1. INFSO-RI-508833 Enabling Grids for E-sciencE www.eu-egee.org V. Breton, 30/08/05, seminar at SERONO Grid added value to fight malaria Vincent Breton EGEE Application identification and support activity manager CNRS, France breton@clermont.in2p3.fr

2. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 2 Goals 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

3. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 3 What is the Grid? 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

4. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 4 How does the grid work? 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

5. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 5 Grid impact on drug discovery workflow down to drug delivery (1/2) 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

6. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 6 Grid impact on drug discovery workflow down to drug delivery (2/2) 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

7. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 7 The challenges 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

8. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 8 Underway: in silico virtual screening (EGEE, Bioinfogrid) Clermont-Ferrand 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 Grid for malaria, neglected disease of the developing world To be done: support to local centres in plagued areas (epidemiology, genomics research, clinical trials and vector control) SCAI Fraunhofer Local research centres In plagued areas Contacts established with: WHO, research institutes on tropical diseases, TATRC, Argonne, SDSC, SERONO, NOVARTIS, Hospitals in subsaharian Africa,...

9. Enabling Grids for E-sciencE INFSO-RI-508833 V. Breton, 30/8/05 9 The first step : Wide In Silico Docking On Malaria 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