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EGEE-2 NA4 Biomed Bioinformatics Applications

EGEE-2 NA4 Biomed Bioinformatics Applications. Christophe Blanchet Institute of Biology and Chemistry of Proteins Lyon, April 28, 2006. Outlines. Bioinformatics applications Pilot Internal External Bioinformatics requirements Defining priorities Next Step. EGEE Biomedical Activity.

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EGEE-2 NA4 Biomed Bioinformatics Applications

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  1. EGEE-2 NA4 BiomedBioinformatics Applications Christophe Blanchet Institute of Biology and Chemistry of Proteins Lyon, April 28, 2006

  2. Outlines • Bioinformatics applications • Pilot • Internal • External • Bioinformatics requirements • Defining priorities • Next Step EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  3. EGEE Biomedical Activity • Chair: • Johan Montagnat • Christophe Blanchet (deputy) • Biomedical activity area • Bioinformatics • Medical imaging • Other health related areas • Three types of application • Pilots: LCG-2 compliant applications at day 0 • Internal: from project partners, to be deployed on EGEE • External: from other projects, to go through a selection procedure • EGEE User Forum, CERN, March 1-3th, 2006http://egee-intranet.web.cern.ch/egee-intranet/User-Forum EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  4. Pilot Applications • There are 3 pilot applications on the EGEE grid platform, running since the beginning of the project (April 2004) • CDSS: Clinical Decision Support System • Contact: Ignacio Blanquer (iblanque@dsic.upv.es) • GATE: Geant4 Application for Tomographic Emission • Contact: Lydia Maigne (maigne@clermont.in2p3.fr) • GPS@: Bioinformatics grid portal • Contact: Christophe Blanchet (christophe.blanchet@ibcp.fr) EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  5. Internal Applications (1) • There are 9 internal applications on the EGEE grid platform, carried by the partners of the EGEE project • SiMRI 3D: Magnetic Resonance Image simulator • Contact: Hugues Benoit-Cattin • gPTM 3D: interactive radiological image visualization and processing tool • Contact: Cécile Germain-Renaud • xmipp_MLrefine: Macromolecular 3D structure analysis • Contact: Angel Merino • GridGRAMM: Molecular Docking web • Contacts: Jose R Valverde, David Garcia • GROCK: Mass screenings of molecular interactions web • Contacts: Jose R Valverde, David Garcia EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  6. Internal Applications (2) • Xmipp_assign_multiple_CTFs :  Micrographia CTF calculation • Contact: tbd • Pharmacokinetics: Contrast agent diffusion in abdominal MR Images • Contact: Ignacio Blanquer • Docking platform for tropical diseases: grid-enabled docking platform for in sillico drug discovery • Contact: Nicolas Jacq • Bronze Standard: Evaluation of medical image registration algorithms • Contact: Tristan Glatard EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  7. External Applications (1) • There are 8 external applications on the EGEE grid platform, carried by other Research Institutes or Projects, to go through a selection procedure by the EGEE project. • Join us: http://egee-na4.ct.infn.it/biomed/na4-biomed-questionnaire.html • SPLATCHE: genome evolution modeling • Contacts: Nicolas Ray, Laurent Excoffier • The Mammogrid project • Contact: Jose Galvez • Markov chain Monte Carlo simulations in phylogeny • Contact: Itay Mayrose • ByoDyn, a systems biology simulator • Contact: Jordi Villa • Large-scale pathway analysis • Contact: Ralf Herwig EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  8. External Applications (2) • MEX: motif extraction and protein classification • Contact: Vered Kunik • bioDCV: molecular oncology • Contact: Cesare Furlanello • Phylojava application: Phylogenetic analysis • Contact: Manolo Gouy EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  9. Bioinformatics Applications • Today, 9 bioinformatics applications in EGEE-2 • 1 pilot • 1 internal • 7 external ones !! • Collaboration • Critical point • Need involvement from these applications • AND FEEDBACK !! • It is mandatory to their participation ! • With biomed experts • Evaluation of the relevance about the grid aspect • With middleware experts • Training, operation, support EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  10. Plus … • 1. (…) EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  11. EU GRID Related EU projects ISSeG BEinGRID EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  12. Plus … • 1. Related EU Projects • 2. (…) EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  13. EMBRACE (EU FP6) • « A European Model for Bioinformatics Research and Community Education » • Objectifs: • simplify and standardize the way in which biological information is served to the researchers who use it. • Integrating biological data and bioinformatics tools in grid • Network of Excellence (20055-2010) • Feb 1st, 2005 • partners: EBI, EMBL, SIB, CNRS, INRA, Lion Bioscience, ... • Leaded by EBI • Funded by the European Union with the contract number LHSG-CT-2004-512092. EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  14. Bioinformatics Applications • Today, 9 bioinformatics applications in EGEE-2 • 1 pilot • 1 internal • 7 external ones !! • Plus: • 1 related EU project: Bioinfogrid • 1 Network of Excellence: EMBRACE • Collaboration • Critical point • Need involvement from these applications • AND FEEDBACK !! • It is mandatory to their participation ! • With biomed experts • With middleware experts • Training, operation, support EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  15. Challenge • Very different applications • Different requirements and priorities • Different resources involved • Hardware • Human • Different scientific communities adressed • But all are biologist • Don’t care of the « infra »-structure • But some common required services • Data • Deploying updatable databases • Security of medical or industrial data • Tools • Integrating small and numerous programs • Legacy programs • Portal as user interface • MPI • … EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  16. Plans • Working on requirements (TCG) • Each application has to fill the requirement matrix • Prioritizing the requirements • Deploy applications on the production platform • Training • Collaboration with ROC • Add new resources • Give strong FEEDBACK of GRID-ADDED value • Work on prioritary services post-poned at the project scale,proposed order of priority: • Deploying updatable databases • Deploying legacy programs with special I/O • Security of medical and industrial data • Deploying small and numerous programs • Portal as user interface • … • Give strong FEEDBACK of GRID-ADDED value to the Project ! EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

  17. Next • Next meeting of EGEE « bioinfo » • « Managing updatable databases on the grid » • Pisa, May 26, 2006 • Associated with EMBRACE NoE and Constanza dvlpers • Organisation: F. Donno, G. Pucciani • http://www.pi.infn.it/~pucciani/workshop/index.htm EGEE-2, Bioinformatics area, IBCP, Lyon, April 28th, 2006

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