The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe

Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk

What is EMBL-EBI?

• Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory

Heidelberg Hamburg Hinxton, Cambridge

Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO

EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states

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 Who we are

~500 members of staff ~400 work in services & support

>53 nationalities ~120 focus on basic research EMBL-EBI’s mission

• Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science

www.ebi.ac.uk/services Browse our services

9 What services do we provide? Labs around the world send us …provide their data and tools to help we… researchers use it

A virtuous Archive it circle Analyse it

Classify it Share it with other data providers Bioinformatics underpins research

Literature Genomes Protein sequence and proteomes Nucleotide sequence Protein structure Gene expression

Protein families, Chemical entities domains and motifs

Protein-protein interactions Systems

Pathways Standards – international collaborations

Genome annotation Genomics Standards Consortium (GSC) www.geneontology.org http://gensc.org

Protein sequence Nucleotide sequence www.uniprot.org www.insdc.org HUPO- Proteomics Standards Initiative Protein structure (PSI) Functional Genomics www.wwpdb.org Data Society www.psidev.info/ www.fged.org

Cheminformatics Pathways www.ebi.ac.uk/chebi www.reactome.org www.biopax.org Systems modelling Metabolomics Standards Initiative (MSI) standards www.metabolomicssociety.org www.sbml.org EMBL-EBI users: Live stats

http://wwwdev.ebi.ac.uk/ebiwebtrafficmap/kmlvector.html

Key facts about our services

• Freely available • A comprehensive collection of molecular databases • Globally coordinated data collection and dissemination • Produced in collaboration with other world leaders:

• NCBI (US) • National Institute of Genetics (Japan) • SIB Swiss Institute of Bioinformatics • Wellcome Trust Sanger Institute Data resources

DNA & RNA Systems genes, genomes & variation reactions, interactions &

Gene expression Chemical biology RNA, protein & metabolite expression chemogenomics & metabolomics

Proteins Ontologies sequences, families & motifs taxonomies & controlled vocabularies

Structures Literature molecular & cellular structures Scientific publications & patents

Other software cross-domain tools & resources pathways DNA & RNA

• European Genome-phenome Archive (EGA) • European Nucleotide Archive (ENA) • Ensembl • Ensembl Genomes • Metagenomics portal Genomes: Ensembl • Explore human, mouse and other chordate (and selected invertebrate) genomes.

Gene models Browse a genomic region

Comparative data gene trees, homologues, alignments, synteny Sequences genomes, genes, transcripts, proteins

Tools Variation data BLAST/BLAT sequence search, Regulatory data short and structural Variant Effect Predictor ENCODE variants, phenotypes

Access: website, BioMart, Perl and REST API

www.ensembl.org Genomes: Ensembl Genomes • Explore genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoan.

Genome portals Variation data for plant, for the five metazoan and fungal kingdoms of life species

Pan-taxonomic comparative analysis Multi-way comparison of whole bacterial chromosomes

Access: website, BioMart, Perl and REST API

www.ensemblgenomes.org Bioinformatics tools

• Over 100 analysis tools • Results enriched with data from EBI resources

Nucleotide sequence search Protein sequence search e.g. BLAST nucleotide e.g. BLAST protein, PSI-Search

Multiple sequence alignment Pairwise sequence alignment e.g. Clustal Omega, MUSCLE e.g. Needle

Protein functional analysis Functional genomics tools e.g. InterProScan e.g. Expression Atlas Molecular structure analysis Text mining e.g. PDBeFold e.g. EBIMed, Whatizit Programmatic access: EBI Web Services

• Run tasks on EBI servers, using EBI data • Ideal for large scale analyses, repetitive tasks and internal pipelines • Programmatically retrieved data • Ensembl API • Biomart API

Research Data-driven discovery

PhD and postdoctoral programmes

www.ebi.ac.uk/research Research themes Proteins, structures & chemical biology Alex Bateman Genes & gene Gerard Kleywegt expression John Overington Paul Bertone Christoph Steinbeck Ewan Birney Sarah Teichmann Alvis Brazma Janet Thornton Anton Enright Paul Flicek Nick Goldman

Systems biology Pedro Beltrao John Marioni Julio Saez-Rodriguez Oliver Stegle Research Group Leaders

Genomes

Ewan Paul Nick Birney Flicek Goldman

Expression

Alvis Anton John Oliver Brazma Enright Marioni Stegle

Proteins & structures

Alex Pedro Gerard Janet Bateman Beltrao Kleywegt Thornton

Pathways & systems Chemical biology

Paul Julio Saez- Sarah John Christoph Bertone Rodriguez Teichmann Overington Steinbeck Examples of EMBL-EBI research How do the neurons of someone with What is the Parkinson’s disease molecular basis signal differently of ageing? from healthy neurons?

Which of these What makes a stem cell proteins will make Which of these decide to become skin or changes to a genome’s good targets for muscle? drugs? structure drive cancer? PhDs and Postdocs

• EMBL International PhD programme: www.embl.de/training/eipp • Postdoctoral positions available from: www.ebi.ac.uk/jobs • Or apply for a postdoctoral fellowship: • EIPOD EMBL sponsored: interdisciplinary • ESPOD EBI–Sanger: combined experimental/computational User training For scientists working at all levels

www.ebi.ac.uk/training

Bioinformatics training

Train at EMBL-EBI Train at your place Train online

Gain hands-on Choose the training Learn in your own time, experience in our state- that’s right for you and at your own pace with of-the-art facilities. your colleagues - and our our freely available experts will come to you. online courses. www.ebi.ac.uk/training Train online

• Free online courses • Learn in your own time, at your own pace • Created for life- science researchers • No previous knowledge of bioinformatics needed

www.ebi.ac.uk/training/online Interactions with industry Support and collaboration

www.ebi.ac.uk/industry

The EMBL-EBI Industry Programme

• Helping industry make the most of innovations in bioinformatics • Neutral ground for members to explore developments and concepts • Standards development • Technical development “The Programme’s regular • Input into services development meetings foster inter-company interactions as we collaborate on special projects and liaise on other industry initiatives.” - Bertram Industry Programme members

• Astellas Pharma Inc. • Merck Serono S.A. • AstraZeneca • Nestlé Research Centre • Bayer Pharma AG • Novartis Pharma AG • Boehringer Ingelheim • Novo Nordisk • Eli Lilly and Company • Syngenta • F. Hoffmann-La Roche • Sanofi-Aventis Recherche & Développement • GlaxoSmithKline • UCB • Johnson & Johnson • • Pharmaceutical R&D Unilever With thanks to our funders

• EMBL member states • The European Commission • The Wellcome Trust • Research Councils UK • US National Institutes of Health Thank you!

www.ebi.ac.uk Twitter: @emblebi Facebook: EMBLEBI YouTube: EMBLMedia