1. Biomedical grid initiatives in Europe
V. Breton
GGF7 – Life Sciences Symposium
March 5th 2003

2. Issues to address in the talk
1.      Identify clear examples and the diverse use of the grid within the life science
2.      Identify how the grid is being challenged by the life sciences, and where there is need for activity
3.      Identify linkages to other research and working groups.

3. DataGrid, prototype of a biomedical grid
DataGrid is a european funded project
DataGrid has three ambitious goals :
Develop a middleware
Deploy a testbed
Have large scale applications running on this testbed
The biomedical work package faces three challenges
Make the middleware meet biomedical specific requirements
Run biomedical applications
Deploy grid nodes in biomedical laboratories

4. Biomedical technical requirements
Critical for development
Mid-term requirement
Long-term requirement
5. High priority jobs
privileged users
6. Interactivity
communication between user interface and CE’s
7. Parallelization
MPI site-wide / grid-wide
8. Pipeline processing
pipeline description language / scheduling
1. Large user community
anonymous/group login
2. Data management
data updates and data versioning
3. Security
disk / network encryption
4. Limited response time
fast queues

5. Analysis and design of biomedical data management grid services
Use cases
EDG Middleware Status
Remote processing of a data set
Available
Image registration
Available / Next release
A patient retrieves one of its images
Next release
A physician retrieves all medical files of a patient
Image search on public metadata
Automatic indexation of new images
Algorithm registration
Not planned
Automatic data parallelization
Pipeline processing
Interactive modeling
J. Montagnat CREATIS

6. Status of biomedical applications
Applications deployed
Applications tested on EDG
Applications under preparation
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. Laboratories involved in DataGrid biomedical activites …
Dublin
Hinxton(EBI)
Montpellier
Moscow
Kosice
Lyon
Uppsala
Stockholm
(Karolinska)
Madrid(CNB)
Clermont
Lausanne(EPFL,SIB)
CERN
Evry(CNG)
Padova
Saclay (CEA)
Laboratories testing EDG Middleware
Other labs.

8. The Health-Grid cluster
Gathers 8 grid-related, EC funded, health projects
The goals :
Share experience in deploying biomedical applications on grids
Identify specific middleware requirements for health
Address security and legal issues
Business model for an health grid
Dissemination
A web site :
Contacts : V. B., H-C Hoppe (Pallas), G. Lonsdale (NEC), R. McClatchy (UWE)
First initiative : healthgrid conference in Lyon January 16th –17th 2003

9. 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.

10. Health centered EU grid projects
GEMSS : a GRID enabled medical simulation system
MammoGRID : European federated mammogram database implemented on a GRID infrastructure
BioGRID : Development of an information and knowledge GRID for genomics and proteomics

11. GEMSS Project Objectives
Demonstrate that the Grid can improve pre-operative planning & near- real-time surgical support by providing access to advanced simulation and image-processing services
Build middleware on existing/developing Grid technology standards to provide support for authorisation, workflow, security and Quality of Service aspects
Develop, evaluate and validate a test-bed for the GEMSS system, including its deployment in the end-user’s working environment
Anticipate privacy, security and other legal concerns by examining and incorporating into its Grid services the latest laws and EU regulations related to providing medical services over the Internet.
Credit : Guy Lonsdale (NEC)

12. Advantages of the Grid-based Medical Service Approach
Medical community end-users are provided with advanced tools at their workplace through easy-to-use interfaces.
They do not need to acquire IT and/or engineering specialist know-how
Their Institute does not have to invest in (additional) computing resources and the related IT support facilities
The reliable, pervasive and interoperable Grid infrastructure can accommodate new services as they become available
Credit : Guy Lonsdale (NEC)

13. Mammogrid Epidemiology of breast cancer from a European perspective
Open source architecture
Use of Grid in developing quality control techniques for breast cancer screening
Development of some CADe techniques
Participants:
CERN & University of West of England - Grid infrastructure.
Mirada Solutions - Image analysis workstation and key technologies.
Universities of Pisa and Sassari - Image analysis algorithms
University Hospitals of Cambridge, Udine & Ospedale Valdese Torino - Clinical validation
University of Oxford – Grid-based quality control
Credit : Richard McClatchey (UWE)

14. The challenges of tomorrow…
Health grid
Patient
related data
PublicHealth
Patient
Tissue, organ
Cell
Molecule
Association
Modelling
Computation
Databases
PublicHealth
Patient
Tissue, organ
Cell
Molecule
S. Norager
Y. Paindaveine
DG- INFSO
INDIVIDUALISED HEALTHCARE
MOLECULAR MEDECINE
Computational
recommandation

15. The European Commission vision on grids for health Sofie Nørager, European Commission, Directorate General Information Society, eHealth Unit
Application of the existing GRID technology to health for both computing intensive applications and knowledge discovery.
to connect databases of heterogeneous content (biology and medicine) enabling new knowledge discovery (research, drug design), better guidance and information (healthcare professionals).
to increase computing power for imaging, simulation and modelling thus allowing these fields to take into account more data and therefore to provide more accurate results.
Development of new middleware and new applications required to meet specific request from the Health domain. (Ex. Security, heterogeneity of data …) .

16. Possible HealthGRID Applications
INTEROPERABILITY
eMOLECULE
Molecular biology databases - knowledge discovery
Molecular Medicine (e-Pharmacology)
eCELL
Pathway simulations, virtual cell - computing power
eINDIVIDUAL
Medical imaging
Combination of genetic and clinical data
ePOPULATION
Environmental Influences
Vision: Person-centered Healthcare

17. Grid applications require grid services
Middleware
First level applications :
Distributed computing,
Grid web portal,
Medical simulations
Basic grid services :
Resource Broker, Data replication,
Relational databases
Second level applications
Database mirroring,
Enhanced grid portals
Grid services :
Metadata management,
pipelining, interactivity,
security
Third level applications :
EPR,
bio-informatics platform
Mygrid,
BioGrid, …
DataGrid,
EuroGrid,
GEMSS,
Mammogrid,
Medigrid,
Gripps …

18. Europe willing to play a major role in grid applications to life sciences
Healthgrid cluster of EC projects (
Medical simulation on a grid (GEMSS)
Distributed database of mammograms (Mammogrid)
Knowledge grid for bio-informatics (BioGrid)
And also CrossGrid, DataGrid, Eurogrid and grid-related projects
Many biomedical grid projects in national initiatives
ACI Grid (GenoGrid, Gripps, Medigrid, GLOP,…)
UK e-science (Mygrid,eDiamond, …) …
Grid technology identified by EC as one of the key technologies for reaching individualized healthcare
Users communities willing to experiment the technology