1. The European Molecular Biology Laboratory (EMBL) is supported by sixteen countries. Consists of the main Laboratory in Heidelberg (Germany), Outstations in Hamburg (Germany), Grenoble (France) and Hinxton (U. K.), and an external Research Programme in Monterotondo (Italy). http://www.embl.de/ from 1974 http://www.ebi.ac.uk/ from 1996

2. The EBI Mission  To provide Bioinformatics Facilities for the Scientific Community  To become a flagship laboratory for research in bioinformatics  To provide bioinformatics training  To help disseminate standards & technologies

3. Role of Bioinformatics  To Support Experimental Biology  To Collect and Archive Data  To provide Framework and Integration  To give Easy Access to Data  To make New Discoveries through Data Analysis  To predict through modelling  To facilitate application and exploitation of academic research in Medicine, Agriculture, Health and Environment

4. Dramatic Changes in Biology over last 5 years  Data Explosion & New Types of Data  Move towards High-Throughput Biology  Move towards Systems Biology  Much larger community – often naïve users  Growth of Applied Biology – molecular medicine, agriculture, food, environmental sciences

5. Genomes Hypotheses and in silico models Bioinformatics Expression- profiling Comparative genomics Mutant/RNAi data Metabolic data Literature Proteome data Biochemistry

6. Molecules to Cells to Organisms E.coli Genome Protein Genomes

7. Systems Biology Output Input CheZ CheW CheB ATP ADP Pi Methyl CheR Methyl Adaptor Flim C Pi CheY CheA

8. Molecular Basis of Disease p53 tumour suppressor core domain – cancers of many types Cu-Zn Superoxide Dismutase - Autosomal dominant Amyotrophic lateral sclerosis

9. From Structure to Functional Annotation

10. PQS biological assemblies MSDchem ligand data Electron Density Visualisation AstexViewer MSDPro, MSDlite SSM fold matchingSurface MatchingMSDsite Active sites Linking to Domain data, eFamily Sequence Mapping, SIFTS

11. From Structure To Biochemical Function Gene  Protein  3D Structure  Function Given a protein structure:  Where is the functional site?  What is the multimeric state of the protein?  Which ligands bind to the protein?  What is biochemical function?

12. High throughput  A new sequence every 4 seconds  600 000 web requests a day  100 000 users  5-10 core databases  20 000 000 cross-references  About 160 other databases

13. Data Growth

14. Web requests per day (excluding Ensembl)

15. ftp year million files; Terabytes 2001 4.5 11914 2002 5.6 11809 2003 13.5 43860 2004 17.3 60508 2005 26.3 85396

16. Web Servers Requestsmillions 2002118631650118 2003255399724 255 2004354235704 354 2005482076196 482

17. Distinct hosts served Number users(millions) 20021586883 1.5 20032784974 2.7 20043656109 3.6 200539195643.9

18. dynamic pages domains (2005) 1..uk (United Kingdom) 21.14% 2..com (Commercial) 17.16% 3. [unknown domain] 13.37% 4.[unresolved numerical addresses] 11.05% 5..edu (USA Higher Education) 5.29% 6..net (Networks) 5.27% 7..fr (France) 4.76% 8..it (Italy) 4.68% 9..de (Germany) 2.81% 10..nl (Netherlands) 2.00%

19. The Services of the EBI  Nucleotide sequences  Genes  Transcription information  Protein sequences  Protein families  Macromolecular structures  Molecular interactions  Pathways  Metabolic information  Scientific Literature

20. Structure of EBI: Services

21. Apweiler, Stoesser Brazma Birney Henrick Database Integration and External Services Lopez Stoehr, Zhu

22. Structure of EBI: Research

23. Text MiningComputational Genomics Structural Proteomics Neuroinformatics Phylogeny & Evolution

24. EBI DATA BASES

26. EMBL-Bank DNA sequences

27. SWISS-PROT + TrEMBL Protein Sequences

28. EMBL-Bank DNA sequences SWISS-PROT + TrEMBL Protein Sequences EMSD Macromolecular Structure Data

29. EMBL-Bank DNA sequences SWISS-PROT + TrEMBL Protein Sequences Array-Express Microarray Expression Data EMSD Macromolecular Structure Data

30. EnsEMBL Human Genome Gene Annotation EMBL-Bank DNA sequences SWISS-PROT + TrEMBL Protein Sequences Array-Express Microarray Expression Data EMSD Macromolecular Structure Data

31. EnsEMBL Human Genome Gene Annotation EMBL-Bank DNA sequences SWISS-PROT + TrEMBL Protein Sequences Array-Express Microarray Expression Data EMSD Macromolecular Structure Data IntAct Protein Interactions

32. GKB Pathways EnsEMBL Human Genome Gene Annotation EMBL-Bank DNA sequences SWISS-PROT + TrEMBL Protein Sequences Array-Express Microarray Expression Data EMSD Macromolecular Structure Data IntAct Protein Interactions

33. Integration

34. Integrative science demands integrative resources  EBI databases have a backbone of integrative links  20 000 000 cross-references support trans- database navigation  Is this good enough?  sparse and coarse-grain  not straight-forward to use

35. Integrative science demands integrative resources Major efforts involved in integration  Interpro: database of protein families, domains and functional sites.  Interg8: data integration project co-ordinated by the EBI, to provide an integrated layer for the exploitation of genomic and proteomic data.  GRID technologies

36. European Patent Office  Support the inclusion of sequence data in the public databases  Development of tools to capture sequence data  Run their searches at the EBI  (similar arrangements in USA and Japan ensure exchange)  Analogous systems being developed for structure information

37. Industry Support

38.  Current successful Industry programme for Pharma  Quarterly meetings  R&D Training - workshops  Industry Forum  Funded by subscriptions  New SME programme under development

39. New Data Expression Data Proteomic Data Metabolome Data Chip-on- Chip AtlasesElectron tomographs Human Variation Disease Links ??

40. http://www.ebi.ac.uk/2can/

41. The Magic Search Box