Buffalo Center of Excellence in Bioinformatics
| Russ Miller | |
| Director, Center for Computational Research | |
| UB Distinguished Professor, Computer Science & Engineering | |
| Senior Research Scientist, Hauptman-Woodward Medical Inst | |
Recent Biomedical
Advances
(Buffalo, NY)
| PSA Test (screen for Prostate Cancer) | ||
| Avonex: Interferon Treatment for Multiple Sclerosis | ||
| Artificial Blood | ||
| Nicorette Gum | ||
| Fetal Viability Test | ||
| Edible Vaccine for Hepatitis C | ||
| Timed-Release Insulin Therapy | ||
| Anti-Arrythmia Therapy | ||
| Tarantula venom | ||
| Direct Methods Structure Determination | ||
| Listed on “Top Ten Algorithms of the 20th Century” | ||
| Vancomycin | ||
| Gramacidin A | ||
| High Throughput Crystallization Method: Patented | ||
| NIH National Genomics Center: Northeast Consortium | ||
| Howard Hughes Medical Institute: Center for Genomics & Proteomics | ||
Animal Models and Preclinical Toxicology
| Center for Advanced Bioengineering & Biomedical Technologies | ||
| UB CAT | ||
| $1M/yr NYS | ||
| Medical Technologies for Product Development & Commercialization | ||
| WNY STAR Center in Disease Modeling & Therapy Discovery | ||
| UB, HWI, RPCI, Kaleida | ||
| $15.3M NYS | ||
| Software, device development, and drug therapies | ||
| Buffalo Center of Excellence in Bioinformatics | ||
| UB, HWI, RPCI | ||
| $61M NYS | ||
| $3M Federal Government | ||
| $151 Corporate Funding | ||
| $53M/yr Peer-Reviewed Grants | ||
Buffalo Center of Excellence
in Bioinformatics (BCOEB)
| Act as a research, development, education, and economic resource for industries based on bioinformatics, including information technology, biotech, and pharmaceuticals. | |
| Combine state-of-the-art computational facilities with high-throughput experimental facilities to enable the development of new medical treatments. | |
| Develop and exploit new algorithms for data acquisition, storage, management, and transmission. |
| Core Partners | ||
| Hauptman-Woodward Medical Research Institute | ||
| Roswell Park Cancer Institute | ||
| Corporate Partners | ||
| 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 | ||
| WNY Business Community | ||
Life Sciences
Complex
(Buffalo-Niagara Medical Campus)
| UB $52M CoE in Bioinformatics | |
| Research and business partners | |
| 225 employees and business associates | |
| 150,000 sq ft: 50% labs, 50% computational facilities | |
| Molecular Targeting Laboratory | ||
| Screen 30-50K compounds every 3 months | ||
| Apply compound to cell (different genes treated w fluor markers) | ||
| Rapidly identify effect on specific gene expression pathways | ||
| Gene Expression Laboratory | ||
| High-throughput microarray and gene chip | ||
| Discover new genes, their functions, and pathways | ||
| Proteomics and Molecular Kinetics Lab | ||
| Identify molecular targets found in Gene Expression Lab | ||
| Disease Modeling Laboratory | ||
| In vivo testing (flies, mice, baboons,…) | ||
| Gene targeting and genetic mapping facilities | ||
| Bioengineering Support Laboratory | ||
| Capabilities in photonics and nano-tech research | ||
| E.g., handheld devices to test for diseases | ||
| Protein Scale-Up and Purification | ||
| High-Throughput Robotic Combinatorial Chemistry/Parallel Synthetic Chemistry Capabilities | ||
| Drugs created robotically; Tested for interaction with target protein | ||
| Rapid identification of a large number of potential drugs | ||
| Public Health and Molecular Pathology | ||
| Tissue repositories; disease gene maps; medical informatics | ||
| High-Throughput Search Process for Structural Biology | ||
| Tests 1536 “chemical cocktails” to determine effective parameters for crystallization | ||
| Center for Computational Research | ||
| Leading Academic Supercomputing Center | ||
| High-Performance Computing (9TF; 250TB) | ||
| High-End Visualization | ||
| Support ~100 Groups in ~25 Depts | ||
| $42M Grants; $46M Vendor Support | ||
| Education/Outreach/Training | ||
| H.S. Summer Program | ||
| Host Meetings/Provide Tours | ||
| Work with Local Industry & Local Colleges | ||
| M.S. Certificate Program in Computational Science | ||
| Dell Linux Cluster | ||
| 5.8TF Peak; 4036 Processors (PIII 1.2GHz + P4 2.4GHz) | ||
| 2TB RAM; 160TB Disk | ||
| 16TB RAID | ||
| Dell Linux Cluster | ||
| 2.9TF Peak; 304 Processors (P4 2.4GHz) | ||
| Myrinet2000 | ||
| 600GB RAM; 40TB Disk | ||
| HP/Compaq SAN (Oct, 2002) | ||
| 25TB Disk | ||
| 250TB Tape | ||
| HP/Compaq 1TF EV7 Alpha System (3/03) | ||
| Fakespace ImmersaDesk | |
| Portable Systems | |
| SGI 3300W | |
| Access Grid Node | |
| Tiled Display Wall | |
| Onyx2 / Onyx300 |
Molecular Structure Determination
| SnB Software by UB/HWI | ||
| “Top Algorithms of the Century” | ||
| Critical to Rational Drug Design | ||
| Important Link in Structural Biology | ||
| Current Effort | ||
| Grid | ||
| Collaboratory | ||
| Intelligent Learning | ||
| Vancomycin solved with SnB | ||
| “Antibiotic of Last Resort” | ||
| Original molecular structure required 5 months of computing to solve | ||
| (Re)solved in a single day on CCR’s supercomputers | ||
| Ability of proteins to perform biological function is attributed to their 3-D structure. | |
| Protein folding problem refers to the challenge of predicting 3-D structure from amino-acid sequence. | |
| Solving the protein folding problem will impact drug design. |
| Dynamics of Hemoglobin (Example) | ||
| 50 Days of Processing on 16 Processors (800 CPU Days) | ||
| Key | ||
| White – Heme Groups | ||
| Red – Phe97 | ||
| Red – Oxygen (in the subunit at bottom) | ||
| Green – His 69 and 101 | ||
| Blue – Tyr 72 | ||
| Cyan (Ball) – Water Molecules | ||
| Yellow – Helix E/F | ||
| Interest | ||
| Flip of the Phe97 ring at top | ||
| Water movement around Phe97 | ||
| Heme-heme relative movement | ||
| 3D Reconstruction of CT Dataset | |
| Created with the Visualization Toolkit (VTK) on a Linux Workstation | |
| 3D Isosurface Clearly Shows Structure that is Nearly Impossible to Determine from 2D Slices |
| Master’s Program in Bioinformatics (Sloan) | ||
| Advanced Degrees under development | ||
| Pharmacometrics, Biophotonics, Computational Chemistry, Molecular Biology | ||
| School of Informatics (AT&T curr. dev.) | ||
| UB-HWI Dept. of Structural Biology | ||
| Complementary Degrees | ||
| Canisius College and Niagara University | ||
| miller@buffalo.edu | |
| www.ccr.buffalo.edu | |
| www.bioinformatics.buffalo.edu | |