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The hub for bioinformatics in Europe The EMBL-European Bioinformatics Institute Dr Laura Emery

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Presentation on theme: "The hub for bioinformatics in Europe The EMBL-European Bioinformatics Institute Dr Laura Emery"— Presentation transcript:

1 The hub for bioinformatics in Europe The EMBL-European Bioinformatics Institute Dr Laura Emery

2 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

3 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

4 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

5 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

6 Data and tools for molecular life science Services

7 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

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 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

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

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

11 The EBI Search Service Gene and protein summaries Data organised by: gene expression protein structure literature Data organised by: gene expression protein structure literature Species selector allows for easy comparison Explore the data and return easily to your results 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 Download FASTA files for chosen sequences Submit data to the archive

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

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

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

17 Expression Atlas A curated subset of the ArrayExpress data Search for gene expression changes under different biological/experimental conditions. Search by gene, organism and/or biological condition Gene page Baseline Atlas Prototype

18 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

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 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 Programmatic access: EBI Web Services

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 Desk

22 Data-driven discovery PhD and postdoctoral programmes Research

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

24 Research at EMBL-EBI Molecular basis of ageing Stem cell differentiation Cancer genome structure DNA data storage Neurons in Parkinson’s disease Protein targets for new drugs

25 PhDs and Postdocs EMBL International PhD programme: Postdoctoral positions available from: Postdoctoral fellowships: EIPOD EMBL sponsored: interdisciplinary ESPOD EBI–Sanger: combined experimental/computational

26 User 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.

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 e

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! Facebook: EMBLEBI YouTube: EMBLMedia


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