The Virtual Laboratory Project

Enabling "Molecular Modelling for Drug Design" on the World Wide Grid

Introduction

The Virtual Laboratory project is engaged in research, design, and development of Grid technologies that help in solving large-scale compute and data intensive science applications in the area of molecular biology. The virtual laboratory environment provides software tools and resource brokers that facilitate large-scale molecular studies on geographically distributed computational and data grid resources. This helps in examining/screening millions of chemical compounds (molecules) in the Chemical Data Bank (CDB) to identify those having potential use in drug design.

Software

Molecular Modelling Tools (DOCK)
Parameter Modelling Tools (Nimrod/enFusion)
Grid Resource Broker (Nimrod-G)
Chemical Data Bank (CDB) Management and Intelligent Access Tools (souce code and binary code--Usage discription )

CDB databse Lookup/Index Table Generation.
CDB and associated index-table Replication.
CDB Replica Catalogue (that maintain record and status of CDB sites and their contents).
CDB Servers (that serve requests of CDB client).
CDB Brokering (Replica Selection).
CDB Clients for fetching Molecule Record (Data Movement).

Grid Middleware (Globus)

Computational Resources

World Wide Grid (WWG) testbed.

Steps for Docking on the Grid

Team Members

Kim Branson, Walter and Eliza Hall Institute of Medical Research (WEHI), Melbourne
Rajkumar Buyya, Monash University, Melbourne
All those involved in creating the software tools.

Publication

Rajkumar Buyya, The Virtual Laboratory Project, IEEE Distributed Systems Online, Vol. 2, No. 5, 2001.
Rajkumar Buyya, Kim Branson, Jon Giddy, and David Abramson, The Virtual Laboratory: A Toolset for Utilising the World-Wide Grid to Design Drugs, 2nd IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2002), 21 - 24 May 2002, Berlin, Germany.
Rajkumar Buyya, Kim Branson, Jon Giddy, and David Abramson, The Virtual Laboratory: Enabling Molecular Modelling for Drug Design on the World Wide Grid, Concurrency and Computation: Practice and Experience (CCPE) Journal, Volume 15, Issue 1, Pages: 1-25, Wiley Press, USA, January 2003.
Hussein Gibbins, Krishna Nadiminti, Brett Beeson, Rajesh Chhabra, Brian Smith, and Rajkumar Buyya, The Australian BioGrid Portal: Empowering the Molecular Docking Research Community, Proceedings of the 3rd APAC Conference and Exhibition on Advanced Computing, Grid Applications and eResearch (APAC 2005), Sept. 26-30, 2005, Gold Coast, Australia.

In News and Press!

Global Grid Forum Newsletter Summer 2001, May 2001.
Cluster Computing and the Grid (CCGrid 2001) Report, Asian Technology Information Program (ATIP), Tokyo, Japan, June 2001.
Technology Research News Mag. interview on the Virtual Laboratory project
Toolset teams computers to design drugs, Technology Research News (TRN), January 16, 2002.

Presentation/Exhibition

Molecular Modeling for Drug Design on P2P Grid, First IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2001), May 15-18, 2001, Brisbane, Australia.
DesignDrug@Home -- A Data Intensive Science on P2P Grid!
Virtual Laboratory: Data Intensive Science during Holiday @ Robinson Village in Italy!, First EuroGlobus Workshop, Robinson Club Apulia Village, Lecce, Italy, June 16-23, 2001. (html version.)
Nimrod-G and Virtual Lab Tools for Data Intensive Computing on Grid: Drug Design Application Case Study, BioGrid Computing Symposium 2001, 26 October 2001, Singapore. Via Teleconference with the Audio version of PPT slides and pure PPT slides.
The Virtual Laboratory: Enabling Molecular Modeling for Drug Design on the World Wide Grid, SuperBioGRID Computing Symposium 2001, National University of SingaporeSingapore, Dec. 10, 2001. Via Teleconference with the Audio version of PPT slides