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Introduction to bioinformatics
- 1. The EMBL-European Bioinformatics Institute Prepared by Chandan N Dipke Assistant Professor MGM’s College of CS & IT Nanded (MS) Email: cdipke@gmail.com
- 2. The science of storing, retrieving and analyzing large amounts of biological information An interdisciplinary science, involving biologists, computer scientists and mathematicians At the heart of modern biology 2 What is bioinformatics?
- 3. 3 Biology is changing • Data explosion • New types of data • High-throughput biology • Emphasis on systems, not reductionism • Growth of applied biology • molecular medicine • agriculture • food • environmental sciences… 0 2000 4000 6000 8000 10000 12000 Disks(TB) Year Growth of raw storage at EMBL-EBI (in terabytes)
- 4. What is EMBL-EBI? 4 • Bioinformatics research and services institute • Non-profit organization • www.ebi.ac.uk/embl and www.ebi.ac.uk • ~ 500 staff • Part of the European Molecular Biology Laboratory
- 5. • Bioinformatics research and services institute the resources of European Molecular Biology Laboratory (EMBL/EBI): divided into two categories – databases and tools or bio-software. EBI’s FTP server provides open access to downloadable databases and bio- software.
- 6. 6 New types of data Genomes Nucleotide sequence Gene expression Proteomes Protein families, domains and motifs Protein structure Protein-protein interactions Chemical entities Pathways Systems Literature Protein sequence
- 7. The five branches of EMBL Mouse biologyStructural biology Bioinformatics Hinxton Structural biology Hamburg • Basic research in molecular biology • Administration • EMBO Heidelberg • 1500 staff • >60 nationalities MonterotondoGrenoble
- 8. 8 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
- 9. 9 EMBL-EBI’s Mission • To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • To contribute to the advancement of biology through basic investigator-driven research in bioinformatics • To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • To help disseminate cutting-edge technologies to industry • To coordinate biological data provision across Europe
- 10. • The key goal of the EMBL nucleotide sequence database is to build, maintain and prepare biological database and other computational services to support data deposition and data analysis make them available to the scientific community. • EMBL-EBI is a huge warehouse of biological data and bio-software. Key Goal
- 11. 1 1 EMBL-EBI Cairns Pavilion (shared) Sanger Institute Sulston building Data centre Sanger labs / informatics The Wellcome Trust Genome Campus © John Freebury
- 12. European node for globally coordinated data collection and dissemination projects Core databases produced in collaboration with other world leaders, including NCBI (US), National Institute of Genetics (Japan), Swiss Institute of Bioinformatics, Cold Spring Harbor Laboratory (US) The world’s most comprehensive collection of molecular databases 12 Key facts about services
- 13. 1 3 Databases: molecules to systems Genomes Ensembl Ensembl Genomes EGA Nucleotide sequence ENA Functional genomics ArrayExpress Expression Atlas Protein Sequences UniProt Protein families, motifs and domains InterPro Macromolecular PDBe Protein activity IntAct , PRIDE Chemical entities ChEBI Pathways Reactome Systems BioModels BioSamples Literature and ontologies CiteXplore, GO Chemogenomics ChEMBL
- 15. 1 5 Standards development – international collaborations Genome annotation www.geneontology.org Functional Genomics Data Society www.fged.org Protein sequence www.uniprot.org HUPO- Proteomics Standards Initiative (PSI) www.psidev.info/ Protein structure www.wwpdb.org Cheminformatics www.ebi.ac.uk/chebi Pathways www.reactome.org www.biopax.org Systems modelling standards www.sbml.orgMetabolomics Standards Initiative (MSI) www.metabolomicssociety.org Genomics Standards Consortium (GSC) http://gensc.org Nucleotide sequence www.insdc.org
- 16. New search service Access from the EBI’s homepage Data organised according to: • gene • expression • protein • structure • literature Species selector allows for easy comparison Explore data, return easily to your results 1 6
- 17. Relevant to ‘wet-lab’ biologists Organises information based around a single gene (or a small number of genes) User-expectation centric (not database centric) Smooth transition to the detailed information in many of EBI’s core databases NOT for bioinformaticians: does not provide programmatic access 17 Goals of the new EBI Search
- 18. A unique environment for bioinformatics research Nine dedicated research groups Seven services teams also carry out R&D Research and services are mutually supportive Key facts about research at EMBL-EBI
- 19. 34 Research themes Genomes Nick Goldman Ewan Birney Paul Flicek Transcriptomes Anton Enright John Marioni Alvis Brazma Proteins Janet Thornton Rolf Apweiler Gerard Kleywegt Chemistry Christoph Steinbeck John Overington Pathways and systems Nicolas Le Novère Nick Luscombe Paul Bertone Julio Saez-Rodriguez Text mining Dietrich Rebholz-Schuhmann Service team leaders who also have research groups are in italics
- 20. Pre- and postdocs at EMBL-EBI • EMBL International PhD Programme • Postdoctoral fellowships: – EIPOD – EMBL-sponsored interdisciplinary fellowships – ESPOD – EBI–Sanger combined experimental and computational fellowships
- 22. REFERENCES http://www.ebi.ac.uk/Information/Brochures www.ebi.ac.uk/support www.ebi.ac.uk/help
- 23. THANK YOU