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EBI resources introductory course

EBI resources introductory course. Pablo Porras Millán pporras@ebi.ac.uk www.ebi.ac.uk. Schedule. The EMBL-European Bioinformatics Institute. The hub for bioinformatics in Europe. Part of the European Molecular Biology Laboratory International , non-profit research institute

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EBI resources introductory course

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  1. EBI resources introductory course Pablo Porras Millán pporras@ebi.ac.uk www.ebi.ac.uk

  2. Schedule

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

  4. 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?

  5. 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

  6. 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

  7. 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

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

  9. 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

  10. Bioinformatics underpins research Literature Genomes Protein sequence and proteomes Nucleotide sequence Protein structure Gene expression Protein families, domains and motifs Chemical entities Protein-protein interactions Systems Pathways

  11. Standards – international collaborations Genomics Standards Consortium (GSC) http://gensc.org Genome annotation www.geneontology.org Protein sequence www.uniprot.org Nucleotide sequence www.insdc.org HUPO- Proteomics Standards Initiative (PSI) www.psidev.info/ Protein structure www.wwpdb.org Functional Genomics Data Society www.fged.org Cheminformatics www.ebi.ac.uk/chebi Pathways www.reactome.org www.biopax.org Systems modelling standards www.sbml.org Metabolomics Standards Initiative (MSI) www.metabolomicssociety.org

  12. EMBL-EBI users: a one-day snapshot

  13. 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 (Switzerland) Wellcome Trust Sanger Institute (UK) Key facts about our services

  14. Data resources DNA & RNAgenes, genomes & variation Gene expressionRNA, protein & metabolite expression Proteinssequences, families & motifs Structuresmolecular & cellular structures Systemsreactions, interactions & Chemical biologychemogenomics & metabolomics Ontologiestaxonomies & controlled vocabularies LiteratureScientific publications & patents Other softwarecross-domain tools & resources pathways

  15. 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

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

  17. 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

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

  19. Research themes Proteins, structures & chemical biology Alex Bateman Gerard Kleywegt John Overington Christoph Steinbeck Sarah Teichmann Janet Thornton Genes & gene expression Paul Bertone Ewan Birney AlvisBrazma Anton Enright Paul Flicek Nick Goldman Systems biology Pedro Beltrao John Marioni Julio Saez-Rodriguez Oliver Stegle

  20. Research leaders Alvis Brazma Janet Thornton Sarah Teichmann Ewan Birney Paul Bertone Anton Enright Gerard Kleywegt PaulFlicek Julio Saez-Rodriguez Nick Goldman John Marioni JohnOverington Alex Bateman Oliver Stegle Pedro Beltrao ChristophSteinbeck

  21. Examples of EMBL-EBI research How do the neurons of someone with Parkinson’s disease signal differently from healthy neurons? What is the molecular basis of ageing? Which of these proteins will make good targets for drugs? Which of these changes to a genome’s structure drive cancer? What makes a stem cell decide to become skin or muscle?

  22. 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

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

  24. 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

  25. 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

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

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

  28. AstellasPharma Inc. AstraZeneca Bayer Pharma AG BoehringerIngelheim Bristol-Meyers-Squibb Eli Lilly and Company F. Hoffmann-La Roche GlaxoSmithKline Johnson & Johnson Pharmaceutical R&D Merck Serono S.A. Nestlé Institute of Health Sciences Novartis Pharma AG Novo Nordisk Syngenta Sanofi-Aventis Recherche & Développement UCB Unilever Industry Programme members

  29. EMBL member states The European Commission The Wellcome Trust Research Councils UK US National Institutes of Health With thanks to our funders • Supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement for Affinomics(FP7-241481).

  30. A brief introduction to standards and data integration

  31. Lazebnik, Biochemistry (Mosc). 2004, PMID: 15627398

  32. Really Important Component Undoubtedly Most Important Component Most Important Component Serendipitiously Recovered Component

  33. The biologist’s model A model that reflects reality

  34. Standards Images from: http://archive.nrc-cnrc.gc.ca/eng/projects/inms/mass.html http://commons.wikimedia.org/wiki/File:Ce-logo.jpg http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/FastaFormat

  35. Standards in bioinformatics • Common identifiers • Controlled vocabularies / ontologies • Common formats • Common schemas • Minimum information guidelines • Common query interfaces Control vocabulary Schema Identifiers Format Reporting guideline Data distribution

  36. DB DB DB DB DB The problem of data integration Reality Ideally I I I I I I Interface Database User

  37. Utility of Bioinformatics Scientific impact Too little bioinformatics Too many databases Too diverse interfaces Tim Hubbard

  38. DB DB DB DB DB DB DB DB DB Data integration Combining data residing in different sources … providing users with a unified view of these data. Compromise Ideally Reality I I I I I SHARED CONTROLLED VOCABULARIES!! I Database I Interface User

  39. The danger with standards… From xkcd: http://xkcd.com/927/

  40. IntAct … InnateDB PRIDE … EMBL MINT GPMDB DIP Molecular interactions IMEx DDBJ Tranche NCBI PeptideAtlas Protein indentifications ProteomeXchange Nucleotide sequences INSDC Collaboration among data providers Access, exchange, sharing, portability, interoperability, annotation, comparison, verification, representation, integration, reusability. • More data coverage • Less redundancy • Less inconsistency • Better data management

  41. Example of community development of standards standards: PSI-MI http://www.psidev.info/MI • Work group of the Proteomics Standards Initiative • Community coordination to ensure deposition of Molecular Interaction data in public repositories • Concentrating on … • Annotation and representation of published MI data • Accessibility of MI data to the user community MIAPE Reporting guideline Control vocabulary Data format/schema PSI-MI CV MIMIx IMEx PSI-MI XML PSI-MITAB Data distribution Scoring PSICQUIC PSISCORE

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

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