Transcript The New Internet and Biomedical Research

The New Internet and
Biomedical Research
Briefing to the
Dean’s Advisory Board
School of Medicine, UCSD
San Diego, CA
March 1, 2001
www.soe.uiuc.edu/~lsmarr
The Emerging Global Information Grid
A Mobile Internet Powered by a Planetary Computer
• Wireless Access--Anywhere, Anytime
• Broadband to the Home and Small Businesses
• Vast Increase in Internet End Points
– Embedded Processors
– Sensors and Actuators
– Information Appliances
• A Core of Optical Fiber Carrying Parallel Light Waves
• Emergence of a Distributed Planetary Computer
– Storage everywhere
– Scalable computing power
Complex Problems Require
a New Research and Education Framework
220 UCSD & UCI Faculty
Working in Multidisciplinary Teams
With Students, Industry, and the Community
www.calit2.net
A Broad Partnership Response
from the Private Sector
Akamai
Boeing
Broadcom
AMCC
CAIMIS
Compaq
Conexant
Copper Mountain
Emulex
Enterprise Partners VC
Entropia
Ericsson
Global Photon
IBM
IdeaEdge Ventures
Intersil
Irvine Sensors
Leap Wireless
Litton Industries
MedExpert
Merck
Microsoft
Computers
Communications
Software
Sensors
Biomedical
Startups
Venture Firms
Mission Ventures
NCR
Newport Corporation
Orincon
Panoram Technologies
Printronix
QUALCOMM
Quantum
R.W. Johnson Pharmaceutical RI
SAIC
SciFrame
Seagate Storage
Silicon Wave
Sony
STMicroelectronics
Sun Microsystems
TeraBurst Networks
Texas Instruments
UCSD Healthcare
The Unwired Fund
WebEx
$140 M Match From Industry
Elements of the
Cal -(IT)2 Industrial Partnerships
• Endowed Chairs for Professors
• Start-Up Support for Young Faculty
• Graduate Student Fellowships
• Research and Academic Professionals
• Sponsored Research Programs
• Equipment Donations for Cal-(IT)2 and Campus
• Named Laboratories in new Institute Buildings
• Pro Bono Services and Software
Developing the Grid Cyber Architecture
To Support Medical Imaging Retrieval
Method-Form a National Scale Testbed for Federating Large Databases
Using NIH High Field NMR Centers
Stanford
U. Of MN
NCRR Imaging
and Computing
Resources UCSD
Harvard
Cal Tech
SDSC
Surface Web
Cal-(IT)2
Deep Web
UCLA
Duke
Source: Mark Ellisman, UCSD
Wireless “Pad”
Web Interface
Cellular Signaling Pathway Database,
Analysis Tools and User Interface
Genes
(Proteins)
Sequence
Annotation
Interactions
Motif
Libraries
Signaling
Pathways
Organism
Data Structure
Database
Query Tools
Interaction
Modules
Pathway
GUI
Temporary
Storage
Editing
Tool
Legacy
Pathways
Signaling
Networks
Bulletin
Board
Annotations
System
Expression
Profiles
Comparison
Tool
Analysis Tools
Data Store
Other
Analysis
Tools
Shankar Subramaniam, UCSD, Director,
Data Coordination & Bioinformatics Lab,
Alliance for Cell Signaling
Cell & Tissue
Specificity
Molecular
Diseases
Proteomics
Profiles
Interaction
Profiles
The Perfect Storm:
Convergence of Engineering with BioMed, Physics, & IT
500x
Magnification
Nanogen MicroArray
2 mm
VCSELaser
400x
Magnification
IBM Quantum Corral
Iron Atoms on Copper
Human Rhinovirus
5 nanometers
From MEMS to Nanotech
As Our Bodies Move On-Line
Bioengineering and Bioinformatics Merge
• New Sensors—Israeli Video Pill
– Battery, Light, & Video Camera
– Images Stored on Hip Device
• Next Step—Putting You On-Line!
– Key Metabolic and Physical Variables
– Wireless Internet Transmission
– Model -- Dozens of 25 Processors and 60
Sensors / Actuators Inside of our Cars
• Post-Genomic Individualized Medicine
– Combine Your Genetic Code &
Noninvasive Imaging Techniques, with
Your Body’s Data Flow
– Use Powerful AI Data Mining Techniques
www.givenimaging.com
The UCSD Cal-(IT)2 Building
The Capstone of the Engineering Quad
Occupancy 2004
220,000 Gross SF
Integrate Cross-Cutting Teams
SDSC / Faculty Joint Projects
Nanofabrication Clean Rooms
Telecommunications Laboratories
Advanced Visualization
Antenna Farm
From Telephone Conference Calls to
Access Grid International Video Meetings
Linking Researchers with IP Multicast
Access Grid Lead-Argonne
NSF STARTAP Lead-UIC’s Elec. Vis. Lab
The UCSD “Living Grid Laboratory”—
Fiber, Wireless, Compute, Data, Software
•Commodity Internet, Internet2
•High-speed WAN (OC48+)
•Remote Wireless Data Ingestion
SDSC
• High-speed optical core
• 8 Gigabit now
• 80 Gigabit in 18 months
• 1 Terabit in 36 Months
CS
Eng. / Cal-(IT)2
Hosp
Med
Chem
• Campus Wireless
SIO
½ Mile
Source: Phil Papadopoulos, SDSC
Extending the Grid to Planetary Dimensions
Using Distributed Computing and Storage
AutoDock Application Software Has Been Downloaded to Over 12,000 PCs
Nearly 1.5 Million CPU-Hours Computed
In Silico
Drug Design
Art Olson,
TSRI