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Enabling Grids for E-sciencE Grid added value to fight malaria Vincent Breton EGEE Application identification and support activity manager CNRS, France [email protected] www.eu-egee.org INFSO-RI-508833 V. Breton, 30/08/05, seminar at SERONO Goals Enabling Grids for E-sciencE • Speed-up the development and deployment of new drugs and vaccines – Improve collection of epidemiological data for research (modeling, molecular biology) – Improve the deployment of clinical trials on plagued areas • Improve disease monitoring – Monitor the impact of policies and programs – Collect data on drug delivery and vector control – Improve epidemics warning and monitoring system • Strengthen the integration of african life science research laboratories in the world community – Access to resources – Access to bioinformatics services INFSO-RI-508833 V. Breton, 30/8/05 2 What is the Grid? Enabling Grids for E-sciencE • The World Wide Web provides seamless access to information that is stored in many millions of different geographical locations • In contrast, the Grid is a new computing infrastructure which provides seamless access to computing power, data and other resources distributed over the globe • The name Grid is chosen by analogy with the electric power grid: plug-in to computing power without worrying where it comes from, like a toaster INFSO-RI-508833 V. Breton, 30/8/05 3 How does the grid work? Enabling Grids for E-sciencE • The Grid relies on advanced software, called middleware, which ensures seamless communication between different computers and different parts of the world • The Grid search engine not only finds the data the scientist needs, but also the data processing techniques and the computing power to carry them out • It distributes the computing task to wherever in the world there is available capacity, and sends the result back to the scientist INFSO-RI-508833 V. Breton, 30/8/05 4 Grid impact on drug discovery workflow down to drug delivery (1/2) Enabling Grids for E-sciencE • Grids provide the necessary tools and data to identify new biological targets – Bioinformatics services (database replication, workflow, ...) – Resources for CPU intensive tasks such as genomics comparative analysis, inverse docking, ... • Grids provide the resources to speed up lead discovery – Large scale in silico docking to identify potentially promising compounds – Molecular Dynamics computations to refine virtual screening and further assess selected compounds INFSO-RI-508833 V. Breton, 30/8/05 5 Grid impact on drug discovery workflow down to drug delivery (2/2) Enabling Grids for E-sciencE • Grids provide environments for epidemiology – Federation of databases to collect data in endemic areas to study a disease and to evaluate impact of vaccine, vector control measures, – Resources for data analysis and mathematical modelling • Grids provide the services needed for clinical trials – Federation of database to collect data in the centers participating to the clinical trials • Grids provide the tools to monitor drug delivery – Federation of database to monitor drug delivery INFSO-RI-508833 V. Breton, 30/8/05 6 The challenges Enabling Grids for E-sciencE • Challenge in terms of infrastructure – Bandwidth is a prerequisite • Challenges in terms of technology – Grid technology must provide the services • Challenges in terms of human involvment – Research laboratories and hospitals must be willing to commit to the program and provide the needed information INFSO-RI-508833 V. Breton, 30/8/05 7 Grid for malaria, neglected disease of the developing world Enabling Grids for E-sciencE Underway: in silico virtual screening (EGEE, Bioinfogrid) SCAI Fraunhofer Clermont-Ferrand To be done: support to local centres in plagued areas (epidemiology, genomics research, clinical trials and vector control) Contacts established with: WHO, research institutes on tropical diseases, TATRC, Argonne, SDSC, SERONO, NOVARTIS, Hospitals in subsaharian Africa, ... Local research centres In plagued areas The grid impact : •Computing and storage resources for genomics research and in silico drug discovery •Federation of patient databases for clinical trials and epidemiology in developing countries •cross-organizational collaboration space to progress research work INFSO-RI-508833 V. Breton, 30/8/05 8 The first step : Wide In Silico Docking On Malaria Enabling Grids for E-sciencE • Large scale in silico drug discovery initiative on malaria on EGEE infrastructure during the summer 2005 –Biological goal : Proposition of new inhibitors for a family of proteins produced by plasmodium falciparum – Biomedical informatics goal : Deployment of in silico virtual screening on the grid – Grid goal : Deployment of a CPU consuming application generating large data flows to test the grid infrastructure and services. • First numbers (http://wisdom.eu-egee.fr) –Total of about 46 million ligands docked –Equivalent to about 80 CPU years –Up to 1000 computers in 15 countries –Millions of files adding up to a few TB of data –Average crunching factor ~600 • Analysis under way INFSO-RI-508833 V. Breton, 30/8/05 9