The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Dr Laura Emery Laura.Emery@EBI.ac.uk 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 Administration EMBO Structural biology Bioinformatics Grenoble Monterotondo, Rome Structural biology Mouse biology EMBL staff: 1500 people >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 their data and we… …provide tools to help researchers use it A virtuous circle Archive it Analyse it Share it with other data providers Classify it Data resources at EMBL-EBI Genes, genomes & variation •European Nucleotide Archive (ENA) •EBI Metagenomics •Ensembl •Ensembl Genomes •European Genome– phenome Archive •Non-redundant patent sequence databases Proteins • UniProt: the Universal Protein Resource • InterPro • Pfam Expression • • • • ArrayExpress Expression Atlas MetaboLights PRIDE Chemical biology • • • ChEBI ChEMBL Patent compounds Cross-domain resources • Europe PubMed Central • Gene Ontology Systems • • • BioModels BioSamples Database Enzyme Portal Molecular & cellular structure • Protein Data Bank in Europe • Electron Microscopy Data Bank Reactions, interactions & pathways • • IntAct Reactome Where to start? use Firefox or Google Chrome Search here The EBI Search Service Gene and protein summaries Explore the data and return easily to your results Data organised by: • gene • expression • protein • structure • literature Species selector allows for easy comparison The EBI Search Service Gene and protein summaries Species selector allows for easy comparison Data organised by: • gene • expression • protein • structure • literature Explore the data and return easily to your results Accessing our services the services tab programmatic access European Nucleotide Archive • Comprehensive catalogue of nucleotide sequence data • Covers raw reads, sequence assembly and functional data Search for DNA sequence Locate gene sequences Submit data to the archive Download FASTA files for chosen sequences www.ebi.ac.uk/ena Ensembl • Explore human, mouse and other chordate (and selected invertebrate) genomes Gene models Comparative data Browse a genomic region gene trees, homologues, alignments, synteny Sequences genomes, genes, transcripts, proteins Regulatory data ENCODE www.ensembl.org Variation data Tools short and structural variants, phenotypes BLAST/BLAT sequence search, Variant Effect Predictor Access: website, BioMart, Perl and REST API Ensembl Genomes • Explore genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoan Genome portals for the five kingdoms of life Variation data for plant, metazoan and fungal species Pan-taxonomic comparative analysis Multi-way comparison of whole bacterial chromosomes Access: website, BioMart, Perl and REST API www.ensemblgenomes.org 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 Expression Atlas • A curated subset of the ArrayExpress data • Search for gene expression changes under different biological/experimental conditions. Gene page Search by gene, organism and/or biological condition Baseline Atlas Prototype www.ebi.ac.uk/gxa 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 Programmatic access: EBI Web Services • Run tasks on EBI servers, using EBI data • Ideal for large scale analyses, repetitive tasks and internal pipelines • Integration of EBI resources and data • EBI Search, tools, data retrieval • Same programs, data and results enrichment as running via the web pages • www.ebi.ac.uk/tools/webservices 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 themes Genomes • Nick Goldman • Ewan Birney • Paul Flicek Chemical biology Transcriptome s • • • • Anton Enright John Marioni Oliver Stegle Alvis Brazma Proteins & structures • • • • Janet Thornton Pedro Beltrao Alex Bateman Gerard Kleywegt • Christoph Steinbeck • John Overington Pathways & systems • Paul Bertone • Julio Saez-Rodriguez • Sarah Teichmann Research at EMBL-EBI Protein targets for new drugs Molecular basis of ageing Neurons in Parkinson’s disease Stem cell differentiation Cancer genome structure DNA data storage PhDs and Postdocs • EMBL International PhD programme: www.embl.de/training/eipp • Postdoctoral positions available from: www.ebi.ac.uk/jobs • Postdoctoral fellowships: • 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 Gain hands-on Choose the training that’s experience in our state-ofright for you and your the-art facilities. colleagues - and our experts will come to you. www.ebi.ac.uk/training Train online Learn in your own time, at your own pace with our freely available online courses. 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