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Bioinformatics & systems biology Pål Puntervoll

Bioinformatics & systems biology Pål Puntervoll. Outline. Bergen Center for Computational Science Computational Biology Unit Bioinformatics From sequence analysis to systems biology eSysbio – e-infrastructure for systems biology Software development; integration/work flows.

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Bioinformatics & systems biology Pål Puntervoll

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  1. Bioinformatics & systems biology PålPuntervoll

  2. Outline • Bergen Center for Computational Science • Computational Biology Unit • Bioinformatics • From sequence analysis to systems biology • eSysbio – e-infrastructure for systems biology • Software development; integration/work flows

  3. Department of UNIFOB AS • Four research units: • CBU – Computational Biology Unit • CMU – Computational Mathematics Unit • BCPL – Bergen Computational Physics Laboratory • Parallab – high performance computing laboratory • These groups share significant needs for: • Computational resources • Methods • Algorithms • Software • A main objective of BCCS: boost cross-disciplinary activity

  4. BCCS Administration Research director: Petter Bjørstad 4 staff members CBU CMU BCPL Parallab Leader: Researchers: Engineers: PostDocs: PhD students: Total staff: Inge Jonassen 8 3 2 12 25 Øyvind Thiem 5 2 2 9 Csaba Anderlik 1 2 2 5 Klaus Johannsen 4 5 2 11 BCCS: 55 employees

  5. Research groups: Inge Jonassen Pattern discovery in molecular biology data Nathalie Reuter Molecular modeling of proteins Boris Lenhard Transcription and transcriptional gene regulation Igor Berezovsky Protein stability and adaptation, protein-protein interactions, and evolution of protein function Rein Aasland Functional annotation of proteins and protein domains

  6. Service group: Services to Norwegian researchers: - molecular biology/biochemistry - biomedicine - microbiology Types of services: - consultancy/support - analysis - programming - online web tools Courses/work shops Pål Puntervoll leader Yvan Strahm service scientist Svenn Helge Grindhaug system engineer/programmer Alexandr Oltu system engineer

  7. The central dogma of molecular biology DNA Genes RNA Protein Molecular machines of the cell

  8. The central dogma of molecular biology DNA

  9. The central dogma of molecular biology …atg ggg ctc agc gac ggg gaa tgg cag ttg… ||| ||| ||| ||| ||| ||| ||| ||| ||| ||| …tac ccc gag tcg ctg ccc ctt acc gtc aac… DNA RNA …aug ggg cuc agc gac ggg gaa ugg cag uug… Protein M G L S D G E W Q L …

  10. Myoglobin < 90% identical

  11. 83% identical 89% similar

  12. 41% identical 62% similar

  13. DNA sequence databases GenBank EMBL DDBJ

  14. Growth of GenBank bases “… from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months.” year

  15. Data in GenBankDecember 2007 • More than 190 billion bases • More than 570 complete microbial genomes • 200 added in the last year • More than 190 eukaryotic genomes • With significant coverage • More than 260,000 named species • 1,700 new species per month

  16. Challenges in bioinformatics • Typical analysis involve many resources • Local tools and databases • Web tools and databases • No common data model for biological data • Some exceptions

  17. Stein, L., Nature. 2002 417(6885):119-120

  18. “EMBRACE is an EU-sponsored Network of Excellence aimed at enabling bioinformatics research through better operability of databases, servers, and services.”

  19. Taverna Workbench a free software tool for designing and executing workflows

  20. Workflow for identifying candidate human pathways from differentially expressed genes Paul Fisher http://www.myexperiment.org/workflows/143

  21. Metabolism map Metabolism: “the set of chemical reactions that occur in living organisms in order to maintain life” KEGG, http://www.genome.jp/kegg/atlas/

  22. DNA microarrays: differential gene expression

  23. Systems biology “Systems biology is the science of discovering, modelling, understanding and ultimately engineering at the molecular level the dynamic relationships between the biological molecules that define living organisms.” Leroy Hood, President Institute for Systems Biology

  24. eSysbioan e-science environment for systems biology “The key to performing excellent systems biology research is the ability to exploit all available sources of information, and to integrate existing knowledge with newly generated experimental data.” “To facilitate the interdisciplinary interaction … we propose to construct a collaborative virtual workspace … an integrated environment for entering, analysing and accessing data.”

  25. The buzzword slide • Web services • XML • WSDL • SOAP (XML messages) • Service-oriented architecture • GRID technology (distributed computing) • Semantic web

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