BioSimGrid: a distributed database for biomolecular simulations

Bing Wu, Kaishu Tai, Stuart Murdock, Muan Hong Ng, Steven Johnston, Hans Fangohr, Paul Jeffreys, Simon Cox, Jonathan Essex, Mark S. P. Sansom

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Biomolecular simulations provide data on the conformational dynamics and energetics of complex biomolecular systems. We aim to exploit the e-science infrastructure developing in the UK to enable large scale analysis of the results of such simulations. In particular, the BioSimGrid project (www.biosimgrid.org) will provide a generic database for comparative analysis of simulations of biomolecules of biological and pharmaceutical interest. In order to address the challenges of distributed computing on large amounts of simulation data the project is building an open software framework system based on OGSA (Open Grid Service Architecture) and OGSA-DAI (Open Grid Service Architecture Database Access and Integration). The system will have a service-oriented computing model using Grid-based Web service technology to deliver data analysis. Data mining services will be provided for the biomolecular simulation and structural biology communities. To address the security problem of the heterogeneous BioSimGrid environment, a Grid certificate-based and a user/pass based authentication mechanism will be integrated across the system. Furthermore, a distributed authorization and accounting mechanism is discussed to enhance the security.
Original languageEnglish
Title of host publicationProceedings of UK E-science All Hands Meeting, Nottingham 2-4 September 2003
Place of PublicationSwindon, UK
PublisherEngineering and Physical Sciences Research Council
ISBN (Print)1904425119, 9781904425113
Publication statusPublished - Sep 2003

Keywords

  • grid
  • biomolecular simulation
  • molecular dynamics
  • protein
  • ogsa
  • ogsa-dai
  • distributed database
  • web service
  • middleware
  • digital certificate

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