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High-Performance Computing for Biomedical Research

High-Performance Computing for Biomedical Research

Pittsburgh Supercomputing Center 300 South Craig Street Pittsburgh, PA 15213 www.psc.edu Grant No. P41 RR006009

Principal Investigator Joel Stiles, M.D., Ph.D. 412-268-4960; Fax: 412-268-5832 Additional Contacts David W. Deerfield II, Ph.D. 412-268-4786; Fax: 412-268-8200 E-mail: deerfiel@psc.edu or biomed@psc.edu Joel R. Stiles, M.D., Ph.D. 412-268-4960; Fax: 412-268-8200 E-mail: stiles@psc.edu

Research Emphasis

The National Resource for Biomedical Supercomputing (NRBSC) pursues leading-edge research in high performance computing and the life sciences and fosters exchange between Pittsburgh Supercomputing Center (PSC) expertise in computational science and biomedical researchers nationwide. The resource focus on computational biomedical research and on outreach to the national biomedical community through education and publications. Research at the NRBSC is centered in three areas: microphysiology, volumetric visualization and analysis, and computational structural biology.

Current Research

Current research in microphysiology and volumetric visualization are linked through software development that targets scalable, interactive mesh generation and annotation for spatially realistic cell modeling as well as terabyte-scale interactive volume visualization and analysis based on distributed server technology. The primary software packages under development by the Center for Quantitative Biological Simulation include MCell, PSC_DX, and DReAMM and the PSC Volume Browser. Research applications currently include synaptic physiology, metabolic and signaling networks, and multidimensional volumetric data analysis including cardiac chamber segmentation and volume estimation from high-resolution computed tomography and magnetic resonance imaging time series. Structural biology research (www.nrbsc.org/sb/index.htm) includes software development centered on the CHARMM and DYNAMO packages and includes applications focused on computational enzymology using hybrid quantum mechanical/molecular mechanical methods, ion channel kinetics using polarizable molecular mechanics force fields, and structural bioinformatics.

Resource Capabilities

Instruments

The PSC Cray XT3 supercomputer has a peak speed of 10 Tflops, 2 terabytes (TB) of memory, and ~ 200 TB of disk space. Its two thousand-sixty-eight 2.4 Ghz Opteron processors are linked by Cray's low-latency interconnect and thus deliver very high scalability for large-scale applications. PSC's Terascale Computing System supercomputer has a peak speed of 6 teraflops, 3 TB of memory, and ~ 70 TB of disk space. PSC also has four 64-processor HP GS1280s, each of which has 256 gigabytes (GB) of shared memory and a peak speed of 150 gigaflops. Several smaller Opteron clusters are available for bioinformatics and other biomedical research. The PSC data archival system can store up to 2.4 petabytes. The PSC has over 3.7 gigabits per second of external commodity network connectivity.

Software

See Current Research above for an overview of in-house software development. The major PSC supercomputers support more than 350 packages in quantum chemistry, molecular modeling, and genetic sequencing, including most commercial packages for fluid dynamics, structural analysis, finite element analysis, mathematics libraries, equation solvers, tools, and graphics. PSC also hosts all major sequence and structural databases.

Available Resources

New NRBSC Gateways are available for all major software development projects. These gateways include information on research projects, software training and downloads, project staff and contact information, and access to PSC hardware resources.

Training Opportunities and Workshops

The NRBSC hosts at least 3 workshops per year. Some bioinformatics workshops are held at outside universities, whereas research and software application workshops are held at the PSC's Computer Training Center. Expanding efforts in distance education can be accessed through a wide variety of detailed scientific and software tutorials available through the NRBSC Gateways.

Publications

1. Munshi, R., Coalson, R. D., Ermentrout, G. B., Madura, J. D., Meirovitch, H., Stiles, J. R., et al., An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnology Program 22:179–185, 2006.

2. Coggan, J. S., Bartol, T. M., Esquenazi, E., et al., Evidence for ectopic neurotransmission at a neuronal synapse. Science 309:446–451, 2005.

3. Wymore, T., Hempel, J., Cho, S. S., MacKerell, A. D. Jr., Nicholas, H. B. Jr., and Deerfield, D. W. II, Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation. Proteins: Structure, Function, and Bioinformatics 57:758–771, 2004.

4. Brothers, E. N., Suarez, D., Deerfield, D. W. II, and Merz, K. M. Jr., PM3-compatible zinc parameters optimized for metalloenzyme active sites. Journal of Computational Chemistry 25:1677–1692, 2004.