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WP10 Status Report

WP10 Status Report. Vincent Breton (WP10 manager) breton@clermont.in2p3.fr Presentation address https://agenda.cern.ch/age?a021814. WP10 Initial goals. Make a list of requirements for biomedical grids (Task 10.1 ending PM6)

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WP10 Status Report

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  1. WP10 Status Report Vincent Breton (WP10 manager) breton@clermont.in2p3.fr Presentation address https://agenda.cern.ch/age?a021814

  2. WP10 Initial goals • Make a list of requirements for biomedical grids (Task 10.1 ending PM6) • Identify and characterize a first biomedical application to deploy on DataGrid testbed (Task 10.2 ending PM12) • Deploy this first application on DataGrid testbed2 (Task 10.3 ending PM24) and testbed3 (Task 10.4 ending PM 36)

  3. Summary of WP10 status • Key achievements • We have shown the relevance of the grid concept for biomedical applications (see demo) • We have established a fruitful dialog with • Biology and medical imaging (25 laboratories involved) • The other applications and middleware work packages of DataGrid • The group has found cohesion and coherence despite the various backgrounds of the actors (biologists, computer scientists, physicists) • Key challenges for the lifetime of the DataGrid project • Deploy a true biomedical testbed involving genomics, bio-informatics and medical imaging laboratories • Run the applications described in D10.2 to demonstrate the use of a grid in genomics and medical imaging

  4. Difficulties in addressing the key challenges • Delay in testbed1 release (Aug. 2002) • Complexity of deployment of a biomedical testbed • Scalability/Robustness problems on testbed1 • Replica Manager scalability issues • Scalability issues when stressing the Res. Broker • Testbed instability related to info. service • Need to make a very large scale test this year • Competition for testbed resources - HEP applications are often the highest priority • Support for MPI-based job submission is vital for some applications • Programmable APIs to access middleware services • Support by the Storage Element for medical databases • Ports to RH7 and 8 needed Strong expectations on EDG 2.0 components

  5. Successes addressing the key challenges • Four groups able to deploy their applications on EDG testbed • Implementation of a web portal for phylogenetics • Comparison of genomes of parasite and bacteria • Management of medical images (see WP10’s demo tomorrow) • Search for primers • Interaction with the middleware packages • Feedback on our job submission problems • Discussion on metadata management (spitfire) • On-going discussion through the architecture group (ATF) on biomedical data integration and related security issues

  6. Applications deployed Applications tested on EDG Applications under preparation Status of WP10 applications • Bio-informatics • Phylogenetics : BBE Lyon (T. Sylvestre) • Search for primers : Centrale Paris (K. Kurata) • Statistical genetics : CNG Evry (N. Margetic) • Bio-informatics web portal : IBCP (C. Blanchet) • Parasitology : LBP Clermont, Univ B. Pascal (N. Jacq) • Data-mining on DNA chips : Karolinska (R. Médina, R. Martinez) • Geometrical protein comparison : Univ. Padova (C. Ferrari) • Medical imaging • MR image simulation : CREATIS (H. Benoit-Cattin) • Medical data and metadata management : CREATIS (J. Montagnat) • Mammographies analysis ERIC/Lyon 2 (S. Miguet, T. Tweed) • Simulation platform for PET/SPECT based on Geant4 : GATE collaboration (L. Maigne)

  7. Phylogenetics (fastDNAm algorithm) Elapsed time (mn) complexity Addressing the key challenges… • More successes… • More than 15 WP10 users trained • Several system administrators initiated to the installation procedure of a grid node • First evaluation of performance Credit : T. Silvestre BBE

  8. A major success in 2002 : dissemination • Active participation to the creation of the HealthGrid cluster of EC projects • CNRS, active co-organizer of the European HealthGrid conference (with CERN, EMBnet and the help of the European Community) in Lyon (January 2003). More than 200 participants. • Three demos shown at HealthGrid, more than 10 papers submitted (4 accepted) to workshops and conferences

  9. The growing interest of the community … Uppsala Stockholm (Karolinska) Hinxton(EBI) Moscow Dublin Evry(CNG) Lausanne(EPFL,SIB) CERN Kosice Padova Lyon Clermont Montpellier Madrid(CNB)

  10. Pending problems • No EDG nodes installed in biomedical laboratories • Delays in EDG 1.2 middleware releases • Middleware is RH6.2 based, RH7.3 happening now, no RH8 release yet foreseen • Complexity of the configuration, despite a tutorial for system engineers • User/site administration support is needed • WP10 human resources limited to 2 funded engineers • Need more synergy between the applications working groups • It is time to revive a cross-application workgroup

  11. Work program for 2003 • March 2003 : deliverable D10.3 « Report on the first bio-testbed release » • Production (large scale) test in phylogenetics • Deployment of all 7 applications described in D10.2. Applications still to be deployed : • data mining on DNA chips (MPI support needed) • GPSA : web portal for protein structure analysis (EDG interface) • MRI simulator (MPI support needed) • Installation of EDG nodes in biomedical laboratories • We must be able to deploy and maintain our own production platform • To make the community aware of the need for a computing infrastructure • First « WP10 » node expected at LPC Clermont-Ferrand

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