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EMBL’s European Bioinformatics Institute
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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
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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…
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New types of data Nucleotide sequence Genomes Protein sequence
Gene expression Protein structure Protein families, motifs and domains Chemical entities Protein interactions Pathways Systems
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What is the EBI? Non-profit organization
Part of the European Molecular Biology Laboratory Based on the Wellcome Trust Genome Campus near Cambridge, UK
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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.
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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.
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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.
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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
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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
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Ontologies and standards
The EBI’s structure Ontologies and standards EMBL-Bank Reactome Ensembl IntAct InterPro ArrayExpress MSD UniProt DATA RESOURCES
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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
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Ontologies and standards
The EBI’s structure Ontologies and standards EXTERNAL SERVICES RICE GROUP TRAINING OUTREACH Data resources Research Groups
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Ontologies and standards
The EBI’s structure Ontologies and standards External Services Rice group Training Outreach COLLABORATIONS Data resources Research Groups
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Services
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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
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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
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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
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User support 2Can bioinformatics – an online primer www.ebi.ac.uk/2Can
Services site map – Online help pages – support –
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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
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Research
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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
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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
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Training
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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
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User training 2Can Bioinformatics: online training resource: Courses run by Services groups Industry Programme workshops Training for schools
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Industry support
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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
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Industry programme members
Procter & Gamble Bayer Healthcare
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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
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