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 Least bioinformatics experience Most bioinformatics experience

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

4. Genome Campus

5. Registration desk EXIT

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

7. EXIT Registration desk

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

14. 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

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

16. 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

17. 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

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

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 Expression ArrayExpress Expression Atlas MetaboLights PRIDE Proteins UniProt: the Universal Protein Resource InterPro Pfam Chemical biology ChEBI ChEMBL Patent compounds Cross-domain resources Europe PubMed Central Gene Ontology Molecular & cellular structure Protein Data Bank in Europe Electron Microscopy Data Bank Reactions, interactions & pathways IntAct Reactome Systems BioModels BioSamples Database Enzyme Portal

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

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

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

23. Bioinformatics tools Over 100 analysis tools Results enriched with data from EBI resources Nucleotide sequence search e.g. BLAST nucleotide Protein sequence search e.g. BLAST protein, PSI-Search Multiple sequence alignment e.g. Clustal Omega, MUSCLE Pairwise sequence alignment e.g. Needle Protein functional analysis e.g. InterProScan Functional genomics tools e.g. Expression Atlas Molecular structure analysis e.g. PDBeFold Text mining e.g. EBIMed, Whatizit

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 Desk www.ebi.ac.uk/support/ www.ebi.ac.uk/support/

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

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

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