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Russ Miller |
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Director, Center for Computational Research |
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Supercomputing |
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www.gapcon.com: |
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6th Worldwide (JAMSTEC, LLNL, NSA,
IBM, LANL) |
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#1 Academia |
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9 Teraflops Aggregate Compute Capacity |
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High-End Visualization |
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Scientific Visualization |
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Urban Planning |
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Education/Outreach/Training |
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H.S. Summer Program |
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Hosts Meetings/Provides Tours |
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Work with Local Industry & Local Colleges |
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Wide-Variety of Degree Programs |
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Support/Expand HPC at UB |
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90 Research Groups in 25 Depts |
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Leverage $300K NSF Grant Þ |
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$46M Vendor Donations |
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$30M Equipment |
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$42M Grants (Peer-Reviewed) |
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Funding |
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NSF, NIH, NIMA, EPA, Keck, Sloan |
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NYS, SUNY, UB |
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IBM, SGI, Sun, DELL, HP (Compaq), Nortel, Myricom |
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Dell Linux Cluster |
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5.8TF Peak; 4036 Processors (PIII 1.2GHz + P4
2.4GHz) |
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2TB RAM; 160TB Disk |
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16TB RAID |
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Dell Linux Cluster |
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2.9TF Peak; 610 Processors (P4 2.4GHz) |
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Myrinet2000 |
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600GB RAM; 40TB Disk |
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HP/Compaq SAN (Oct, 2002) |
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25TB Disk |
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250TB Tape |
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HP/Compaq 1TF EV7 Alpha System (3/03) |
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Fakespace ImmersaDesk |
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SGI 3300W |
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Portable Systems |
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Access Grid Node |
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Tiled Display Wall |
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Onyx2 / Onyx300 |
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Groundwater Flow Modeling |
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Predict contaminant flow in groundwater &
possible migration into streams and lakes. |
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Geophysical Mass Flows |
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Study of geophysical mass flows for risk
assessment of lava flows and mudslides. |
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Astrophysics |
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Determine whether interacting astrophysical jets
in dense star environments can generate turbulence in surrounding medium |
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Bioinformatics |
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Protein Folding (Computer simulations determine
the 3D structure of proteins.) |
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Pharmacology |
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Computational Chemistry |
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Algorithm Development & Simulations |
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Fluid Dynamics |
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Modeling turbulent flows and combustion to
improve design of chemical reactors, turbine engines, and airplanes. |
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The creation and development of advanced
information and computational technologies to solve problems in biology. |
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The use of advanced computational resources and
techniques 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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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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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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Center for Advanced Bioengineering &
Biomedical Technologies |
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UB CAT |
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$1M/yr NYS |
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Medical Technologies for Product Development
& Commercialization |
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WNY STAR Center in 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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$3M Federal Government |
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$151 Corporate Funding |
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$53M/yr Peer-Reviewed Grants |
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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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Core Partners |
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Hauptman-Woodward Medical Research Institute |
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Roswell Park Cancer Institute |
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Corporate Partners |
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Amersham Pharmacia, AT&T, Beckman Coulter,
BioPharma Ireland, Bristol Myers Squibb, Confederation of Indian
Industries, Dell, General Electric, Human Genome Sciences, HP, Immco,
InforMax, Invitrogen, Pfizer Pharmaceutical, Q-Chem, Sloan Foundation, SGI, Stryker, Sun, 3M, Veridian, Wyeth Lederle,
Zeptometrix |
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WNY Business Community |
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UB $52M CoE in Bioinformatics |
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Research and business partners |
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225 employees and business associates |
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150,000 sq ft: 50% labs, 50% computational
facilities |
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Molecular Targeting Laboratory |
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Screen 30-50K compounds every 3 months |
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Apply compound to cell (different genes treated
w fluor markers) |
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Rapidly identify effect on specific gene
expression pathways |
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Gene Expression Laboratory |
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High-throughput microarray and gene chip |
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Discover new genes, their functions, and
pathways |
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Proteomics and Molecular Kinetics Lab |
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Identify molecular targets found in Gene
Expression Lab |
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Disease Modeling Laboratory |
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In vivo testing (flies, mice, baboons,…) |
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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 nano-tech research |
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E.g., handheld devices to test for diseases |
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Protein Scale-Up and Purification |
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High-Throughput Robotic Combinatorial
Chemistry/Parallel Synthetic Chemistry Capabilities |
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Drugs created robotically; Tested for
interaction with target protein |
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Rapid identification of a large number of
potential drugs |
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Public Health and Molecular Pathology |
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Tissue repositories; disease gene maps; medical
informatics |
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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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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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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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Institute of Lasers, Photonics, and Biophotonics
(www.photonics.buffalo.edu) |
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MEMS, Data Storage, Chem/Bio Sensors,
Nanotechnology, Spintronics |
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National Center for Geographic Information
Analysis (www.geog.buffalo.edu/ncgia) |
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UB, UC Santa Barbara, Univ. of Maine |
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Center for Multisource Information Fusion
(www.infofusion.buffalo.edu) |
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Center for Excellence in Document Analysis and
Recognition (www.cedar.buffalo.edu) |
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Database and Multimedia Laboratory (www.cse.buffalo.edu/DBGROUP/index.html) |
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Content based image retrieval |
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Advanced data mining algorithm development |
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Center
of Excellence in Bioinformatics (www.bioinformatics.buffalo.edu) |
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NSA
Center of Excellence in Information Systems Assurance Research and
Education (cyberterrorism) |
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Laboratory for Advanced Network Design
(www.cse.buffalo.edu/faculty/qiao/) |
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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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miller@buffalo.edu |
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www.ccr.buffalo.edu |
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Notes
