V. Breton, Budapest, September 2002

WP10 status

V. Breton

DataGrid conference

V. Breton, Budapest, September 2002

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

V. Breton, Budapest, September 2002

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)

V. Breton, Budapest, September 2002

GATE, a PET/SPECT simulation platform

• Goal : dGoal : 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

V. Breton, Budapest, September 2002

GATE unique potentialities take advantage of GEANT4 toolkit and new developments

SCANNER DESCRIPTIONSCANNER DESCRIPTION Geometry

script (detectors, materials, …)

Properties spectral resolution…

RADIOACTIVE SOURCESRADIOACTIVE SOURCES Radioactive decay Digital images

complex emission and absorption cards

TIMETIME Physical dynamics : decay Biological dynamics : drug kinetics Movements

DYNAMICSDYNAMICS Detector continuous movement

rotation: SPECT, PET specific moves

Source movement patient (heart beat…) external source

USER FRIENDLYUSER FRIENDLY graphical interfacegraphical interface user guide, examplesuser guide, examples

V. Breton, Budapest, September 2002

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

V. Breton, Budapest, September 2002

The challenges of tomorrow

• Understanding the genome

• Integrating genetic data into medical records

• To reach individualized health care

Bioinformatics

Medical Imaging

Medicalinformatics

Public Health

Martin-Sanchez et al,MIM 41 (2002) 25-30

V. Breton, Budapest, September 2002

What could be individualized health care…

INDIVIDUALISED HEALTHCAREMOLECULAR MEDECINE

Databases

Association

Modelling

Computation

Computational recommandation

Patient related data

PublicHealth

Patient

Tissue, organ

Cell

Molecule

PublicHealth

Patient

Tissue, organ

Cell

Molecule

S. NoragerY. PaindaveineDG- INFSO

V. Breton, Budapest, September 2002

• 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

Toward individualized health care

V. Breton, Budapest, September 2002

EC vision of HealthGrid w.r.t. GridStart cluster

EUROGRID

DATAGRID

DAMIEN

CROSSGRID

GRIDSTART

Only health related GRID’s

Multidisciplinary GRID’s

GEMSS

HEALTHGRID CLUSTER

BIOGRID

MAMMOGRID

Public Health

Patient

Tissue, organ

Cell

Molecule

Public health informatics

Medical Informatics

Medical Imaging

Bio-informatics

Figure 1

ETC.

V. Breton, Budapest, September 2002

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

V. Breton, Budapest, September 2002

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

V. Breton, Budapest, September 2002

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

V. Breton, Budapest, September 2002

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