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The EMBL-European Bioinformatics Institute

The EMBL-European Bioinformatics Institute. The hub for bioinformatics in Europe. Dr Laura Emery Laura.Emery@EBI.ac.uk www.ebi.ac.uk. Part of the European Molecular Biology Laboratory International , non-profit research institute Europe’s hub for biological data, services and research.

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The EMBL-European Bioinformatics Institute

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  1. The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Dr Laura Emery Laura.Emery@EBI.ac.uk www.ebi.ac.uk

  2. Part of the European Molecular Biology Laboratory International, non-profit research institute Europe’s hub for biological data, services and research What is EMBL-EBI?

  3. The European Molecular Biology Laboratory Hinxton, Cambridge Hamburg Heidelberg Bioinformatics Structural biology Basic research Administration EMBO Grenoble Monterotondo, Rome EMBL staff: 1500 people >60 nationalities Structural biology Mouse biology

  4. 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-EBI’s mission

  5. 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 EMBL member states

  6. Services Data and tools for molecular life science www.ebi.ac.uk/services

  7. What services do we provide? Labs around the world send us their data and we… …provide tools to help researchers use it A virtuouscircle Archive it Analyse it Classify it Share it with other data providers

  8. 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 • Molecular & cellular structure • Protein Data Bank in Europe • Electron Microscopy Data Bank • Reactions, interactions & pathways • IntAct • Reactome • Chemical biology • ChEBI • ChEMBL • Patent compounds • Cross-domain resources • Europe PubMed Central • Gene Ontology • Systems • BioModels • BioSamples Database • Enzyme Portal

  9. Where to start? use Firefox or Google Chrome Search here

  10. The EBI Search ServiceGene and protein summaries Explore the data and return easily to your results Species selector allows for easy comparison • Data organised by: • gene • expression • protein • structure • literature

  11. The EBI Search ServiceGene 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

  12. Accessing our services the services tab programmatic access

  13. 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

  14. Ensembl • Explore human, mouse and other chordate (and selected invertebrate) genomes Gene models Comparative data gene trees, homologues,alignments, synteny Browse a genomic region Sequences genomes, genes, transcripts, proteins Variation data short and structural variants, phenotypes Tools BLAST/BLAT sequence search, Variant Effect Predictor Regulatory data ENCODE Access: website, BioMart, Perl and REST API www.ensembl.org

  15. Ensembl Genomes • Explore genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoan Variation data for plant, metazoan and fungal species Genome portals for the five kingdoms of life Pan-taxonomic comparative analysis Multi-way comparison of whole bacterial chromosomes Access: website, BioMart, Perl and REST API www.ensemblgenomes.org

  16. ArrayExpress • Archive of functional genomics data – RNA-Seq, ChIP-Seq and array-based technologies • MIAME- and MINSEQE- standard compliant Expand results Search experiments Apply filters to refine a search Read descriptions of sample properties www.ebi.ac.uk/arrayexpress

  17. 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

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

  19. 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

  20. 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

  21. 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 Deskwww.ebi.ac.uk/support/

  22. Research Data-driven discovery PhD and postdoctoral programmes www.ebi.ac.uk/research

  23. Research themes • Genomes • Nick Goldman • Ewan Birney • Paul Flicek • Chemical biology • Christoph Steinbeck • John Overington • Transcriptomes • Anton Enright • John Marioni • Oliver Stegle • AlvisBrazma • Pathways & systems • Paul Bertone • Julio Saez-Rodriguez • Sarah Teichmann • Proteins & structures • Janet Thornton • Pedro Beltrao • Alex Bateman • Gerard Kleywegt

  24. 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

  25. 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

  26. User training For scientists working at all levels www.ebi.ac.uk/training

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

  28. 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

  29. EMBL member states The European Commission The Wellcome Trust Research Councils UK US National Institutes of Health With thanks to our funders

  30. Thank you! www.ebi.ac.uk Twitter: @emblebi Facebook: EMBLEBI YouTube: EMBLMedia

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