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Russ Miller, Director |
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Professor, Comp Sci & Eng |
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Senior Research Scientist @ Hauptman-Woodward
Inst. |
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Adj Prof., Electrical Engineering and Structural
Biology |
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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 at UB |
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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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Funding |
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Initial $300K Provided by NSF (CS/Chem) |
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UB Faculty/Staff have Leveraged CCR to Acquire
$40M in Funding |
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UB Investment: ~$2M (renovation, invest,
personnel) |
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CCR Vendor Donations: ~$6M |
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CCR Projects: ~$2.7M |
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NYS Funding: $15.3 NYSTAR; $2.7 NYSCEDII; $4M+
CCR |
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Federal Funding: ~$13M |
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NSF, NIH, EPA, NIMA, Sloan, Keck, Woodrow
Wilson, NYS, Vendors, Industry |
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Corporate Partners/Relationships: |
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IBM, SGI, Sun, Alias|Wavefront, Nortel, Myricom,
InforMax, Celera |
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Q-Chem, Praxair, Sarnoff, Occidental, M&T,
Tops Markets, Performance Technologies, Believe, Kodak, Xerox,Veridian,
Children’s Hospital, First Interstate Data Systems, Buffalo Medical
Consortium, artN |
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Peace Bridge Authority, Parsons Engineering,
Bermann Associates, eMedia Inc., IBC Digital |
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Third Science (Theoretical and Laboratory) |
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Focuses on Scientific Problems, combining: |
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Mathematics qComputer Science |
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Disciplinary Science |
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Biology qChemistry |
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Applied and Eng. Fields qPhysics |
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Impact (Simulation) |
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Structural Biology qMaterials Science |
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Fluid Dynamics qHigh Energy Physics |
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Pharm. Drug Design qGlobal Climate Change |
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NSF: “proving to be an effective way to generate
new knowledge” |
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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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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 |
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determine what protein a gene regulates |
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determine protein function |
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determine structure |
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devise drugs to block or enhance protein
function |
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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 - Antibiotic of Last Resort |
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Collaboratory – Incorporated in Backend of
System |
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HWI, CSE, CCR |
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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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Diffusion-Collision Model |
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Both Simulations: 5 CPU Hours |
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Collapse-Reorganization Model |
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Biophysics |
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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 Shows Structure that is Nearly
Impossible to Determine from 2D Slices |
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Children’s & CCR |
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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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Photonics & CCR |
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1901 Celebration |
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Hightlighted Americas |
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Featured all Aspects of Life |
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Arts to Technology |
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Buffalo |
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1st American City to Light
Streets with Electricity |
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Most Paved Streets in World |
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Walk Through |
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PSCHologram |
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Pan Am Temple of Music |
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3D & LightBox |
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Burchfield Art Gallery |
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Media & CCR |
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Document and Publish Unique Historical
Perspective of Best-Preserved Assyrian Palace |
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Create a Multimedia Interactive Educational and
Scholarly Research Tool |
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Combine Traditional Research with Modern
Computer Graphics |
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Completely Immersive |
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Animated Characters |
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Interactive Storyboard |
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Classics, VR Lab, CCR |
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VR Interactive Fiction |
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User as Protagonist |
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Emotional Relationship between User &
Virtual Character |
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CAVE library, Performer, XP |
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Media Study |
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International Crossing (USA/Canada) |
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Existing Bridge: Old (75yrs) & Small (3
lanes) |
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Existing USA Plaza: Small & Poor Design |
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IBC, VR Lab, CCR |
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Proposed Options |
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Relocate USA Plaza |
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Build a 3 Lane Companion & Rehab Original |
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Build a 6 Lane Signature Span |
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CCR Provides Immersive 3D Viz |
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All Bridge & Plaza Options |
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Realtime Visualization of the Downtown Medical
Complex |
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Photorealistic Representation |
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Alias|Wavefront and Multigen |
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3D Tool for Future Development |
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IBC & CCR |
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Commodity Cluster-Based Viz |
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$2.3M/yr Subcontract |
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Parallel File Database Servers |
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High-Redundancy/Low-Failure |
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IBM Intel Linux Cluster |
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28 Pentium III Processors (1 GHz) |
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28 GB RAM, 2.2 TB Disk storage |
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Emulex + 100BT Ethernet |
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CCR |
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Hardware |
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2-6TFlops of Cluster Computing |
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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