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Structural Biology on the Grid

e-Infrastructure project Virtual Organization Virtual Research Community. Structural Biology on the Grid. Christophe Schmitz Bijvoet Center for Biomolecular Research Faculty of Science, Utrecht University The Netherlands c.p.f.schmitz@uu.nl. e-BioGrid Workshop 2011.

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Structural Biology on the Grid

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  1. e-Infrastructure project Virtual Organization Virtual Research Community Structural Biology on the Grid Christophe Schmitz Bijvoet Center for Biomolecular Research Faculty of Science, Utrecht University The Netherlands c.p.f.schmitz@uu.nl e-BioGrid Workshop 2011

  2. The scientific objectives

  3. The molecular machines and network of life

  4. Exploiting GRID resources in structural biology… NMR data collection and processing SAXS data analysis # Number of dimensions 2 # INAME 1 1H # INAME 2 1H 12 2.137 2.387 1 T 0.000e+00 0.00e+00 - 0 2756 2760 0 14 2.387 4.140 1 T 0.000e+00 0.00e+00 - 0 2760 2752 0 32 1.849 4.432 1 T 0.000e+00 0.00e+00 - 0 2259 2257 0 36 1.849 3.143 1 T 0.000e+00 0.00e+00 - 0 2259 2587 0 39 1.760 4.432 1 T 0.000e+00 0.00e+00 - 0 2260 2257 0 40 1.760 1.849 1 T 0.000e+00 0.00e+00 - 0 2260 2259 0 43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0 46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0 47 1.649 1.849 1 T 0.000e+00 0.00e+00 - 0 2583 2259 0 Data interpretation assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y ) ( resid 2 and name CA ) -0.1400 0.15000 assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y ) ( resid 3 and name CA ) -0.0100 0.15000 Computations • Structure, dynamics & interactions •  impact on research and health: • origin of disease • - design of new experiments • - drug design …

  5. The institute and the users

  6. The Institute Partner Institute BCBR Utrecht, The Netherlands BMRZ Frankfurt, Germany CIRMMP Florence, Italy INFN Padova, Italy RUN Nijmegen, The Netherlands UCAM Cambridge, United Kingdom EMBL Hamburg, Germany Alexandre Bonvin, WeNMR coordinator

  7. BCBR institute resources • LB • CREAM-CE • SITE-BDII • TOP-BDII • APEL • UI • SE • WMS • 22 NODES (8 CPUs each) + 4 NODES (16 CPUs) • 240 CPUs • 1.8 Tb of data Vitual Machines (XEN) with Glite 3.2

  8. The users Australia: 2 Brazil: 5 Canada: 2 China: 1 Germany: 48 France: 12 Italy: 59 Netherlands: 41 Turkey: 21 United Kingdom: 40 United States: 37 South Africa: 4 Today: 352 Users, growth ~ 10 users per month

  9. The users BCBR Utrecht, The Netherlands BMRZ Frankfurt, Germany CIRMMP Florence, Italy INFN Padova, Italy RUN Nijmegen, The Netherlands UCAM Cambridge, United Kingdom EMBL Hamburg, Germany Structural biologists http://www.wenmr.eu/wenmr/user-survey

  10. The software

  11. Software packages AMBER -> Molecular dynamics GROMACS -> Molecular Dynamics ROSETTA -> protein folding prediction CSROSETTA -> Structure Calculation CNS -> Structure Calculation XPLOR -> Structure calculation HADDOCK-> protein-protein docking + =

  12. The Web Portals

  13. Haddock web portal

  14. Software characteristics • CPU intensive • Possibly parallel jobs • Small internet transfer (except for software deployment) • Usually low I/O • Usually no storage required

  15. Typical use case 1. A scientific problem requires protein-protein docking calculation (HADDOCK) 2. User wants to use a GRID enabled software of our VO (HADDOCK) 3. User obtains a grid certificate 4. User joins enmr.eu VO 5. User registers for a software (HADDOCK) 7. User gets results Behind the scene 6. User provides calculation parameters

  16. Behind the scene: the grid

  17. Required resources Lots of CPUs! Short queues

  18. WeNMR platform operational and well used! • Largest global VO in the life sciences • Over 352 registered users from 38 nationalities, and growing • >33 000 CPUs • >700 (normalized) CPU years over the last 12 months • 1.4 million jobs over the last 12 months • 150Tb of storage space • ~20% of Life Sciences on the Grid • User-friendly access to e-Infrastructure via web portals

  19. Acknowledgments Prof. AlexandreBonvin (WeNMR coordinator) All the Bijvoet Center in Utrecht Utrecht University, Bijvoet Center for Biomolecular Research, NL Johann Wolfgang Goethe Universität Frankfurt a.M., Center for Biomolecular Magnetic Resonance DE University of Florence, Magnetic Resonance Center, IT Istituto Nazionale di Fisica Nucleare , Padova, IT Raboud University, Nijmegen, NL University of Cambridge UK European Molecular Biology Laboratory, Hamburg, DE Spronk NMR Consultancy, LT

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