e-Infrastructures for e-Science: A Global View

In the last 10 years, a new way of doing science is spreading in the world thank to the development of virtual research communities across many geographic and administrative boundaries. A virtual research community is a widely dispersed group of researchers and associated scientific instruments working together in a common virtual environment. This new kind of scientific environment, usually addressed as a "collaboratory", is based on the availability of high-speed networks and broadband access, advanced virtual tools and Grid-middleware technologies which, altogether, are the elements of the e-Infrastructures. The European Commission has heavily invested in promoting this new way of collaboration among scientists funding several international projects with the aim of creating e-Infrastructures to enable the European Research Area and connect the European researchers with their colleagues based in Africa, Asia and Latin America. In this paper we describe the actual status of these e- Infrastructures and present a complete picture of the virtual research communities currently using them. Information on the scientific domains and on the applications supported are provided together with their geographic distribution

Large Scale In Silico Screening on Grid Infrastructures

Large-scale grid infrastructures for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale in silico docking within the framework of the WISDOM initiative against Malaria and Avian Flu requiring about 105 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large-scale grid infrastructures for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large-scale deployment.Comment: 14 pages, 2 figures, 2 tables, The Third International Life Science Grid Workshop, LSGrid 2006, Yokohama, Japan, 13-14 october 2006, to appear in the proceeding

WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures

<p>Abstract</p> <p>Background</p> <p>Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the <it>Plasmodium </it>parasite, some are promising targets to carry out rational drug discovery.</p> <p>Motivation</p> <p>Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase.</p> <p>Methods</p> <p>In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate <it>in silico </it>docking and in information technology to design and operate large scale grid infrastructures.</p> <p>Results</p> <p>On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, <it>In vitro </it>results are underway for all the targets against which screening is performed.</p> <p>Conclusion</p> <p>The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.</p

D19 final plan for using and disseminating knowledge

This document presents the Final Plan for Using and Disseminating Knowledge acquired throughout the development of the CYCLOPS project as deliverable D19. It includes a description of the main achievements in disseminating knowledge, and the consortium and each participant’s plans for the exploitation of the results for the consortium as a whole, or for individual participants or groups of participants. It updates the Plan for Using and Disseminating Knowledge that was presented as Deliverable D4 and describes the final dissemination plan of the CYCLOPS project. This deliverable provides a strategy aimed at addressing various target communities in order to achieve the project dissemination and exploitation goals. After an update of the dissemination instruments employed, the deliverable focuses on the description of the dissemination activities carried out. In addition to the normal dissemination and exploitation of the work through scientific journals and professional bodies, Civil Protection Community will be specifically targeted for dissemination of the CYCLOPS deliverables, and their future exploitation of the results. Other written deliverables focus on presenting dissemination activities in specific subject areas. In particular deliverable D17 reports “the results of the dissemination of EGEE towards the Civil Protection community, and about the coordination between the EGEE and CYCLOPS activities”, deliverable D18 focuses on “collecting the CYCLOPS project results for dissemination towards different interested audiences such as Grid communities, other Civil protection agencies, but also national and international initiative and projects, SMEs, etc.” and deliverable D20 that reports “the extent to which actors beyond the research community have been involved to help spread awareness and to explore the wider societal implications of the proposed work