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Innovative Bioinformatics Applications in the Biomedical Field

Explore the diverse range of bioinformatics applications in the biomedical field, including pilot initiatives, internal projects, and external collaborations. Learn about cutting-edge tools and platforms enhancing healthcare research and practice.

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Innovative Bioinformatics Applications in the Biomedical Field

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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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