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WP10 Status Report. Vincent Breton (WP10 manager) [email protected] 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

WP10 Status Report

Vincent Breton (WP10 manager)

[email protected]

Presentation address https://agenda.cern.ch/age?a021814

Wp10 initial goals
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)

Summary of wp10 status
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

Difficulties in addressing the key challenges
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


Successes addressing the key challenges
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

  • Status of wp10 applications

    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)

    Addressing the key challenges

    Phylogenetics (fastDNAm algorithm)

    Elapsed time (mn)


    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

    A major success in 2002 dissemination
    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

    The growing interest of the community
    The growing interest of the community …
















    Pending problems
    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

    Work program for 2003
    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