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

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.

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

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

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

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)

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.

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 : www.healthgrid.org Contacts : V. B., H-C Hoppe (Pallas), G. Lonsdale (NEC), R. McClatchy (UWE) First initiative : healthgrid conference in Lyon January 16th –17th 2003

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.

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

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)

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)

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)

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

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 …) .

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

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 …

Europe willing to play a major role in grid applications to life sciences Healthgrid cluster of EC projects (http://www.healthgrid.org) 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