University of Utah
50 S. Central Campus Drive, Room 3490
Salt Lake City, UT 84112-9205
Grant No. P41 RR012553
Chris R. Johnson, Ph.D.
801-581-7705; Fax: 801-585-6513
801-585-5983; Fax: 801-585-6513
The overall goal of the Center for Bioelectric Field Modeling, Simulation, and Visualization is
to develop and disseminate new methods, algorithms, and software systems for use in the study of
experimental, clinical, and computational bioelectric field problems.
Develop and implement the following techniques for the efficient manipulation and processing of
bioelectric field data: geometric model generation and manipulation, bioelectric field simulation,
and scalar and vector field visualization. Use the resulting software modules in supporting research
projects within the center and in combination with center collaborators in computational, clinical,
and basic electrocardiology and electroencephalography. Develop, disseminate, and support BioPSE
(biomedical problem solving environment), an integrated, extensible, computation workbench that features
a computational steering framework for interactive modeling, simulating, and visualizing bioelectric
field problems; and map3d, a surface-based visualization package for qualitative and quantitative
visualization and interrogation of time-dependent bioelectric field data.
The center conducts research on and disseminates state-of-the-art software for geometric modeling,
simulation, and visualization in basic and clinical bioelectric field research. Specific software tools include:
Modeling tools: Semi-automatic segmentation, surface generation, automatic mesh generation, and
model editing, manipulation, and re-sampling tools.
Simulation tools: Finite element, finite difference, and boundary element techniques for the
numeric solution of bioelectric field problems. Regularization techniques to constrain the effects
produced by the ill-posed nature of ECG and EEG inverse problems; currently supported techniques include
Tikhonov and Greensite regularization methods. Future directions include admissible solution approaches,
and adaptive refinement techniques for forward and inverse approximation methods.
Visualization tools: Interactive scalar field display; isocontour and isosurface extraction;
volume and surface rendering; vector field visualization. Current initiatives include quantitative
spatio-temporal visualization, and methods for the characterization, representation, and presentation
of error and uncertainty due to modeling, simulation, and visualization. Efforts are also being applied
toward remote visualization tools.
Pittsburgh Supercomputing Center (PSC)
Mellon Institute Building
4400 Fifth Avenue
Pittsburgh, PA 15213
Grant No. P41 RR006009
Ralph Z. Roskies, Ph.D.
412-268-4960; Fax: 412-268-5832
David W. Deerfield II, Ph.D.
412-268-4960; Fax: 412-268-8200
The resource抯 mission is to develop new methods, optimize existing approaches, and undertake
research projects in biomedical areas that require high-performance computing, broadly construed to
include large-scale data management, high-speed networking, and visualization. The resource also
identifies new biomedical application areas that could benefit from high-performance computing, and
speed the introduction of high-performance computing techniques into these areas.
Current efforts are in structural biology, bioinformatics, cellular microphysiology, neural modeling,
the Visible Human Project, and pathology. Specific projects include development and application of
algorithms for sequence-sequence, sequence-structure, and multiple sequence alignment; classification
and analysis of gene and protein superfamilies; understanding divalent metal ion binding sites in proteins
and nucleic acids; incorporation of polarization effects in simulations of biopolymers; simulation of neural
transmission (Mcell); simulation of neural networks on parallel platforms (NEOSIM); analysis of multi-electrode
recordings of brain activity; display of anatomic (visible human) images; image analysis of
pathology slides; databasing and retrieval of medically relevant images.
PSC抯 Terascale Computing System has a peak speed of 6 Teraflops, 3 Terabytes of physical memory, and
almost 70 TB of disk space. Currently the most powerful computer in the nation dedicated to open scientific
research, it consists of 750 HP/COMPAQ ES-45 nodes, each with 4 processors rated at 2 Gflops peak, 4 GB of
memory, and over 50 GBs of local disk. PSC also offers a 512 processor Cray T3E. Each processor is a 450-MHz
alpha processor, with a peak speed of 900 Mflops and 128 MB of memory. For bioinformatics, the resource provides
a dedicated 4-processor minisupercomputer with 6 GB of memory and 158 GB of disk; 525 Mb/s of commodity connectivity,
with connectivity to two leading-edge networks (Abilene and vbns); archival system that can currently store
165 terabytes without human intervention, based on two storage-Tek silos, and Cray Research J90 file server
with 20 processors and more than 500 GB of disk.
More than 350 packages in quantum chemistry, molecular modeling, and genetic sequencing. All
major sequence and structural databases. Most commercial packages for fluid dynamics, structural
analysis, finite element analysis, mathematics libraries, equation solvers, tools, and graphics.
28 Silicon Graphics Indy graphics workstations for teaching workshops including graphically intensive subjects.
- Gomez, C. M., Maselli, R., et al., A novel delta subunit mutation in slow-channel syndrome causes
severe weakness by novel mechanisms. Annals of Neurology 51:102112, 2002.
- Nicholas Jr., H. B., Ropelewski, A. J., and Deerfield II, D. W., Strategies for multiple sequence
alignment. Biotechniques 32:592603, 2002.
- Wetzel, A. W., Pomerantz, S. M., et al., Distributed multiuser visualization of time varying anatomical
data 30th AIPR workshop: Analysis and understanding of time varying imagery, Oct. 10�, 2001, Washington DC,
IEEE Computer Society Press, pp. 109114.
Case Western Reserve University
Metro Health Medical Center
2500 Metro Health Drive
Cleveland, OH 44109-1998
Grant No. P41 RR003655
Robert C. Elston, Ph.D.
216-778-3863; Fax: 216-778-3280
The resource is developing a user-friendly software package, S.A.G.E., that may be used to analyze
family data to determine if the variability of a trait, either quantitative or qualitative, is significantly
due to Mendelian segregation at a single genetic locus; if there is association between a quantitative or
qualitative trait and a known polymorphic genetic marker; and if there are genetic loci linked to a known
genetic marker that underlie variability in a trait.
Theoretical development of statistical methods for the analysis of family data, especially to detect
and identify genetic components that underlie disease susceptibility. Incorporating these methods
into appropriate computer programs and making the programs generally available to other human
geneticists and genetic epidemiologists in a well-documented and user-friendly form. Testing
the validity, power, and robustness of the statistical procedures, especially to differentiate
genetic causes from alternative environmental causes for familial aggregation. Application of
methods and programs in collaborative projects to identify single genes that play roles in the
etiology of various diseases.
The Human Genetic Analysis Resource (HGAR) utilizes a wide array of operating systems including
Digital UNIX, Microsoft Windows 95/98 and NT, Sun Solaris, IBM AIX, SGI IRIX, and Linux. For large-scale
simulations and computations, MOSIX Cluster Management Software is used to distribute workloads over a
dedicated CPU cluster. Software development at HGAR proceeds in a variety of languages including C, C++,
Python, Java, Perl, PHP, Fortran, and LotusScript. HGAR staff have access to a wide variety of math and
statistical packages including Mathematica, SAS, and SPlus, usually utilizing the high-speed server
systems directly from their desktops natively and via X-Windows emulation. Secure, distributed medical
and research databases are being developed using Lotus Domino, Oracle8, and MySQL.
- Olson, J. M., Goddard, K. A. B., and Dudek, D. M., A second locus for very-late-onset Alzheimer disease:
A genome scan reveals linkage to 20p and epistasis between 20p and the amyloid precursor protein region.
American Journal of Human Genetics 71:154�1, 2002.
- Keen, K. J. and Elston, R. C., A problem in ascertainment. Communications in Statistics 30:1615�31, 2002.
- Burton, P. R., Palmer, L. J., et al., Ascertainment adjustment: Where does it take us?
American Journal of Human Genetics 67:1505�14, 2001.
- Buxbaum, S., Elston, R. C., Tishler, P. V., and Redline, S., Genetics of the apnea hypopnea index
in Caucasians and African Americans. Genetic Epidemiology 22:243�30, 2001.
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037
Grant No. P41 RR012255
Investigator and Contact
Charles L. Brooks III, Ph.D.
858-784-8035; Fax: 858-784-8688
Problems in structural biology increasingly require researchers to move between models of
low-resolution and detailed atomic models to fully explore and exploit experimental information.
This resource focuses on development of new and integrated approaches to multiscale modeling, with
an emphasis on modeling large-scale assemblies of nucleic acids and proteins with nucleic acids;
developing methods that combine lattice-based dynamic Monte Carlo and all atom molecular dynamics;
studying physical processes involved in and developing models for the interactions associated with
virus assembly; and establishing new tools for the combined treatment of crystallographic and low-resolution
structural models from cryo-electron microscopy. These research threads are tied together through the
development and distribution of computer codes to make such multiscale simulations and modeling readily
accessible to the scientific community at large.
Modeling very large conformational changes occurring in proteins, nucleic acids, and their assemblies;
developing methods and models to explore virus swelling and associated large-scale capsid dynamics
during viral maturation; exploring of meso-scale distortions of molecular assemblies using low-resolution
data from electron microscopy, in the absence of any atomic level structural information; providing links
between low-resolution images of functional states of the ribosome during translocation and the near-atomic
structural distortions that comprise these motions; characterization of protein-protein interfaces in
assembled virus capsids from an energetic and structural standpoint, providing a basis for understanding
large-scale molecular assembly. Ongoing development of methods for, and applications to, protein folding,
loop, and homology modeling, including participation in CASP5, to perfect and 揾arden� physics-based
approaches to structural genomics. Develop and test software to extend the range of atom-based modeling
methods to larger systems.
This resource is equipped with high-performance parallel Linux clusters of 32 and 64 processors as
well as several dual-processor Silicon Graphics graphics servers. Large-scale modeling and simulation
studies are performed on TSRI servers, which include a 256-node SGI Origin cluster.
Software under development includes lattice-based Monte Carlo sampling codes, nab (a software package
to rapidly construct nucleic acid structures at atomic resolution), yammp (a molecular mechanics and modeling
code directed toward low-resolution modeling of RNA and DNA), SITUS (for multiscale modeling of atomic and
cryo-electron microscopy structural models), X-ray visualization and refinement software, and modules for
CHARMM and AMBER. Much of this software is integrated for large-scale 揺nsemble� modeling, as relevant to
structural genomic efforts, through the MMTSB tool set. The tool set, a suite of Perl libraries and routines
that integrate and control the execution and management of large molecular simulations, is available at the
MMTSB web site (http://mmtsb.scripps.edu/).
- Tama, F. and Brooks, C. L. III, Mechanism and pathway of pH induced swelling in cowpea
chlorotic mottle virus. Journal of Molecular Biology 318:733�7, 2002.
- Tama, F., Brooks, C. L. III, and Wriggers, W., Exploring global distortions of biological macromolecules
and assemblies from low-resolution structural information and elastic network theory.
Journal of Molecular Biology 321:297�5, 2002.
- Fiser, A., Feig, M., Brooks, C. L. III, and Sali, A., Evolution and physics in comparative protein
structure modeling. Accounts of Chemical Research 35:413�1, 2002.
- Skolnick, J. and Kolinski, A., A unified approach to the prediction of protein structure
and function. Advances in Chemical Physics 120:131�2, 2002.
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0043
Grant No. P41 RR008605
Peter W. Arzberger, Ph.D.
858-534-1079; Fax: 858-822-4767
858-534-5034; Fax: 858-822-5407
The mission of the National Biomedical Computation Resource (NBCR) at the University of California,
San Diego (UCSD) is to conduct, catalyze, and enable biomedical research by harnessing advanced computational
technology. To fulfill this mission, NBCR efforts are focused on four key activities: integrate computational
and visualization tools in a transparent, advanced computing environment to enhance access to distributed data,
computational resources, and instruments; develop and deploy advanced computational tools for modeling, data
query, linking of data resources, 3-D image processing, and interactive visualization; provide access to
and support of advanced computational infrastructure for biomedical researchers; and train a cadre of new
researchers to have interdisciplinary knowledge of biology and the latest computation technologies.
The ultimate goal of the resource is to facilitate biomedical research by providing access to advanced
computational and data grid capabilities via easy-to-use web portals, thereby enabling researchers
to focus on the essential aspects of the biological/biomedical problem.
NBCR is part of UCSD抯 Center for Research on Biological Structure, and its technology development
activities involve collaborations among researchers at UCSD, the San Diego Supercomputer Center (SDSC),
the California Institute of Telecommunications and Information Technology (Cal-(IT)2), and The Scripps
Research Institute, with a general interest in performing basic biomedical research from atomic to
organismic levels. Core research projects include methods for pattern recognition in protein and
nucleic acid structure, parallel tomographic methods for reconstruction of 3-D images, distributed
database for cell-centered data, development/enhancement of cardiac electromechanics, parallel
quantum mechanical modeling methods including environmental effects, development of platform-independent
visualization tools, and the creation of portals for the biomedical community.
NBCR provides web portals to a variety of analyses performed on its high-performance computing
systems and servers. Software and services (see web site) include MEME, MAST, MetaMEME and SeqWeb, EULER,
CE, MSMS, MIA, CMSMBR, GAMESS, QMView, PVM.
- Yerushaimi, R., Noy, D., Baldridge, K., and Scherz, A., A mutual control of axial and equatorial
ligands: Model studies with [Ni]-bacteriochlorophyll-a. Journal of American Chemical Society 124:8406�15, 2002.
- Martone, M. E., Gupta, A., et al., A cell-centered database for electron tomographic data. Journal of
Structural Biology 1-2:145155, 2002.
- Sanner, M. F. and Olson, A., ViPEr, a visual programming environment for python. Proceedings of the
10th International Python Conference, Alexandria VA, Feb 47, 2002.
- Baker, N. A., Sept, D., et al., Electrostatics of nanosystems: Application to microtubules and
the ribosome. Proceedings of the National Academy of Sciences USA 98:1003710041, 2001.
- McCulloch, A. D., Sung, D., et al., Computational and experimental modeling of ventricular
electromechanical interactions. In N. Virag, O. Blanc, and L. Kappenberger, Eds. Computer Simulation
and Experimental Assessment of Cardiac Electrophysiology (pp. 89�). Armonk, NY: Futura Publishing, 2001.
- Reddy, B. V. B., Li, W. W., et al., Conserved key amino acid positions (CKAAPs) derived from analysis of
common substructures in proteins. Proteins 42:148163, 2001.
- Reiter, L. T., Potocki, L., Chien, S., Gribskov, M., and Bier, E., A systematic analysis of
human disease-associated gene sequences in Drosophila melanogaster. Genome Research 11:114125, 2001.
University of Connecticut Health Center
Center for Biomedical Imaging Technology
Farmington, CT 06030-1507
Grant No. P41 RR013186
Leslie M. Loew, Ph.D.
Ann E. Cowan, Ph.D.
860-679-1452; Fax: 860-679-1039
The National Resource for Cell Analysis and Modeling
(NRCAM) is developing methods for modeling cell
physiological processes in the context of the actual 3-D
structure of individual cells. Approaches in computational
cell biology are coupled with high-resolution light
microscopy to facilitate the interplay between experimental
manipulation and computational simulation of specific
NRCAM is developing the Virtual Cell, a general computational framework for modeling cell biological
processes. This new technology associates biochemical and electrophysiological data describing individual
reactions with experimental microscopic image data that describes their subcellular locations. Individual
processes are integrated within a physical and computational infrastructure that will accommodate any molecular
mechanism. Current development of the Virtual Cell is focused on expanding the generalized mathematical
descriptions to include additional cell biological mechanisms, enhancing accessibility to biologists studying
different biological processes, and integrating the interface with a database of images and reaction mechanisms.
Current applications of the Virtual Cell include studies of calcium dynamics in neuroblastoma cells and Purkinje
cells, and studies of intracellular RNA trafficking in oligodendrocytes. Additional collaborative research projects
include modeling diffusional processes in mitochondria, nuclear transport, and aspects of cell motility.
Microscopy instrumentation includes 3 confocal laser scanning microscopes including UV excitation,
nonlinear optical microscopy utilizing a titanium sapphire pulsed laser, confocal-based fluorescence
correlation spectroscopy, wide-field imaging workstation with cooled CCD and rapid excitation filter
wheel, and dual-wavelength spectrofluorometer. Access to the facilities and technical staff is open to
Computational resources include a Compaq Alpha cluster of 8 dual-processor DS20s, 2 RAID fileservers, 2
database servers and 2 primary servers, and multiple PC and Linux platforms running a variety of imaging
processing and development software.
Authorized access to the Virtual Cell Modeling software is available via the Internet through a JAVA-based
- Slepchenko, B. M., Schaff, J. C., Carson, J. H., and Loew, L. M., Computational cell biology:
Spatiotemporal simulation of cellular events. Annual Review of Biophysics and Biomolecular Structure
- Smith, A. E., Slepchenko, B. M., Schaff, J. C., Loew, L. M., and Macara, I. G., Systems
analysis of Ran transport. Science 295:488�1, 2002.
- Schaff, J. C., Slepchenko, B. M., and Loew, L. M., Physiological modeling with the Virtual
Cell framework. Methods in Enzymology 321:1�, 2000.
Beth Israel Deaconess Medical Center
Department of Medicine
330 Brookline Avenue
Boston, MA 02215
Grant No. P41 RR013622
Ary L. Goldberger, M.D.
617-667-4267; Fax: 617-667-7268
George B. Moody
617-253-7424; Fax: 617-258-7859
The objective of this multicenter resource (Beth Israel Deaconess Medical Center/Harvard Medical School;
Massachusetts Institute of Technology, Division of Health Sciences and Technology; Boston University, Center
for Polymer Studies; and McGill University, Department of Physiology) is to accelerate current research progress
and catalyze new investigations in the quantitative study of complex physiologic signals. The resource has three
interdependent components: PhysioBank is a large and growing archive of well-characterized digital recordings of
physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes
databases of multiparameter cardiopulmonary, neural, and other signals from healthy subjects and from patients with
a variety of conditions with major public health implications, including life-threatening arrhythmias, sleep apnea,
neurologic disorders, and aging. PhysioToolkit is a library of open-source software for physiologic signal processing
and analysis, and detection of physiologically significant events using both classical techniques and novel methods
based on statistical physics and nonlinear dynamics. PhysioNet is an online forum for dissemination and exchange
of recorded biomedical signals and open-source software for analyzing them.
The resource is developing new algorithms that quantify the transient and local properties of
nonstationary physiologic signals and the cross-interactions among multiparameter signals. These techniques
will be used to detect changes that may precede the onset of catastrophic physiologic events, including epilepsy
and sudden cardiac death. Complementary studies are aimed at developing techniques to quantify the nonlinear
dynamics of physiologic control, with an emphasis on modeling these mechanisms and identifying new measures
that have diagnostic/prognostic utility in life-threatening cardiopulmonary pathologies, such as sleep apnea
and congestive heart failure. Another core area of research is the development of methods for assessing signal
quality in multiparameter data.
The PhysioNet web site creates an online community for the dissemination and exchange of recorded
biomedical signals and the software for analyzing them by providing facilities for cooperative analysis
of data and evaluation of proposed new algorithms. Much of the PhysioBank and PhysioToolkit software
utilizes standard networking protocols, allowing interactive display and analysis of physiologic signals
at remote locations on the Internet.
- Goldberger, A. L., Amaral, L. A. N., et al., Fractal dynamics in physiology: Alterations with
disease and aging. Proceedings of the National Academy of Sciences USA 99[suppl 1]:2466�72, 2002.
- Bub, G., Shrier, A., and Glass, L., Spiral wave generation in heterogeneous excitable media.
Physical Review Letters 88:058101, 2002.
- Costa, M., Goldberger, A. L., and Peng, C. K., Multiscale entropy analysis of complex physiologic
time series. Physical Review Letters 89:068102, 2002.
- Moody, G. B., Mark, R. G., and Goldberger, A. L., PhysioNet: A web-based resource for the
study of physiologic signals. IEEE Engineering in Medicine and Biology 20:70�, 2001.
- Amaral, L. A. N., Ivanov, P. Ch., Aoyagi, N., Hidaka, I., Tomono, S., Goldberger, A. L., Stanley,
H. E., and Yamamoto, Y., Behavioral-independent features of complex heartbeat dynamics. Physical Review
Letters 86:6026�29, 2001.
Computer Graphics Laboratory
University of California, San Francisco
San Francisco, CA 94143-0446
Grant No. P41 RR001081
Thomas E. Ferrin, Ph.D.
415-476-2299; Fax: 415-502-1755
The Resource for Biocomputing, Visualization, and Informatics (RBVI) creates innovative computational
and visualization-based data analysis methods and algorithms; implements these as professional-quality,
easy-to-use software tools; and applies these tools for solving a wide range of genomic and molecular
recognition problems within the complex sequence-structure-function triad. Application areas include
gene characterization and interpretation, drug design, variation in drug response due to genetic
factors, protein engineering, biomaterials design, and prediction of function from sequence and structure.
Sequence analysis and bioinformatics: The characterization and interpretation of genomic data,
including knowledge discovery and transfer in nucleic acid and protein sequence analysis, pharmacogenomics,
identifying gene and regulatory motifs, protein family/superfamily relationships, and gene expression patterns.
Structural informatics: The development, application, and dissemination of analysis methodologies
and software tools in computational structural biology, including algorithm development for low- and
high-resolution protein structural models and their comparison, molecular visualization for structural
analysis and the integration of sequence and tertiary structural information, and facilitation of
collaborative research, especially with distant scientists, through use of high-performance network technology.
Functional informatics: Theoretical and applied research in how protein structures deliver function,
including the identification and characterization of protein superfamilies, the generation of new computational-based
representations of protein chemistry, and the development of structurally contextual definitions of protein function.
High-performance cluster of symmetric multiprocessor Hewlett-Packard AlphaServer computers for performing theoretical
studies on protein and nucleic acid structure and function, and for storing, searching, and analyzing various
sequence and structure databases. High-performance interactive three-dimensional graphics workstations equipped
with special glasses for viewing in stereo for visualization of complex molecular structures. All systems are
interconnected via a high-performance network and are capable of distributed computations.
Commercial applications for database searching and analysis, and several locally developed packages
disseminated as documented source code to allow others to use the resource抯 software both for their own
research applications and as a starting point and training tool for specialized applications. Local packages
include MidasPlus, a molecular visualization application used to display and interactively manipulate macromolecules
such as proteins and nucleic acids, and Chimera, an advanced molecular visualization system that can easily be
extended for specialized molecular modeling needs.
- Stryke, D., Huang, C. C., et al., SNP analysis and presentation in the pharmacogenetics
of membrane transporters project. In Pacific Symposium on Biocomputing 2003 (R. B. Altman, A. K. Dunker, L.
Hunter, K. Lauderdale, and T. E. Klein, eds.). Singapore: World Scientific Publishing, December 2002.
- Konerding, D. E., Huang, C. C., and Ferrin, T. E., Chimera: Affordable desktop molecular
modeling on Linux workstations. Proceedings of the 5th Annual Linux Showcase and Conference,
Usenix Association, November 2001. Available from www.cgl.ucsf.edu/home/tef/pubs/konerding.pdf.
University of Illinois at Urbana-Champaign
3147 Beckman Institute
405 North Mathews Avenue
Urbana, IL 61801
Grant No. P41 RR005969
Klaus J. Schulten, Ph.D.
217-244-1604/2212; Fax: 217-244-6078
Emad Tajkhorshid, Ph.D.
217-244-6914; Fax: 217-244-6078
The resource studies large biomolecular processes in living cells, focusing on membrane proteins
that mediate the exchange of materials and information across, in particular, biological membranes as
well as the conversion between electro-osmotic, mechanical, and chemical energy. It also develops
software for large-scale simulations. Software tools include NAMD, a molecular dynamics simulation program
used for classical, atomistic molecular dynamics simulations of large biomolecular aggregates; VMD, a molecular
visualization program for displaying, animating, and analyzing both large and small biomolecular systems using
3-D graphics and built-in scripting; BioCoRE, a web-based, tool-oriented collaboratory for biomedical research
Interactive molecular dynamics (IMD) for the manipulation of molecular simulations with real-time force
feedback and interactive display; investigations of aquaporin channels, mechanosensitive channel, ATP
synthase, chloride channel, photosynthetic proteins, visual receptors, and proteins with mechanical
functions; efficient evaluation of force fields and integration schemes for simulation of very large
biomolecular systems; efficient distributed molecular dynamics programs on workstation clusters and
massively parallel machines; continued development of NAMD, VMD, and BioCoRE.
Three main computational platforms: 100 Athlon PC nodes running as four Scyld Beowulf Linux clusters, the
primary development platform for the group抯 molecular dynamics program, NAMD; 4 Microway Alpha AXP21264-500
dual-processor nodes, two with 4 GB of memory, primarily used for large-memory jobs such as quantum simulations;
and 2 dual-processor SunBlade 2000 systems with XVR1000 video cards and 4 GB of memory, used for both visualization
and large memory jobs. These systems are controlled using a shared queueing system. Four Sun Enterprise 250 servers
with a combined total of 2.75 TB of disk space serve the network-wide home and project directories. The servers are
backed up daily on four DLT4000 tape changers. The key graphics platforms include aforementioned SunBlade 2000
systems; one Sun Ultra 80 and one Ultra 60 system, each with Expert 3-D graphics; and an eight-processor SGI
Onyx2 with InfiniteReality graphics. Nearly all researcher workstations are equipped with 3-D video cards and
are capable of real-time stereoscopic visualization. The Sun Ultra 80 drives a stereo-capable Electrohome
Marquee 8500LC projector in the resource抯 3-D projection facility.
IMD, interactive molecular dynamics; VMD, a visualization program for interactive display and animation of
molecules; NAMD, a parallel message-driven molecular dynamics program reaching teraflop performance; and BioCoRE,
an integrated set of computational tools that functions as an interactive visual computing environment for the
simulation and collaborative study of biopolymers over distance and as a training platform.
- Phillips, J. C., Zheng, G., Kumar, S., and Kale, L. V., NAMD: Biomolecular simulation on thousands
of processors. Proceedings of the IEEE/ACM SC2002 Conference at
- Tajkhorshid, E., Nollert, P., et al., Control of the selectivity of the aquaporin water channel
family by global orientational tuning. Science 296:525�0, 2002.
- Jensen, M. O., Park, S., Tajkhorshid, E., and Schulten, K., Energetics of glycerol conduction
through aquaglyceroporin GlpF. Proceedings of the National Academy of Sciences USA 99:6731�36, 2002.