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Russ Miller, Director |
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Center for Computational Research |
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Edible Vaccine for Hepatitis C |
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PSA Test |
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Avonex: Interferon Treatment for Multiple
Sclerosis |
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NIH National Genomics Center: Northeast
Consortium |
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Howard Hughes Medical Institute: Center for
Genomics & Proteomics |
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Artificial Blood |
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Fetal Viability Test |
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Anti-Arrythmia Therapy – tarantula venom |
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Direct Methods Structure Determination (Dr.
Herbert Hauptman) |
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Listed on poster “Top Ten Algorithms of the 20th
Century” |
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Vancomycin |
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Gramacidin A |
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High Throughput
Crystallization Method: patented |
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Timed release Insulin therapy |
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The use of HPC to analyze data generated by the
Human Genome Project to improve medical treatment. |
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Precise sequence of ~30K human genes have been
mapped |
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Critical to elucidate the function of each gene. |
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Leads to greater understanding of human
development. |
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Potential to treat many diseases, including AIDS
cancer, MS, and Alzheimer’s and provide personalized treatment. |
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From Human Genome |
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Locate genes (tens of thousands in human body) |
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Determine what protein a gene regulates
(millions of proteins in body) |
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Determine structure |
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Determine protein function |
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Devise drugs to block or enhance protein
function |
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WNY STAR Center for Advanced Medical
Technologies |
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$1M NYS; UB & RPCI |
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Medical Technologies for Product Development and
Commercialization |
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NYSTAR in Disease Modeling and Therapy Discovery |
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$15.3M NYS; UB, HWI, RPCI, Kaleida |
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Software, device development, and drug therapies |
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Buffalo Center of Excellence in Bioinformatics |
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$75M NYS, $3M US; UB, HWI, RPCI, Industry |
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www.bioinformatics.buffalo.edu |
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Goal: Develop New Treatments for Disease |
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Act as a research, development, education, and
economic resource for industries based on bioinformatics, including
information technology, biotechnology, and pharmaceuticals. |
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Generate medically and biologically important
information |
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Genomics: Identify Gene |
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Molecular Biology: Express protein (gene
product) |
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Structural Biology: Determine shapes of protein |
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Indicates use of protein in body |
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Suggests drug designs to assist or inhibit
protein action |
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Drugs interact strongly with proteins in
structure-specific ways |
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Center for Computational Research |
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Top 10 Academic Supercomputing Center |
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High-Performance Computing & High-End Viz |
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High-Speed Communication |
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I2, vBNS, Abilene, NYSERNET |
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WNY Regional Fiber Network Initiative |
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UB, City of Buffalo, Erie County |
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Molecular Targeting Laboratory |
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Screen 30-50K compounds every 3 mos |
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Determine effects on specific gene expression
pathways |
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Gene Expression Laboratory |
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Dissection of target gene product & gene
expression pathway |
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Proteomics and Molecular Kinetics Lab |
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Identify molecular targets found in Gene Ex. Lab |
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Disease Modeling Laboratory |
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Gene targeting and genetic mapping facilities |
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Bioengineering Support Laboratory |
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Capabilities in photonics and BioMEMs |
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High-Throughput DNA Micro-Array |
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Full spectrum analysis of genomes and expression |
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Protein Scale-Up and Purification |
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High-Throughput Robotic Combinatorial
Chemistry/Synthetic Chemistry Capabilities |
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High-Throughput Search Process for Structural
Biology |
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Tests 1536 “chemical cocktails” to determine
effective parameters for crystallization |
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Matching Funds ($151M) |
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Amersham Pharmacia, AT&T, WNY Business
Community, Compaq, Dell, InforMax, Sloan Foundation, SGI, Stryker, Sun,
Q-Chem, Veridian |
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Research |
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Amersham, Bristol-Myers Squibb, Compaq, Human
Genome Sciences, Immco, InforMax, Invitrogen, Pfizer Pharmaceutical, Wyeth
Lederle, Zeptometrix |
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New York State ($50M + $25M) |
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Federal ($3.1M + ?) |
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Proteomics ($1.5M) |
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Disease Pathogens and Physiology ($27M) |
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Drug Discovery ($6M) |
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Genomic and Proteomic Infra. ($1.8M) |
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Genomics ($4.7M) |
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Information Technology ($12.3M) |
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STOR: Office of Science, Tech Transfer, and
Economic Outreach |
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Support product and business development |
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BuffLink: Private sector will promote
commercialization of cutting-edge research |
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Venture Capital |
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Compaq ($10M) |
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Buffalo Business Community ($15M) |
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Corporate Partnerships |
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WNY Regional Fiber Network Initiative |
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Buffalo Center of Excellence in Bioinformatics |
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$42M Building for research and business partners |
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200 employees and business associates |
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150,000 sq ft: 50% research labs, 25%
computational facilities; 25% workforce training |
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Roswell Park Cancer Institute Research Bldg |
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$60M Building to replace outmoded facilities |
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60 PIs and 200 support staff |
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170,000 sq ft: 85% research labs and 15% support |
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Master’s Program in Bioinformatics (Sloan) |
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Advanced Degrees under development |
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Pharmacometrics, Biophotonics, Computational
Chemistry, Molecular Biology |
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School of Informatics (AT&T curr. dev.) |
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UB-HWI Dept. of Structural Biology |
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Complementary Degrees: |
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Canisius College and Niagara University |
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SnB Software by UB/HWI |
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“Top Algorithms of the Century” |
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Critical to Rational Drug Design |
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Important Link in Structural Biology |
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Vancomycin solved with SnB |
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“Antibiotic of Last Resort” |
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Original molecular structure required 5 months
of computing to solve |
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(Re)solved in a single day on CCR’s
supercomputers |
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Ability of proteins to perform biological
function is attributed to their 3-D structure. |
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Protein folding problem refers to the challenge
of predicting 3-D structure from amino-acid sequence. |
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Solving the protein folding problem will impact
drug design. |
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Dynamics of Hemoglobin (Example) |
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50 Days of Processing on 16 Processors (800 CPU
Days) |
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Key |
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White – Heme Groups |
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Red – Phe97 |
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Red – Oxygen (in the subunit at bottom) |
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Green – His 69 and 101 |
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Blue – Tyr 72 |
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Cyan (Ball) – Water Molecules |
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Yellow – Helix E/F |
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Interest |
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Flip of the Phe97 ring at top |
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Water movement around Phe97 |
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Heme-heme relative movement |
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3D Reconstruction of CT Dataset |
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Created with the Visualization Toolkit (VTK) on
a Linux Workstation |
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3D Isosurface Clearly Shows Structure that is
Nearly Impossible to Determine from 2D Slices |
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3D Reconstruction of an Oral Epithelial Cell |
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Translucent White Surface Represents the Cell
Membrane |
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Reddish Surface Represents Groups of Bacteria |
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Leading U.S. Academic Supercomputing Center |
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High-Performance Computing |
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High-End Visualization |
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Support ~80 Groups in ~25 Depts |
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Education/Outreach/Training |
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H.S. Summer Program |
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Work with Local Industry & Local Colleges |
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Hosts Meetings/Provides Tours |
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M.S. Certificate Program in Computational
Science |
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Structural Biology |
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Molecular Structure Determination & DNA
Sequence Analysis |
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Protein Folding |
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Computer simulations determine the 3D structure
of proteins. |
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Environmentally Friendly Solvents |
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Study supercritical CO2 as a solvent
to reduce the need for toxic solvents. |
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Groundwater Modeling |
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Predict contaminant flow in groundwater &
migration into streams and lakes. |
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Industrial Design Optimization |
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Design, modify, and perfect new products at
reduced cost. |
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Fluid Dynamics |
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Modeling turbulent flows and combustion in order
to improve design of chemical reactors, turbine engines, and airplanes. |
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Volcanology |
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Study of volcanoes for risk assessment. Modeling
of lava flows and mudslides. |
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Financial Analysis |
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Datamining analaysis for prediction. |
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Dental Implant Design |
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Simulation and modeling of a dental implant in a
jawbone to reduce failure rate. |
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Physiology |
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Flow & regulation in kidney. Flow altered by aneurysm. |
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Biophysics |
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Measure protein conformational dynamics. |
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Visualization & Multimedia |
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Peace Bridge, Buffalo Medical Corridor, CCR,
Events. Networked media. Art. |
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Semiconductor Manufacturing |
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New processes & chemicals to improve the
manufacturing of computer chips. |
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Classics |
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Digital reconstruction of Assyrian Palace. |
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SGI Origin2000 |
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128 Processors (250 MHz) |
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32 GB RAM |
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400 GB Fibre Channel Disk Storage |
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IBM RS/6000 SP |
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78 Processors |
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26 GB Ram, 640 GB Disk Storage |
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Sun Microsystems Cluster |
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48 Sun Ultra 5 Workstations (333MHz) |
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32 Sunblades (750MHz) |
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Myrinet + 100BT Ethernet |
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SGI Intel Linux Cluster |
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150 Pentium III Processors (1 GHz) |
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75 GB RAM, 2.5 TB Disk Storage |
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Myrinet2000 + 100BT Ethernet |
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Manufacturing |
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Medical Imaging |
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Computational Science |
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Simulation & Modeling |
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Historical Reenactments |
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Multimedia Presentations |
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Hardware |
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Cluster Computing: 2-6TFlops |
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ACCESS Grid |
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Commodity Viz Clusters |
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Portable Viz Systems |
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Additional Viz Workbench |
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Commodity Projection Systems |
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Software |
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Bioinformatics |
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Modeling and Simulation Packages |
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Database & Data Mining |
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Storage Management |
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Notes