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WP10 status

WP10 status. V. Breton DataGrid conference. WP10 goals between now and the end of the year. Deploy the applications listed in deliverable D10.2 Test algorithms on a significant scale (several tens of CPU) to get biomedically meaningful results

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WP10 status

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  1. WP10 status V. Breton DataGrid conference

  2. WP10 goals between now and the end of the year • Deploy the applications listed in deliverable D10.2 • Test algorithms on a significant scale (several tens of CPU) to get biomedically meaningful results • Demonstrate the relevance of grids to handle biomedical data and metadata • Have DataGrid nodes in biomedical laboratories • Need for training of system engineers to install EDG in their lab • Write D10.3 deliverable describing our results on the testbed

  3. List of applications • Bio-informatics • Bio-informatics web portal : IBCP (C. Blanchet) • Parasitology : LBP Clermont (N. Jacq) • Phylogenetics : BBE Lyon (T. Sylvestre) • Search for primers : Centrale Paris (K. Kurata) • Statistical genetics : CNG Evry (N. Margetic) • Update and mirroring of genomics data bases : LPC Clermont (Y. Legrè) • Medical imaging • MR image simulation: CREATIS (H. Benoit-Cattin) • Medical data and metadata management : CREATIS (J. Montagnat) • Simulation platform for PET/SPECT based on Geant4 : GATE collaboration (L. Maigne)

  4. GATE, a PET/SPECT simulation platform • Goal : develop a generic simulation platform for nuclear medecine based on GEANT4 • Crystal Clear ClearPET project of a microPET for small animals imaging • Deploy CPU intensive simulations on a grid environment • 9 laboratories involved • From CC ClearPET : IPHE Lausanne (Spokesman : C. Morel), Univ. Bruxelles, Univ. Gent, CERMEP Lyon, Sungkyunkwan University and CHU Nantes (U463 INSERM) • Outside Crystal Clear : LPC Clermont-Fd, INSERM U494 Pitié-Salpêtrière, SHFJ Orsay

  5. SCANNER DESCRIPTION • Geometry • script (detectors, materials, …) • Properties • spectral resolution… • DYNAMICS • Detector continuous movement • rotation: SPECT, PET • specific moves • Source movement • patient (heart beat…) • external source • USER FRIENDLY • graphical interface • user guide, examples • RADIOACTIVE SOURCES • Radioactive decay • Digital images • complex emission and absorption cards • TIME • Physical dynamics : decay • Biological dynamics : drug kinetics • Movements GATE unique potentialities take advantage of GEANT4 toolkit and new developments

  6. Status of GATE gridification • Successful test of Geant4.4.0 execution on testbed1 at CC-IN2P3 (July 2002) • To be done • a web portal for GATE/GEANT4 simulations on DataGrid

  7. The challenges of tomorrow • Understanding the genome • Integrating genetic data into medical records • To reach individualized health care Bioinformatics Medical Imaging Medical informatics Public Health Martin-Sanchez et al, MIM 41 (2002) 25-30

  8. Patient related data PublicHealth Association Modelling Computation Databases PublicHealth Patient Patient Tissue, organ Tissue, organ Cell Cell Molecule Molecule INDIVIDUALISED HEALTHCARE MOLECULAR MEDECINE Computational recommandation What could be individualized health care… S. Norager Y. Paindaveine DG- INFSO

  9. Toward individualized health care • The bottlenecks • The complexity and diversity of life • Exponential growth of the volume of data coming from genomics and post-genomics • The lack of synergy between the scientific communities • Physicians legitimately focussed on improving daily practice • Biologists legitimately focussed on long term understanding • The steps toward individualized healthcare • Foster the synergy between bio-informatics and medical informatics • Provide the environment where medical and bio-informatics data can be stored and analyzed together

  10. Only health related GRID’s Multidisciplinary GRID’s HEALTHGRID CLUSTER Public Health Patient GEMSS Tissue, organ MAMMOGRID Cell Molecule BIOGRID DAMIEN ETC. GRIDSTART DATAGRID CROSSGRID EUROGRID Figure 1 Public health informatics Medical Informatics Medical Imaging Bio-informatics EC vision of HealthGrid w.r.t. GridStart cluster

  11. Calendar • September • Cluster meeting of the 5 health related grid projects approved in 2002 • DataGrid invited to present its experience in deploying biomedical applications on a grid • EC starts writing first calls for proposals • November • BioInfoMed white paper circulated • December • Open meeting on health grids in Brussels • Official call for proposal • In the mean time, healthgrid distribution list used to identify a community for an health grid

  12. WP10 concerns… • That quality becomes the reason why developments needed by WP9/WP10 are postponed beyond the end of the project. • That LHC data challenges saturate the testbed although we understand their importance

  13. Application Technical Working Group • Several discussions between application WPMs and technical coordination to refocus the ATWG on the common needs of all applications • Proposal is being circulated among the members of TWG HEP EO Bio Common applicative layer EDG software Globus

  14. Conclusion • WP10 is ready to deploy its applications and to get more strongly involved in ATWG • WP10 is willing to promote EDG middleware within the biomedical community … • New healthgrid cluster started by the EC • But we need your help for this task • Room for medium to large scale tests on testbed • Training and support for system administrators • Continuous interest for WP10 requirements

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