Biomedical subjects

Vincent Breton

Publications and source records attributed to Vincent Breton.

5 recordsLinked to original sources

PubMed2006

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.

Animals↗

PubMed2006

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

Encouraged by the success of the first EGEE biomedical data challenge against malaria (WISDOM), the second data challenge battling avian flu was kicked off in April 2006 to identify new drugs for the potential variants of the influenza A virus. Mobilizing thousands of CPUs on the Grid, the six-week-long high-throughput screening activity has fulfilled over 100 CPU years of computing power and produced around 600 gigabytes of results on the Grid for further biological analysis and testing. In the paper, we demonstrate the impact of a worldwide Grid infrastructure to efficiently deploy large-scale virtual screening to speed up the drug design process. Lessons learned through the data challenge activity are also discussed.

Binding Sites↗

PubMed2006

Demonstration of in silico docking at a large scale on grid infrastructure.

WISDOM stands for World-wide In Silico Docking On Malaria. First step toward enabling the in silico drug discovery pipeline on a grid infrastructure, this CPU consuming application generating large data flows was deployed successfully on EGEE, the largest grid infrastructure in the world, during the summer 2005. 46 million docking scores were computed in 6 weeks. The proposed demonstration presents the submission of in silico docking jobs at a large scale on the grid. The demonstration will use the new middleware stack gLite developed within the EGEE project.

Europe↗

PubMed2006

Proposing a roadmap for HealthGrids.

With the regular progress of technology and infrastructures, a growing number of grid applications are developed and deployed for life science and medical research. At the last HealthGrid conference in April 2005 in Oxford, many groups described successful usage of grids for compute intensive calculations. Very large scale deployment of a biomedical application in the area of drug discovery has been achieved on EGEE during 2005. On the other hand, beside a few pioneers, very few data grids have been deployed so far and knowledge grids are still at a conceptual level. This situation is expected to evolve quickly as many projects are focussed on developing data management services and knowledge management tools relevant to biomedical sciences. At this stage, it is important to identify the potential bottlenecks and to define a roadmap for the wide adoption of grids for healthcare. This article presents an analysis of the present adoption of grids for biomedical sciences and healthcare in Europe: it identifies bottlenecks and proposes actions that will be further assessed within the framework of the SHARE European project dedicated to the definition of a roadmap for HealthGrids.

Database Management Systems↗

PubMed2005

The Healthgrid White Paper.

Over the last four years, a community of researchers working on Grid and High Performance Computing technologies started discussing the barriers and opportunities that grid technologies must face and exploit for the development of health-related applications. This interest lead to the first Healthgrid conference, held in Lyon, France, on January 16th-17th, 2003, with the focus of creating increased awareness about the possibilities and advantages linked to the deployment of grid technologies in health, ultimately targeting the creation of a European/international grid infrastructure for health. The topics of this conference converged with the position of the eHealth division of the European Commission, whose mandate from the Lisbon Meeting was "To develop an intelligent environment that enables ubiquitous management of citizens' health status, and to assist health professionals in coping with some major challenges, risk management and the integration into clinical practice of advances in health knowledge." In this context "Health" involves not only clinical procedures but covers the whole range of information from molecular level (genetic and proteomic information) over cells and tissues, to the individual and finally the population level (social healthcare). Grid technology offers the opportunity to create a common working backbone for all different members of this large "health family" and will hopefully lead to an increased awareness and interoperability among disciplines. The first HealthGrid conference led to the creation of the Healthgrid association, a non-profit research association legally incorporated in France but formed from the broad community of European researchers and institutions sharing expertise in health grids. After the second Healthgrid conference, held in Clermont-Ferrand on January 29th-30th, 2004, the need for a "white paper" on the current status and prospective of health grids was raised. Over fifty experts from different areas of grid technologies, eHealth applications and the medical world were invited to contribute to the preparation of this document.

Computer Communication Networks↗