Presentation on theme: "The EMBL-European Bioinformatics Institute"— Presentation transcript:
1The EMBL-European Bioinformatics Institute The hub for bioinformatics in EuropeDr Laura Emery
2What is EMBL-EBI? Part of the European Molecular Biology Laboratory International, non-profit research instituteEurope’s hub for biological data, services and researchThe EBI is based on the Wellcome Trust Genome Campus in Hinxton, which is near Cambridge in UK. The EBI is part of the European Molecular Biology Laboratory and as part of that, we’re a non-profit organisation.
3The European Molecular Biology Laboratory HeidelbergBasic researchAdministrationEMBOHamburgStructural biologyHinxton, CambridgeBioinformaticsGrenobleStructural biologyMonterotondo, RomeMouse biologyEMBL staff:1500 people>60 nationalitiesWe’re the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome, and bioinformatics in Hinxton. There are around 1,500 staff within EMBL and about 520 of those work at the EBI.
4EMBL-EBI’s missionProvide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progressContribute to the advancement of biology through basic investigator-driven research in bioinformaticsProvide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigatorsHelp disseminate cutting-edge technologies to industryCoordinate biological data provision throughout EuropeThe EBI is at the centre of Europe’s efforts to collect, organise and make available all types biological dataWe do this by providing services so researchers can access and make sense of the information, by being active in bioinformatics research, by providing training and by working closely with industry.
5EMBL member statesAustria, 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: AustraliaWe’re the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome, and bioinformatics in Hinxton. There are around 1,500 staff within EMBL and about 520 of those work at the EBI.
6Data and tools for molecular life science ServicesData and tools for molecular life science
7What services do we provide? Labs around the world send us their data and we……provide tools to help researchers use itA virtuous circleArchive itAnalyse itClassify itShare it with other data providers
8Data resources at EMBL-EBI Genes, genomes & variationEuropean Nucleotide Archive (ENA)EBI MetagenomicsEnsemblEnsembl GenomesEuropean Genome– phenome ArchiveNon-redundant patent sequence databasesProteinsUniProt: the Universal Protein ResourceInterProPfamExpressionArrayExpressExpression AtlasMetaboLightsPRIDEMolecular & cellular structureProtein Data Bank in EuropeElectron Microscopy Data BankChemical biologyChEBIChEMBLPatent compoundsReactions, interactions & pathwaysIntActReactomeThe slide shows the core resources at the EBI to show the range of data you can access through the EBI.Cross-domain resourcesEurope PubMed CentralGene OntologySystemsBioModelsBioSamples DatabaseEnzyme Portal
9use Firefox or Google Chrome Where to start?use Firefox or Google ChromeSearch here
10The EBI Search Service Gene and protein summaries Explore the data and return easily toyour resultsSpecies selector allows for easy comparisonData organised by:geneexpressionproteinstructureliteratureThe EBI has a new, ‘biologically aware’ search service that we developed in response to the needs of our bench-biologist users. Our intuitive, ‘biologically aware’ search service provides a huge simplification for users exploring the data. For example, if you enter p53 in the search box, you are most likely looking for the (human) p53 gene, rather than the gene encoding a p53-binding protein or a p53-like protein; the new search engine takes this into account, and ranks the results accordingly.From an uncluttered results 'dashboard', you can explore genes, protein sequences, gene expression, molecular structures and the scientific literature. You can still delve into the individual databases and the original experimental data, but can return easily to the results summary. A species selector allows you to compare key information for human, mouse, fly and other species, and the literature results include links to free full-text articles.
11The EBI Search Service Gene and protein summaries Species selector allows for easy comparisonData organised by:geneexpressionproteinstructureliteratureThe EBI has a new, ‘biologically aware’ search service that we developed in response to the needs of our bench-biologist users. Our intuitive, ‘biologically aware’ search service provides a huge simplification for users exploring the data. For example, if you enter p53 in the search box, you are most likely looking for the (human) p53 gene, rather than the gene encoding a p53-binding protein or a p53-like protein; the new search engine takes this into account, and ranks the results accordingly.From an uncluttered results 'dashboard', you can explore genes, protein sequences, gene expression, molecular structures and the scientific literature. You can still delve into the individual databases and the original experimental data, but can return easily to the results summary. A species selector allows you to compare key information for human, mouse, fly and other species, and the literature results include links to free full-text articles.Explore the data and return easily toyour results
12Accessing our services the services tabprogrammatic access
13European Nucleotide Archive Comprehensive catalogue of nucleotide sequence dataCovers raw reads, sequence assembly and functional dataSearch for DNA sequenceLocate gene sequencesSubmit data to the archiveENA is part of the International Nucleotide Sequence Database Collaboration (INSDC). Comprised of EMBL-Bank, the Short Read Archive (SRA) and the Trace Archive, ENA containsDownload FASTA files for chosen sequences
14Browse a genomic region EnsemblExplore human, mouse and other chordate (and selected invertebrate) genomesGene modelsComparative datagene trees, homologues, alignments, syntenyBrowse a genomic regionSequencesgenomes, genes, transcripts, proteinsEnsembl provides a framework for working with the genomes of higher animals (metazoans).It presents, via an interactive website, the human genome together with other genomes that are important for addressing questions in medical research and molecular biology.It uses automated methods for gene prediction and annotation to provide a consistent view of completely sequenced genomes.Users can view the data at many levels, from entire chromosomes down to single nucleotide polymorphisms.As well as accessing a wealth of data for each species, users can also perform cross-species comparisons.Variation datashort and structural variants, phenotypesToolsBLAST/BLAT sequence search,Variant Effect PredictorRegulatory dataENCODEAccess: website, BioMart, Perl and REST API
15Ensembl GenomesExplore genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoanVariation data for plant, metazoan and fungal speciesGenome portals for the five kingdoms of lifePan-taxonomic comparative analysisMulti-way comparison of whole bacterial chromosomesEnsembl Genomes is the combined repository for non-vertebrate genome data, consisting of five resources: Ensembl Bacteria, Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, and Ensembl Protists, bringing the power of the Ensembl system to all branches of life.Ensembl Genomes re-uses and extends software developed for vertebrate genomes in the context of the Ensembl project, and replaces several pre-existing resources (Genome Reviews and ASTD) thereby unifying services and simplifying data access for users.Access: website, BioMart, Perl and REST API
16ArrayExpressArchive of functional genomics data – RNA-Seq, ChIP- Seq and array-based technologiesMIAME- and MINSEQE- standard compliantSearch experimentsExpand resultsApply filters to refine a searchArrayExpress is the world’s first and largest MIAME-compliant repository for microarray-based data (mostly gene expression data, but it also takes CGH and chip-chIP data). You can search the repository to view and download experiments; a subset of the data in the repository is hand-picked for the Data Warehouse, which can be searched on the basis of gene names and allows you to view gene expression data for different time points or experimental conditions.Read descriptions of sample properties
17Expression Atlas A curated subset of the ArrayExpress data Search for gene expression changes under different biological/experimental conditions.Gene pageSearch by gene, organism and/or biological conditionContains and analysed subsets of the array express dataIt has been analysed to report differential expression genesCurrent expression Atlas reports relative expression levelsThe new baseline Atlas is only based on RNA-seq data and reports absolute expression levelYou can search for a gene, and then you'll see a heat maps to show whether it's under expressed or overexpressed in each of the different conditions listed horizontallyArrayExpress is the world’s first and largest MIAME-compliant repository for microarray-based data (mostly gene expression data, but it also takes CGH and ChIP-ChIP data). You can search the repository to view and download experiments; a subset of the data in the repository is hand-picked for the Data Warehouse, which can be searched on the basis of gene names and allows you to view gene expression data for different time points or experimental conditions.Baseline Atlas Prototype
18Bioinformatics tools Over 100 analysis tools Results enriched with data from EBI resourcesNucleotide sequence searche.g. BLAST nucleotideProtein sequence searche.g. BLAST protein, PSI-SearchMultiple sequence alignmente.g. Clustal Omega, MUSCLEPairwise sequence alignmente.g. NeedleProtein functional analysise.g. InterProScanFunctional genomics toolse.g. Expression AtlasMolecular structure analysise.g. PDBeFoldText mininge.g. EBIMed, WhatizitAs well as providing data itself at EMBL-EBI, we also enable you to analyse your own data using our resources and data collections.The wide-ranging tools are developed internally, externally and by collaboration with leading authors. They are incorporated into our web framework to allow a consistent user experience, access to the latest data and to leverage cross-resource information, for example automatically annotating aligned regions of a BLAST protein search with domain and motif information.Sequence similarity searching:Central to genome annotationCharacterising protein familiesExploring distant evolutionary relationships
19Navigating the EBI EBI resources are linked to one another Allows you to move to other relevant informationGain a greater overview of biological applications
20Programmatic access: EBI Web Services Run tasks on EBI servers, using EBI dataIdeal for large scale analyses, repetitive tasks and internal pipelinesIntegration of EBI resources and dataEBI Search, tools, data retrievalSame programs, data and results enrichment as running via the web pagesWeb Services combines the flexibility of command-line access and scripting with access to our powerful compute and data resources, so you don’t have to worry about maintaining local software or data, you run the latest versions directly on our servers.Since its introduction, Web Services has become extremely popular: for each job submitted via the web pages more than five times as many jobs are submitted via Web Services.They’re ideal for all sorts of tasks – large scale analyses, repetitive tasks, internal pipelines, engines behind your own program or web page front end.
21Getting 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 OnlineRead resource documentationContact EBI Help Desk
22Data-driven discovery PhD and postdoctoral programmes ResearchData-driven discoveryPhD and postdoctoral programmes
23Research themes Genomes Chemical biology Transcriptomes Nick GoldmanEwan BirneyPaul FlicekChemical biologyChristoph SteinbeckJohn OveringtonTranscriptomesAnton EnrightJohn MarioniOliver StegleAlvis BrazmaPathways & systemsPaul BertoneJulio Saez-RodriguezSarah TeichmannHere are the research groups at the EBI.The groups are mapped onto an arrow to demonstrate that our research spans the central dogma of biology - from nucleotides and small RNAs through to genome-scale analysis of regulatory systems.In the next talk by Anton Enright, you’ll get a more in-depth look at research at the EBIProteins & structuresJanet ThorntonPedro BeltraoAlex BatemanGerard Kleywegt
24Research at EMBL-EBI Protein targets for new drugs Molecular basis of ageingNeurons in Parkinson’s diseaseStem cell differentiationCancer genome structureDNA data storage
25PhDs and PostdocsEMBL International PhD programme:Postdoctoral positions available from:Postdoctoral fellowships:EIPOD EMBL sponsored: interdisciplinaryESPOD EBI–Sanger: combined experimental/computationalPhDs: Visit EMBL Heidelberg for 3 months for the core course: to learn about research in molecular biology and to become familiar with EMBL culture (great way to meet other predocs, as we call them). A mixture of lectures, interactive seminars and hands-on rotations through multiple laboratories at EMBL.All EBI PhD students are part of the EMBL programme and receive their PhDs from Cambridge.Active calendar of events, including informal student seminars, visiting speakers, courses, workshops, and of course, social events.Postdocs are advertised on the jobs pages. We also have two formal fellowship programmes:1) EIPODs (the EMBL Interdisciplinary Postdoctoral programme) brings together scientific fields that are usually separate or transfer techniques to a novel context.Each project will have one scientific supervisor who will officially host the EIPOD, but all projects will involve extensive collaboration with the partner labs.Design and propose your project or select from a list of pre-designed projects.2) ESPOD (EBI-Sanger postdoctoral) programme. This builds on our strong collaborative relationships between the two institutions and provides the opportunity to combine experimental and computational approaches. Projects may be selected from predefined areas or proposed by the applicant. Each fellowship will last three years and there will be two such fellowships this year.
26For scientists working at all levels User trainingFor scientists working at all levels
27Bioinformatics training Train at EMBL-EBIGain hands-on experience in our state-of-the-art facilities.Train at your placeChoose the training that’s right for you and your colleagues - and our experts will come to you.Train onlineLearn in your own time, at your own pace with our freely available online courses.
28Train online www.ebi.ac.uk/training/online Free online courses Learn in your own time, at your own paceCreated for life-science researchersNo previous knowledge of bioinformatics needed
29With thanks to our funders EMBL member statesThe European CommissionThe Wellcome TrustResearch Councils UKUS National Institutes of Health