staff >60 nationalities Structural biology Mouse biology

4 What is EMBL-EBI? Bioinformatics research and services institute Non-profit organisation ~ 540 staff; 57 nationalities Part of the European Molecular Biology Laboratory 4

5 EMBL-EBI s mission To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress To contribute to the advancement of biology through basic investigator-driven research in bioinformatics To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators To help disseminate cutting-edge technologies to industry To coordinate biological data provision across Europe 5

6 Molecular biology Literature Genomes Protein sequence Nucleotide sequence Proteomes Gene expression Protein structure Protein families, domains and motifs Chemical entities Protein-protein interactions Pathways Systems 6

7 EMBL-EBI Resource Clusters Genes, Genes, & Variation Proteins & Protein Families Molecular Atlas Molecular & Cellular Structure Chemistry Molecular Systems Cross-domain 7

8 Genes, Genomes & Variation ENA Ensembl + Ensembl Genomes EGA DGVa 1000 Genomes Metagenomics Portal 8

9 Proteins & Protein Families UniProt InterPro 9

10 Molecular Atlas Array Express Atlas PRIDE MetaboLights 10

11 Molecular & Cellular Structure PDBe EMDB 11

12 Chemistry ChEMBL ChEBI 12

13 Molecular Systems IntAct Reactome Microme IntEnz Rhea BioModels Enzyme Portal 13

14 Cross-domain Literature BioSamples Taxonomy Ontologies 14

15 Terabytes Petabytes EMBL-EBI statistics >7 million hits a day from across the world >300,000 unique hosts served per month >800 million database cross-references Year Year 15

16 EMBL-EBI Tools Over 100 tools available for analysis Classic molecular biology search tools BLAST & FASTA Recent advanced tools Exonerate & PSI-Search Protein annotation tools InterProScan Sequence alignment tools Clustal Omega & MUSCLE Sequence translation, analysis and prediction EMBOSS Results enriched with data from EBI resources 16

17 EMBL-EBI Web Services Programmatic access via Web Services Integration of EBI resources and data EBI Search, tools, data retrieval Run tasks on EBI servers, using EBI data SOAP & REST APIs PPre-made clients in Java, PERL, python Galaxy, YABI, Taverna workflow compatible Result enrichment as via webpages 17

18 EMBL-EBI Training Pre-doctoral training programme EMBL International PhD programme Post-doctoral fellowships EIPOD EMBL sponsored: interdisciplinary ESPOD EBI-Sanger: combined experimental/computational 18

19 EMBL-EBI Training Hands-on training courses Held in the EBI IT Training Room Introductory and advanced courses Talks and practicals from EBI experts 19

20 EMBL-EBI Training EBI Roadshows Held in host institutions around the world Modules tailored to user needs and requirements Talks and practicals from EBI experts 20

21 EMBL-EBI Training Train Online Quick Tour 30 minute introductions to EBI resources Learn in your own time and at your own pace No previous bioinformatics experience needed Longer courses for beginners and intermediate levels 21

22 With thanks to support from EBI Industry Programme 22

23 BioMedBridges Building data bridges for biomedicine in Europe 23