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Welcome to EMBL-EBI

Welcome to EMBL-EBI. Dr Laura Emery. Before we start…. Stand up How experienced are you in bioinformatics? Get to know each other by arranging yourselves in order of your confidence with bioinformatics including using linux and R. Most bioinformatics experience.

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Welcome to EMBL-EBI

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  1. Welcome to EMBL-EBI Dr Laura Emery

  2. Before we start… • Stand up • How experienced are you in bioinformatics? • Get to know each other by arranging yourselves in order of your confidence with bioinformatics including using linux and R Most bioinformatics experience Least bioinformatics experience

  3. Welcome to EMBL-EBI Useful information while you are here www.ebi.ac.uk

  4. Genome Campus

  5. EXIT Registration desk EXIT

  6. Welcome to EMBL-EBI • Contacts • Training Team – courses@ebi.ac.uk • Registration Desk – 8553 • Emergency – 3333

  7. EXIT Registration desk EXIT

  8. Fire Assembly: Car Park A

  9. Training room rules

  10. Computer workstation

  11. Logging on to your computer • Your computers should already be logged on • How to access the Penelope shared drive…

  12. Please remember… • The room opens at 8:45am each morning • Sign in at the registration desk each day • The room locks at 7:00pm each evening • Fire alarm test at 11:45am Wednesday morning

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

  14. 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?

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. ChEBI • Dictionary of small chemical compounds • Covers both products of nature and synthetic compounds Target search Wikipedia information Entity information View chemical structure ChEBI Ontology Viewer

  21. ChEMBL • Database of bioactive drug-like molecules • 2D structure, chemical properties, bioactivity Target search Browse targets Compound search www.ebi.ac.uk/chembl

  22. Reactome Compare events in different species Select a pathway Link to source databases Export pathway to your favouritemodelling software View reactions and events in detail www.reactome.org

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

  24. 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

  25. Getting help • EBI resources are vast and can be daunting Take a Quick Tour in Train Online Read resource documentation Contact EBI Help Deskwww.ebi.ac.uk/support/

  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. Expectations activity • What are your expectations of this course? • Think to yourself • Write your thoughts on post-it notes (one expectation per post-it) • Discuss these in small groups • Sort out your post-its to eliminate redundancy • Nominate a spokesperson to present to the rest of the group • Stick them on the whiteboards to the right of the room

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

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

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