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2007 CompTox Forum
Abstract - The National Biomedical Computation Resource: Computing Technology to Support Development of Computational Tissues
Wilfred W. Li, Ph.D.
Executive Director, NBCR
San Diego Supercomputer Center
University of California, San Diego
SDSC 351
9500 Gilman Drive (Mail Code: 0505), La Jolla, CA 92093-0505
Phone: 858-822-0974
E-mail: wilfred@sdsc.edu
Founded in 1994, the mission of the National Biomedical Computation Resource (NBCR) is to conduct, catalyze, and enable multiscale biomedical research by harnessing advanced computation and data cyberinfrastructure through multidiscipline and multi-institutional integrative research and development activities. The development of the cyberinfrastructure is driven by multiscale modeling applications, which focus on scientific research ranging in biological scale from the subatomic to molecular and cellular tissue to organ level. Application examples include: quantum mechanics modeling with the General Atomic and Molecular Electronic Structure System (GAMESS); calculation of protein electrostatic potentials with the Adaptive Poisson-Boltzmann Solver (APBS) and the finite element toolkit (FEtk); protein-ligand docking studies with AutoDock; cardiac systems biology and physiology modeling with Continuity; and molecular visualizations using the Python Molecular Viewer (PMV) and visual workflow programming in Vision. Real use cases are used to demonstrate how these multiscale applications may be made available transparently on the grid to researchers in the biomedicine and translational research arena through integrative projects including: the understanding of the detailed mechanism of action of human immunodeficiency virus (HIV) protease and integrase; neuromuscular junction research in myopathy; heart arrhythmia and failure; and, emerging public health threats, as well as through collaborative projects with other research teams across the world. The adoption of service oriented architecture enables us to develop highly reusable software components and provide an environment for transparent access to grid resources, at both national and international levels. NBCR Web site URL: http://nbcr.net.