The EMBL-European Bioinformatics Institute
The hub for bioinformatics in Europe
Rajesh Radhakrishnan [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-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 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 Services Data and tools for molecular life science
www.ebi.ac.uk/services 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 Data resources at EMBL-EBI
Genes, genomes & Proteins variation • UniProt: the Universal Protein Resource •European Nucleotide • InterPro Archive (ENA) Expression • Pfam •EBI Metagenomics • ArrayExpress •Ensembl • Expression Atlas Molecular & cellular structure •Ensembl Genomes • MetaboLights • Protein Data Bank in Europe •European Genome– • PRIDE • Electron Microscopy Data Bank phenome Archive •Non-redundant patent Reactions, sequence databases Chemical biology • ChEBI interactions & • ChEMBL pathways • Patent compounds • IntAct • Reactome Cross-domain resources • Europe PubMed Central Systems • Gene Ontology • BioModels • BioSamples Database • Enzyme Portal Where to start?
Search here The EBI Search Service Gene and protein summaries Species selector allows for easy comparison
Data organised by: • gene Explore the data and • expression return easily to • protein your results • structure • literature European Nucleotide Archive
• Comprehensive catalogue of nucleotide sequence data • Covers raw reads, sequence assembly and functional data Search for DNA Locate gene sequence sequences
Submit data to the archive
Download FASTA files for chosen sequences
www.ebi.ac.uk/ena ArrayExpress
• Archive of functional genomics data – RNA-Seq, ChIP- Seq and array-based technologies • MIAME- and MINSEQE- standard compliant
Search experiments Expand results
Apply filters to refine a search
Read descriptions of sample properties
www.ebi.ac.uk/arrayexpress 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 e.g. Clustal Omega, MUSCLE alignment 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 Navigating the EBI
• EBI resources are linked to one another • Allows you to move to other relevant information • Gain a greater overview of biological applications Getting help
• EBI resources are vast and very daunting • Don’t worry. We are here to help. Don’t be afraid to ask.
Take a Quick Tour in Train Online
Read resource documentation
Contact EBI Help Desk www.ebi.ac.uk/support/ Research Data-driven discovery
PhD and postdoctoral programmes
www.ebi.ac.uk/research Research at EMBL-EBI
Protein targets for Molecular new drugs basis of ageing
Neurons in Parkinson’s disease
Stem cell differentiation
Cancer genome DNA data storage structure 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 that’s Learn in your own time, experience in our state-of- right for you and your at your own pace with the-art facilities. 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 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