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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

WP10 Status Report

Vincent Breton (WP10 manager)


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