August 2006
Trends and Tools in Bioinformatics and Computational Biology
Wilfred W. Li, University of California, San Diego (UCSD), San Diego Supercomputer Center (SDSC)
Nathan Baker, Washington University in Saint Louis
Kim Baldridge, UCSD, SDSC
J. Andrew McCammon, UCSD
Mark H. Ellisman, UCSD, Center for Research In Biological Systems (CRBS)
Amarnath Gupta, UCSD, SDSC
Michael Holst, UCSD
Andrew D. McCulloch, UCSD
Anushka Michailova, UCSD
Phil Papadopoulos, UCSD, SDSC
Art Olson, The Scripps Research Institute (TSRI)
Michel Sanner, TSRI
Peter W. Arzberger, California Institute for Telecommunications and Information Technology (Calit2), CRBS, UCSD


Abstract — Begun 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. Here we report the more recent research and technology advances in building cyberinfrastructure for multiscale modeling 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, cellular, tissue to organ level. Application examples include quantum mechanics modeling with GAMESS, calculation of protein electrostatic potentials with 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 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 ranging from the understanding of the detailed mechanism of HIV protease and integrase action, to neuromuscular junction research in myopathy, to heart arrhythmia and failure, and to emerging public health threats, as well as through collaborative projects with other research teams across the world.

The adoption of service oriented architecture enables the development of highly reusable software components and efficiently leverages the international grid development activities. We describe an end to end prototype environment, exemplified by the adoption of key components of the Telescience project, that allows existing applications to run transparently on the grid, taking advantage of open source software that provides the following:

  • a portal interface using GridSphere,
  • transparent GSI authentication using GAMA,
  • a web service wrapper using Opal,
  • a metascheduler using CSF4,
  • a virtual filesystem using Gfarm, and
  • a grid-enabled cluster environment using Rocks.

Solutions to complex problems may be developed using workflow tools that coordinate different interoperable services. In addition, we also describe the development of ontology and semantic mediation tools such as Pathsys and OntoQuest for data integration and interoperability, which may be efficiently coupled with the application services provided to the biomedical community.

Pages: 1 2 3 4 5 6 7 8 9 10 11

Reference this article
Li, W. W., Baker, N., Baldridge, K., McCammon, J. A., Ellisman, M. H., Gupta, A., Holst, M., McCulloch, A. D., Michailova, A., Papadopoulos, P., Olson, A., Sanner, M., Arzberger P. W. "National Biomedical Computation Resource (NBCR): Developing End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research," CTWatch Quarterly, Volume 2, Number 3, August 2006. http://www.ctwatch.org/quarterly/articles/2006/08/national-biomedical-computation-resource/

Any opinions expressed on this site belong to their respective authors and are not necessarily shared by the sponsoring institutions or the National Science Foundation (NSF).

Any trademarks or trade names, registered or otherwise, that appear on this site are the property of their respective owners and, unless noted, do not represent endorsement by the editors, publishers, sponsoring institutions, the National Science Foundation, or any other member of the CTWatch team.

No guarantee is granted by CTWatch that information appearing in articles published by the Quarterly or appearing in the Blog is complete or accurate. Information on this site is not intended for commercial purposes.