• Lin, Shien-Fong (PI)
  • Bazan, J. (PI)
  • Knight, Jennifer (PI)
  • Karin, Sidney (PI)
  • Neira, Mauricio (PI)
  • Zvelebil, Marketa (PI)
  • Lagarias, John Clark (PI)
  • Hempel, John (PI)
  • Arzberger, Peter William (PI)
  • Bourne, Philip (PI)
  • Ellisman, Mark (PI)
  • Bailey, Timothy (PI)
  • Baldridge, Kim (PI)
  • Smith, Christopher (PI)
  • Henikoff, Steven (PI)
  • Bazan, J. (PI)
  • Knight, Jennifer (PI)
  • Neira, Mauricio (PI)
  • Zvelebil, Marketa (PI)
  • Lagarias, John Clark (PI)
  • Hempel, John (PI)
  • Selvin, Paul (PI)
  • McMorris, Trevor C. (PI)
  • Berman, Helen (PI)
  • Green, Doug (PI)
  • Sanner, Michel F. (PI)
  • Romesberg, Floyd (PI)
  • Gribskov, Michael (PI)
  • Olson, Arthur J. (PI)
  • Siegel, Jay (PI)
  • Xiang-Dong, Fu (PI)
  • Loomis, William (PI)
  • Fromm, Michael (PI)
  • Henikoff, Steven (PI)
  • Sudholt, Wibke (PI)
  • Miller, D. Craig (PI)
  • Efimov, Igor (PI)
  • Frank, Lawrence R. (PI)
  • Fredrickson, James (PI)
  • Greenough, William (PI)
  • Bassingthwaigthe, James B. (PI)
  • Spirou, George (PI)
  • Del Nido, Pedro J. (PI)
  • Taber, Larry (PI)
  • Sharpless, K. Barry (PI)
  • Ciscione, John (PI)
  • Perkins, Guy (PI)
  • Kohl, Peter (PI)
  • May-Newman, Karen (PI)
  • Pollard, Andrew Emil (PI)
  • Berg, Darwin (PI)
  • Rogers, Jack (PI)
  • Pevzner, Pavel (PI)
  • Bossy-Wetzel, Ella (PI)
  • Benson, Dennis (PI)
  • Houk, Kendall (PI)
  • Ahlquist, Paul G. (PI)
  • Ratcliffe, Mark (PI)
  • Shupliakov, Oleg (PI)
  • Reilly, Peter T.A. (PI)
  • Roberts, William (PI)
  • Wilson, Bridget (PI)
  • Smith, Christopher (PI)
  • Varani, Gabriele (PI)
  • Wickline, Samuel (PI)
  • Kobayashi, C. (PI)
  • Scherz, Avigdor (PI)
  • Baldridge, Kim (PI)
  • Remington, S. James (PI)
  • Chiu, W.A.H. (PI)
  • Paternostro, Giovanni (PI)
  • Ellisman, Mark (PI)
  • Trayanova, Natalia A. (PI)
  • Garfinkel, Alan (PI)
  • Bers, Donald (PI)
  • Wilson, Ian (PI)
  • Holmes, Jeffrey (PI)
  • Bailey, Timothy (PI)
  • McCammon, James (PI)
  • McCulloch, Andrew D. (PI)
  • Westbrook, John D. (PI)
  • Mesirov, Jill P. (PI)
  • Carragher, Bridget Olivia (PI)
  • Gupta, Amarnath (PI)
  • Green, Douglas (PI)
  • Martone, Mary (PI)
  • Aminesh, Ray (PI)
  • Eskin, Eleazar (PI)
  • Taylor, Palmer William (PI)
  • Li, Wilfred (PI)
  • Marshall, Frances (PI)
  • Janda, Kim (PI)
  • Wolynes, Peter G. (PI)
  • Raphael, Benjamin (PI)
  • Murdock, Stuart (PI)
  • Smarr, Larry L. (PI)
  • Wong, Chung (PI)
  • Jensen, Jan (PI)
  • Taylor, Susan (PI)
  • [No Value], Kathryn R. (PI)
  • Brooks, Charles (PI)
  • Omens, Jeffrey (PI)
  • Wong, Chi-Huey (PI)
  • Elder, John (PI)
  • Matsuzawa, Shu-Ichi (PI)
  • Vajragupta, O.P.A. (PI)
  • Tsien, Roger (PI)
  • Abramson, David (PI)
  • Narayan, Sanjiv (PI)
  • Sanner, Michel F. (PI)
  • Borg, Thomas (PI)
  • Cravatt, B.E.N. (PI)
  • Judith, Lin (PI)
  • Moraru, Ion I. (PI)
  • Loew, Leslie (PI)
  • Vaughan-Jones, Richard (PI)
  • Beutler, Bruce (PI)
  • Hirojima, Masahiko (PI)
  • Bajaj, Chandrajit (PI)
  • Kelley, Jennifer (PI)
  • Xiangyang, Wei (PI)
  • Wolynes, Peter (PI)
  • Johnson, John Emil (PI)
  • Sharpless, Karl Barry (PI)
  • Schnaufer, Achim (PI)
  • Sine, Steven (PI)
  • Vogt, Peter (PI)
  • Crouch, Rosalie (PI)
  • Janda, Kim D. (PI)
  • Berman, Helen (PI)
  • Sachse, Frank Bernd (PI)
  • Holst, Michael (PI)
  • Papadopoulos, Philip (PI)
  • Olson, Arthur J. (PI)
  • Markeffisman, [No Value] (PI)
  • Phillips, Andrew (PI)
  • Elkan, Charles (PI)
  • Case, David (PI)
  • Andzelm, J.A.N. (PI)
  • Zuker, Michael (PI)
  • Gribskov, Michael (PI)
  • Olson, Arthur J. (PI)
  • McCulloch, Andrew D. (PI)
  • Ten Eyck, Lynn F. (PI)

Project: Research project

Project Details


Major advances and an explosion of new information in the biomedical
sciences are in part the result of our ability to pose and solve questions
of biological structure and function at all levels and on all scales,
thanks to advanced computation. Today a host of critical problems depend
on large-scale computation and scientific visualization. The most advanced machines of the hour are massively parallel
supercomputers. We propose, therefore, to create an NIH National
Biomedical Computation Resource (NBCR) to accomplish three major purposes:
(1) to carry out important biomedical research programs that will benefit
from and can extend the new technologies for computation and
visualization, (2) to assemble a group of core programs that focus on
different scales of biological activity, with a thrust toward developing
ways of accessing interactions among and between scales, and (3) to use
those programs as drivers to make the new technologies friendly and
accessible to a larger community of biomedical researchers. NBCR will give biomedical researchers access to a 400-processor Intel
Paragon supercomputer at the San Diego Supercomputer Center (SDSC). SDSCs
broad program of research in parallel computing emphasizes the development
of operating systems, applications, and advanced visualization. Thus a
high level of support can be mobilized to aid scientists using the
parallel hardware for modeling, simulation, analysis, and visualization. Core and collaborative research at NBCR will address several important and
often closely related topics. The improvement of methods for calculating
density functional integrals will speed the process of obtaining
geometries and force fields for large molecules of biological interest and
will result in a DFT package on the Paragon for use by NBCR researchers.
The concurrent parallel implementation of the AMBER molecular dynamics
package will enable researchers to combine the virtues of quantum
mechanical and molecular dynamics programs. Improved methods of analyzing
patterns in protein sequences and structures will be developed for use in
genomic studies and modeling homologous protein structures. Visualization
packages will be developed as part of and in conjunction with these
programs. In addition, work will be carried out on the prediction of RNA
structure at kilobase lengths, sizes appropriate to studying gene
expression in RNA viruses (e.g., HIV), RNA processing, and phylogenetics;
and on finite-element modeling of the electromechanics of cardiac muscle,
as a paradigm computational tissue-function study. NBCR will fund a portion of the processor complement of the Paragon,
guaranteeing the allocation of a minimum of 140,000 processor hours
annually to NBCR researchers. Enhancements to the capabilities of SDSCs
VisLab will support NBCR advances in imaging. NBCR staff will port
existing applications to the Paragon and work with core and collaborative
investigators on new or revised applications. Workshops and courses will
be given to train all NBCR researchers to make best use of the resource,
and resource information and research results will be disseminated to
users and the wider biomedical community.
Effective start/end date4/15/944/30/14


  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health


  • Medicine(all)


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