Center for Computational Research

Russ Miller

Director, Center for Computational Research

CCR Overview

Supercomputing

www.gapcon.com:

6^th Worldwide (JAMSTEC, LLNL, NSA, IBM, LANL)

#1 Academia

9 Teraflops Aggregate Compute Capacity

High-End Visualization

Scientific Visualization

Urban Planning

Education/Outreach/Training

H.S. Summer Program

Hosts Meetings/Provides Tours

Work with Local Industry & Local Colleges

Wide-Variety of Degree Programs

General Information

Support/Expand HPC at UB

90 Research Groups in 25 Depts

Leverage $300K NSF Grant Þ

$46M Vendor Donations

$30M Equipment

$42M Grants (Peer-Reviewed)

Funding

NSF, NIH, NIMA, EPA, Keck, Sloan

NYS, SUNY, UB

IBM, SGI, Sun, DELL, HP (Compaq), Nortel, Myricom

"Dell Linux Cluster"

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; 610 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)

CCR Visualization

Fakespace ImmersaDesk

SGI 3300W

Portable Systems

Access Grid Node

Tiled Display Wall

Onyx2 / Onyx300

Sample CCR-Supported Research

Groundwater Flow Modeling

Predict contaminant flow in groundwater & possible migration into streams and lakes.

Geophysical Mass Flows

Study of geophysical mass flows for risk assessment of lava flows and mudslides.

Astrophysics

Determine whether interacting astrophysical jets in dense star environments can generate turbulence in surrounding medium

Bioinformatics

Protein Folding (Computer simulations determine the 3D structure of proteins.)

Pharmacology

Computational Chemistry

Algorithm Development & Simulations

Fluid Dynamics

Modeling turbulent flows and combustion to improve design of chemical reactors, turbine engines, and airplanes.

Bioinformatics

The creation and development of advanced information and computational technologies to solve problems in biology.

The use of advanced computational resources and techniques to analyze data generated by the Human Genome Project to improve medical treatment.

Precise sequence of ~30K human genes have been mapped

Critical to elucidate the function of each gene.

Leads to greater understanding of human development.

Potential to treat many diseases, including AIDS cancer, MS, and Alzheimer’s and provide personalized treatment.

From Human Genome

Locate genes (tens of thousands in human body)

Determine what protein a gene regulates (millions of proteins in body)

Determine structure

Determine protein function

Devise drugs to block or enhance protein function

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 20^th 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

Bioinformatics in Buffalo

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.

BCOEB Partners

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

Experimental Facilities I

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

Experimental Facilities II

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

Protein Dynamics

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

Children’s Hospital CT

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

Groundwater Flow Modeling

Regional-scale modeling of groundwater flow and contaminant transport (Great Lakes Region)

Ability to include all hydrogeologic features as independent objects

Groundwater Modeling

Current work is based on Analytic Element Method

Key features:

High precision

Highly parallel

Object-oriented programming

Intelligent user interface

GIS facilitates large-scale regional applications

Utilized 10,661 CPU days (32 CPU years) of computing in past year on CCR’s commodity clusters

Computational Geophysical Mass Flows

Risk Mitigation

Integrate information from several sources

Simulation results

Remote sensing

GIS data

Develop realistic 3D models of geophysical mass flows

Present information at user appropriate resolutions

UB Centers Working with CCR

Institute of Lasers, Photonics, and Biophotonics (www.photonics.buffalo.edu)

MEMS, Data Storage, Chem/Bio Sensors, Nanotechnology, Spintronics

National Center for Geographic Information Analysis (www.geog.buffalo.edu/ncgia)

UB, UC Santa Barbara, Univ. of Maine

Center for Multisource Information Fusion (www.infofusion.buffalo.edu)

Center for Excellence in Document Analysis and Recognition (www.cedar.buffalo.edu)

UB Centers Working with CCR

Database and Multimedia Laboratory (www.cse.buffalo.edu/DBGROUP/index.html)

Content based image retrieval

Advanced data mining algorithm development

Center of Excellence in Bioinformatics (www.bioinformatics.buffalo.edu)

NSA Center of Excellence in Information Systems Assurance Research and Education (cyberterrorism)

Laboratory for Advanced Network Design (www.cse.buffalo.edu/faculty/qiao/)

Academic Programs

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

Contact Information

miller@buffalo.edu

www.ccr.buffalo.edu


Supercomputing
	www.gapcon.com:
		6^th Worldwide (JAMSTEC, LLNL, NSA, IBM, LANL)
		#1 Academia
	9 Teraflops Aggregate Compute Capacity
High-End Visualization
	Scientific Visualization
	Urban Planning
Education/Outreach/Training
	H.S. Summer Program
	Hosts Meetings/Provides Tours
	Work with Local Industry & Local Colleges
	Wide-Variety of Degree Programs


	Support/Expand HPC at UB
		90 Research Groups in 25 Depts
	Leverage $300K NSF Grant Þ
		$46M Vendor Donations
		$30M Equipment
		$42M Grants (Peer-Reviewed)
	Funding
		NSF, NIH, NIMA, EPA, Keck, Sloan
		NYS, SUNY, UB
		IBM, SGI, Sun, DELL, HP (Compaq), Nortel, Myricom


	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; 610 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
	SGI 3300W
	Portable Systems
	Access Grid Node
	Tiled Display Wall
	Onyx2 / Onyx300


	Groundwater Flow Modeling
		Predict contaminant flow in groundwater & possible migration into streams and lakes.
	Geophysical Mass Flows
		Study of geophysical mass flows for risk assessment of lava flows and mudslides.
	Astrophysics
		Determine whether interacting astrophysical jets in dense star environments can generate turbulence in surrounding medium
	Bioinformatics
		Protein Folding (Computer simulations determine the 3D structure of proteins.)
		Pharmacology
	Computational Chemistry
		Algorithm Development & Simulations
	Fluid Dynamics
		Modeling turbulent flows and combustion to improve design of chemical reactors, turbine engines, and airplanes.


	The creation and development of advanced information and computational technologies to solve problems in biology.
	The use of advanced computational resources and techniques to analyze data generated by the Human Genome Project to improve medical treatment.
	Precise sequence of ~30K human genes have been mapped
		Critical to elucidate the function of each gene.
		Leads to greater understanding of human development.
		Potential to treat many diseases, including AIDS cancer, MS, and Alzheimer’s and provide personalized treatment.
	From Human Genome
		Locate genes (tens of thousands in human body)
		Determine what protein a gene regulates (millions of proteins in body)
		Determine structure
		Determine protein function
		Devise drugs to block or enhance protein function


	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 20^th Century”
	Vancomycin
	Gramacidin A
	High Throughput Crystallization Method: Patented
	NIH National Genomics Center: Northeast Consortium
	Howard Hughes Medical Institute: Center for Genomics & Proteomics


	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


	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


	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


	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


	Regional-scale modeling of groundwater flow and contaminant transport (Great Lakes Region)
	Ability to include all hydrogeologic features as independent objects


	Current work is based on Analytic Element Method
	Key features:
		High precision
		Highly parallel
		Object-oriented programming
		Intelligent user interface
		GIS facilitates large-scale regional applications
	Utilized 10,661 CPU days (32 CPU years) of computing in past year on CCR’s commodity clusters


	Integrate information from several sources
		Simulation results
		Remote sensing
		GIS data
	Develop realistic 3D models of geophysical mass flows
	Present information at user appropriate resolutions


	Institute of Lasers, Photonics, and Biophotonics (www.photonics.buffalo.edu)
		MEMS, Data Storage, Chem/Bio Sensors, Nanotechnology, Spintronics
	National Center for Geographic Information Analysis (www.geog.buffalo.edu/ncgia)
		UB, UC Santa Barbara, Univ. of Maine
	Center for Multisource Information Fusion (www.infofusion.buffalo.edu)
	Center for Excellence in Document Analysis and Recognition (www.cedar.buffalo.edu)


	Database and Multimedia Laboratory (www.cse.buffalo.edu/DBGROUP/index.html)
		Content based image retrieval
		Advanced data mining algorithm development
	Center of Excellence in Bioinformatics (www.bioinformatics.buffalo.edu)
	NSA Center of Excellence in Information Systems Assurance Research and Education (cyberterrorism)
	Laboratory for Advanced Network Design (www.cse.buffalo.edu/faculty/qiao/)


	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