Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria

PCSVInternational audienceComputational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required. The WISDOM project successfully deployed virtual screening at large scale on EGEE grid infrastructures in the summer 2005 and achieved 46 million dockings in 45 days, which is equivalent to 80 CPU years. WISDOM is one good example of a successful deployment of an embarrassingly parallel application. In this paper, we describe the improvements in our deployment. We screened ZINC database against four targets implicated in malaria. During more than 2 months and a half, we have achieved 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tool

Replication and update of molecular biology databases in a grid environment

PCSV, présenté par V. Breton, à paraître dans les proceedingsUpdate of molecular biology databases is a growing burden on the biomedical research community. As the grid allows to share and replicate data, we propose a service to automatically update the biology databases from a single changing reference using web services. In this paper we report the components, the architecture and the deployment of the update service on the french RUGBI grid infrastructure. RUGBI is a computing grid infrastructure based on existing middleware and technologies for the community of scientists in bioinformatics

Grid enabled high throughput virtual screening against four different targets implicated in malaria

PCSVInternational audienceAfter having deployed a first data challenge on malaria and a second one on avian flu, respectively in summer 2005 and spring 2006, we are demonstrating here again how efficiently the computational grids can be used to produce massive docking data at a high-throughput. During more than 2 months and a half, we have achieved at least 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tools; in this case it is the FlexX commercial docking software which is used to dock the whole ZINC database against 4 different targets

Les grilles pour le développement médical

PCSV, présenté par V. Breton, à paraître dans les Comptes-Rendu de la ConférenceLe développement récent des sciences et technologies de l'information et de la communication permet aujourd'hui la création de véritables infrastructures pour le calcul et le stockage de données hétérogènes à l'échelle régionale, nationale et internationale. Ces infrastructures, appelées grilles informatiques, permettront bientôt d'utiliser les ressources informatiques mutualisées avec autant de facilité que nous utilisons aujourd'hui l'électricité. L'utilisation des grilles afin d'accélérer la découverte de médicaments est une voie très prometteuse pour l'avenir. Par cette approche in silico, le nombre de molécules ainsi que la vitesse de test peuvent être grandement augmentés induisant un coût moindre de développement de médicaments. Du 11 Juillet au 31 Août 2005, l'expérience WISDOM (Wide In Silico Docking On Malaria) a permis de tester rien moins qu'un million de ligands (médicaments potentiels) pour le traitement du paludisme: 1700 ordinateurs à travers le monde ont ainsi été associés à cette démarche permettant de réaliser en un mois ce qui aurait nécessité 80 ans sur un ordinateur classique. L'analyse des résultats est en cours. Par cette approche, on peut souhaiter également que les maladies orphelines puissent bénéficier d'un intérêt nouveau de la part des industries pharmaceutiques, à travers notamment la baisse du coût de développement d'un médicament, principal obstacle actuellement à leur mobilisation

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

La grille au service du développement médical en Afrique

PCSV, présenté par F. Jacq, pas de proceedingsObjectives: Telemedicine networks allow to train local physicians and to improve diagnosis by exchanging medical data. But the set-up of multipoint dynamic telemedicine requires moving towards GRID technologies. The objective is to develop telemedicine services for physicians from Burkina Faso and France with the perspective of setting up a grid infrastructure between the participating medical sites. Methods: A web site to exchange diagnosis on diabetic retinopathy was developed in PHP. Another application using web services was developed to exchange patient information on ophthalmology between two databases. Results: The main difficulty comes from limited resources in developing countries including staff skills, bandwidth and funding. But the collaboration with dispensaries opened a door to enhanced collaboration between physicians of France and Burkina Faso Conclusions: These applications are designed with the aim of their use on grids which opens the perspective of multipoint dynamic telemedicine. We are developing a new generation of telemedicine service using experience acquired in the last two years

Grid-enabled high throughput in-silico screening against influenza A neuraminidase

PCSV, présenté par H.-C. Lee, à paraître dans les proceedingsEncouraged by the success of first EGEE biomedical data challenge against malaria[1], the second data challenge was kicked off in April, 2006, fighting against avian flu. In the paper, we demonstrated how to adopt a world-wide deployed Grid infrastructure to efficiently produce a large scale virtual screening to speed up the drug design process. The 6-weeks activity of molecular docking on the Grid has covered over 100 years of computing power required for discovering new drug for avian flu. Around 600 Gigabytes of output has also been produced and archived on the Grid for further biological analysis and test

Demonstration of In Silico docking at a large scale on grid infrastructure

présenté par N. Jac

g-INFO portal: a solution to monitor Influenza A on the Grid for non-grid users

International audienceIn this paper, we introduce a portal for monitoring Influenza A on a grid-based system. Influenza A keeps on being a major threat to public health worldwide; especially if one virus can mutate itself so that it acquires the capacity for human to human transmission of H1N1 as well as the high death rate of H5N1. The existing g-INFO (Grid-based Information Network for Flu Observation) project provides a complete system for monitoring flu virus on the Grid. We present here a portal that operates on top of the g-INFO system as a solution for non-grid users to utilize grid services for analyzing molecular biology data of Influenza A