1. EMBL’s European Bioinformatics Institute

2. What is bioinformatics?
The science of storing, retrieving and analysing large amounts of biological information
It is an interdisciplinary science, involving biologists, computer scientists and mathematicians
It is at the heart of modern biology

3. Biology is changing Data explosion and new types of data
Move towards high-throughput biology
Emphasis on systems, not reductionism
Large community of users with no training in bioinformatics
Growth of applied biology – molecular medicine, agriculture, food, environmental sciences…

4. New types of data Nucleotide sequence Genomes Protein sequence
Gene expression
Protein structure
Protein families,
motifs and domains
Chemical entities
Protein interactions
Pathways
Systems

6. What is the EBI? Non-profit organization
Part of the European Molecular Biology Laboratory
Based on the Wellcome Trust Genome Campus near Cambridge, UK

7. Part of the European Molecular Biology Laboratory
The EBI is part of the European Molecular Biology Laboratory (EMBL), a basic research institute funded by public research monies from 18 member states.

8. The Wellcome Trust Genome Campus
Sanger
Research Support
Facility
RFCGR
IT centre
EMBL-EBI
Labs/informatics
Cairns Pavilion
Thanks to Don Powell, Wellcome Trust Sanger Institute, for providing this image.

9. Funding
In 2004 The EBI received € 24 million in funding. The global importance of our work is reflected in the fact that we attract funds from beyond Europe.

10. Our mission
To provide freely available bioinformatics services to all facets of the scientific community in ways that promote scientific progress
To become a flagship laboratory for 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

11. ONTOLOGIES AND STANDARDS
The EBI’s structure
ONTOLOGIES AND STANDARDS
Gene Ontology
Chemical Ontology
MIAME & MAGE
HUPO Proteomics
Standards Initiative
Systems Biology
Markup Language
Structural data
standards

12. Ontologies and standards
The EBI’s structure
Ontologies and standards
EMBL-Bank
Reactome
Ensembl
IntAct
InterPro
ArrayExpress
MSD
UniProt
DATA RESOURCES

13. Ontologies and standards
The EBI’s structure
Ontologies and standards
Ouzounis
Computational genomics
Rebholz-Schuhmann
Text mining
Huber
Functional genomics
Goldman
Phylogenetics
Le Novère
Computational neurobiology
Luscombe
Regulatory networks
Thornton
Structural bioinformatics
Data resources
RESEARCH GROUPS

14. Ontologies and standards
The EBI’s structure
Ontologies and standards
EXTERNAL SERVICES
RICE GROUP
TRAINING
OUTREACH
Data resources
Research Groups

15. Ontologies and standards
The EBI’s structure
Ontologies and standards
External Services
Rice group
Training
Outreach
COLLABORATIONS
Data resources
Research Groups

16. Services

17. Key facts about services
European node for globally coordinated data collection and dissemination projects
Core databases produced in collaboration with other world leaders, including NCBI (US), National Institute of Genetics (Japan), Swiss Institute of Bioinformatics, Cold Spring Harbor Laboratory (US)
The world’s most comprehensive collection of molecular databases

18. Databases: molecules to systems
Genomes
Ensembl, Integr8
Nucleotide sequence
EMBL-Bank
Protein sequence
UniProt
Gene expression
ArrayExpress
Protein structure
MSD
Protein families,
motifs and domains
InterPro
Chemical entities
ChEBI
Protein interactions
IntAct
Pathways
Reactome
Systems
BioModels

19. Principles of service provision
Accessibility – all data and tools freely available without restriction
Compatibility – we develop and promote the use of standards in bioinformatics
Comprehensive data sets – agreements with other data providers ensure that our resources contain comprehensive and up-to-date data; agreements with publishers ensure that published data are placed in a public repository at the earliest opportunity
Portability – data and software can be downloaded and installed locally
Quality – Our databases are enhanced through annotation and cross-referencing

20. User support 2Can bioinformatics – an online primer www.ebi.ac.uk/2Can
Services site map – 
Online help pages – 
support – 

21. Data management >1 new sequence every 4 seconds
> web requests a day
> users (unique hosts)
5–10 ‘core’ databases
> cross-references (conservative)
> 150 other databases within EBI

22. Research

23. Key facts about research
Seven dedicated research groups that aim to understand biology through new approaches to interpreting biological data
Services teams also carry out R&D to enhance existing services and develop new ones
Research programme complements services and the two are mutually supportive
The EBI provides a unique environment for bioinformatics research

24. Research groups Ouzounis Computational genomics Rebholz-Schuhmann
Text mining
Goldman
Evolutionary sequence analysis
Huber
Functional genomics
Thornton
Structural bioinformatics
Luscombe
Regulatory networks
Le Novère
Computational systems neurobiology

25. Training

26. Predoc and postdoc training
Annual Open Days for bioinformatics masters’ students
PhD studentships through EMBL International PhD Programme
Short-term placements for visiting PhD students though EU-funded Marie Curie Fellowships
Philsoc: internal training for postdocs and other staff

27. User training
2Can Bioinformatics: online training resource:
Courses run by Services groups
Industry Programme workshops
Training for schools

28. Industry support

29. The EBI Industry Programme
Established in 1996 by Paolo Zanella, former Director of the EBI
Membership benefits include:
Research of benefit to industry
Expert training
Standards development
Technical development
Networking opportunities
Membership is by invitation

30. Industry programme members
Procter & Gamble
Bayer Healthcare

31. SME Support Forum Established in 2004
Members ‘dip in’ to benefits on an as-needs basis:
Biannual meetings
Expert training
Dedicated helpdesk
Technical Development
Consultancy
Funded by the UK Department of Trade and Industry’s Biosciences Unit
19 Member companies from all over the world