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Russ Miller, Director |
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Center for Computational Research |
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Pervasive Computing |
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Computer Trends |
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Definition of Supercomputer |
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Overview of Center for Computational Research |
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Sample CCR Projects |
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Center of Excellence in Bioinformatics |
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H.S. Workshop |
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Computers play an important role in your life |
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Currently ~10 processors per person |
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Working with computers can be fun and exciting |
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Science and Engineering |
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Physics, Chemistry, Biology |
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Aerospace, Mechanical, Civil, Environmental |
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Architecture |
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Building and Bridge Design |
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Computer Animation |
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Cartoons, Movies, Advertising |
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Games (Playstation, Nintendo, PC games, etc) |
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Graphic Arts/Design |
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Computer programmers |
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Co-Founder of Intel |
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Predicted (1965/75) that transistor density
would double every 12/18 months |
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Processing speed doubling every 18 mos. |
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Disk storage doubling every 12 mos. |
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Aggregate bandwidth doubling every 9 mos. |
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Industry Standard Hardware and Software |
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PC-Based Components (Intel or AMD) |
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Ethernet or Myrinet |
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Linux, PBS, MPI |
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“Commodity Off-The-Shelf” (COTS) |
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Operates as a Single System |
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Rivals Performance of Traditional Supercomputer
at a Fraction of the Price |
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Fastest computers at any point in time |
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Used to solve large and complex problems |
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Machines 1000 times faster than a PC |
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Machines 10 times slower than what you need to solve the most challenging
problems |
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40TFlops Peak |
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Homogeneous, Centralized, Proprietary, Vector |
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Expensive! |
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CFD-Weather, Climate, Earthquake |
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640 NEC SX/6 Nodes (5120 CPUs) |
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Footprint = 4 tennis courts |
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$6M/year in power |
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High-Performance Computing and High-End
Visualization |
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70 (40+ active) Research Groups in 27 Depts |
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13 Local Companies |
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10 Local Institutions |
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External Funds: $108M |
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Vendor Contributions: $41M |
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Deliverables |
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350 Publications and Presentations |
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Hardware, Software, Algorithms, etc |
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Training |
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Workshops |
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Courses |
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Degree Programs |
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Dell Linux Cluster - #22 in World |
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600 P4 Processors (2.4 GHz) |
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600 GB RAM; 40 TB Disk |
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Dell Linux Cluster - #187 in World |
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4036 Processors (PIII 1.2 GHz) |
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2TB RAM; 160TB Disk; 16TB RD |
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Private Use |
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Computational Chemistry (King, Kofke, Coppens,
Furlani, Tilson, Lund, Swihart, Ruckenstein, Garvey) |
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Algorithm development & simulations |
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Groundwater Flow Modeling (Rabideau, Jankovic,
Becker, Flewelling) |
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Predict contaminant flow in groundwater &
possible migration into streams and lakes |
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Geophysical Mass Flows (Patra, Sheridan, Pitman,
Bursik, Jones, Winer) |
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Study of geophysical mass flows for risk
assessment of lava flows and mudslides |
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Bioinformatics (Zhou, Miller, Hu, Szyperski –
NIH Consortium, HWI) |
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Protein Folding: computer simulations to
understand the 3D structure of proteins |
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Structural Biology; Pharmacology |
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Computational Fluid Dynamics (Madnia, DesJardin,
Lordi, Taulbee) |
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Modeling turbulent flows and combustion to
improve design of chemical reactors, turbine engines, and airplanes |
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Physics (Jones, Sen) |
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Many-body phenomena in condensed matter physics |
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Chemical Reactions (Mountziaris) |
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Molecular Simulation (Errington) |
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Fakespace ImmersaDesk R2 |
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Portable 3D Device |
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Tiled-Display Wall |
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20 NEC projectors: 15.7M pixels |
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Screen is 11’´7’ |
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Dell PCs with Myrinet2000 |
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Access Grid Node |
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Group-to-Group Communication |
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Commodity components |
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SGI Reality Center 3300W |
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Dual Barco’s on 8’´4’ screen |
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VREX VR-4200 Stereo Imaging Projector |
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Portable projector works with PC |
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Computational Science (Patra, Sheridan, Becker,
Flewelling, Baker, Miller, Pitman) |
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Simulation and modeling |
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Urban Visualization and Simulation (CCR) |
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Public projects involving urban planning |
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Medical Imaging (Hoffmann, Bakshi, Glick,
Miletich, Baker) |
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Tools for pre-operative planning; predictive
disease analysis |
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Geographic Information Systems (CCR, Bisantz,
Llinas, Kesavadas, Green) |
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Parallel data sourcing software |
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Historical Reenactments (Paley, Kesavadas, More) |
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Faithful representations of previously existing
scenarios |
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Multimedia Presentations (Anstey, Pape) |
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Networked, interactive, 3D activities |
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Regional-scale modeling of groundwater flow and
contaminant transport (Great Lakes Region) |
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Ability to include all hydrogeologic features as
independent objects |
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Current work is based on Analytic Element
Method |
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Key features: |
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High precision |
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Highly parallel |
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Object-oriented programming |
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Intelligent user interface |
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GIS facilitates large-scale regional
applications |
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Utilized 10,661 CPU days (32 CPU years) of
computing in past year on CCR’s commodity clusters |
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Integrate information from several sources |
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Simulation results |
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Remote sensing |
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GIS data |
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Develop realistic 3D models of geophysical mass
flows |
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Present information at user appropriate
resolutions |
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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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Collaboration with Children’s Hospital |
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Leading miniature access surgery center |
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Application reads data output from a CT Scan |
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Visualize multiple surfaces and volumes |
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Export images, movies or CAD representation of
model |
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Collaboration with Buffalo Neuroimaging Analysis
Center (BNAC) |
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Developers of Avonex, drug of choice for
treatment of MS |
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MS Project examines patients and compares scans
to healthy volunteers |
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International Crossing |
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The Problem |
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75 year old bridge |
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3 lanes – poor capacity |
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Existing US plaza: small and poor design |
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IBC Digital |
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Gov. Pataki Visit |
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Peace Bridge (Early & Current) |
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Buffalo-Niagara Medical Campus |
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Compute Cycles for Animation |
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Bergmann Associates |
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Peace Bridge (Current) |
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NYS Thruway Toll Plaza |
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Azar & More |
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Reenactment of 1901 Pan Am Exhibition |
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PHSCologram & Courses |
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Avid Digital Editing |
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Niagara College |
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Start up |
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Peace Bridge (Current) |
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Hauptman-Woodward Medical Research Institute |
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Computing |
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Collaboratory |
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The Children’s Hospital of Buffalo |
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Medical Visualization |
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Veridian |
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Battlespace Management |
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“This Center [of Excellence in Bioinformatics]
will, through the University of Buffalo’s Center for Computational
Research, create academic and industrial partnerships …” |
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- NYS Gov. George S. Pataki, January 2001 |
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PSA Test (screen for Prostate Cancer) |
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Avonex: Interferon Treatment for Multiple
Sclerosis |
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Artificial Blood |
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Nicorette Gum |
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Fetal Viability Test |
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Implantable Pacemaker |
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Edible Vaccine for Hepatitis C |
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Timed-Release Insulin Therapy |
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Anti-Arrythmia Therapy |
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Tarantula venom |
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Direct Methods Structure Determination |
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Listed on “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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NIH National Genomics Center: Northeast
Consortium |
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Howard Hughes Medical Institute: Center for
Genomics & Proteomics |
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UB Center for Advanced Bioengineering &
Biomedical Technologies |
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$1M/yr NYS |
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Med Tech for Product Dev & Commer. |
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Center Disease Modeling & Therapy Discovery |
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UB, HWI, RPCI, Kaleida |
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$15.3M NYS |
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Software, device development, and drug therapies |
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Buffalo Center of Excellence in Bioinformatics |
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UB, HWI, RPCI |
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$61M NYS |
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$10.6M Federal Government |
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$151 Corporate Funding |
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Significant Local Foundation Support |
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Act as a research, development, education, and economic
resource for industries based on bioinformatics, including information
technology, biotech, and pharmaceuticals. |
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Combine state-of-the-art computational
facilities with high-throughput experimental facilities to enable the
development of new medical treatments. |
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Develop and exploit new algorithms for data
acquisition, storage, management, and transmission. |
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Bachelor’s & Master’s Program in
Bioinformatics |
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Related Disciplines |
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Chemical Biology |
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Computational Chemistry |
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Environmental Analysis (Sloan Support) |
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Medical Informatics (Sloan Support) |
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Advanced Degrees under Development |
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Pharmacometrics, Biophotonics |
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UB-HWI Department of Structural Biology |
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Complementary Degrees |
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Canisius College |
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Niagara University |
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June 30 – July 11 |
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Perl Scripts |
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Public Databases |
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Filtering Results |
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Graphics & Visualization |
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Contact |
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Dr. Bruce Pitman (pitman@buffalo.edu) |
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miller@buffalo.edu |
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www.ccr.buffalo.edu |
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H.S. Program |
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pitman@buffalo.edu |
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Notes
