The New Partnering Between
Biomedicine and Cyberspace
Luncheon Speech to
BioParks 2001
University of California, San Diego
June 23, 2001
The Convergence:
A Challenge for the 21st Century
Information
Technology
Biology &
Medicine
Engineering
National Institutes of Health
Biomedical Information Science and Technology Initiative
• National Needs for Biomedical Research
• Interdisciplinary Teams
– Collaborating to Develop Mathematical Models, Write
Software and Adapt Systems
• Cooperation with Computer Science in:
– Algorithm, Software, Database and System Development
• Improved Access to Computing
– Shared PC Clusters in Biomedical Laboratories to HighPerformance Systems in National Centers
• Workforce Development to Encompasses Every Level
– Technician to Ph.D.
• New Centers for Research and Teaching
– People Competent in Biomedicine and Computation &
Mathematics
www.nih.gov/about/director/060399.htm
The Post-Genome Era
Genomes
Populations
Structure &
& Evolution
Function
Gene
Pathways &
Ecosystems
Products
Physiology
• Bioinformatics Provides The Tools:
– To Extract And Combine Knowledge
– From Isolated Data And Results In Biology
– Into Meaningful Working Models Of Cells And Organisms
– Their Birth, Life And Death
Source: Shankar Subramaniam, UCSD
Bioinformatics –
A Fundamental Post-Genomic Technology
• Comparative and Functional Genomics
– Chromosome Organization and Evolution
– Phylogenetic Relationships From Sequence Comparisons
• Developmental and Integrative Biology
– Expression Profiling in Cells
– Deciphering Multigenic Traits
• Microanalytical Systems
– Sequence Analysis From Microarrays
– Pattern Analysis and Association With Pathways
• Cellular and Molecular Bioengineering
– Metabolic Reconstruction
– Integration of Pathways to Construct a Genome-Based Cell Models
• Molecular Medicine
– Prediction of Phenotypes From Genomic Information
– Polymorphism and Sequence Analysis of Diseased States
Source: Alliance for Cell Signaling
California Has Undertaken a
Grand Experiment in Partnering
The California Institute for Bioengineering,
Biotechnology,
and Quantitative Biomedical Research
The Center for
Information Technology Research
in the Interest of Society
UCD
UCB
UCSF UCM
UCSC
The California
NanoSystems Institute
UCSB
UCLA
UCI
UCSD
The California Institute
for Telecommunications
and Information Technology
Cal-(IT)2
A Integrated Approach to the New Internet
220 UCSD & UCI Faculty
Working in Multidisciplinary Teams
With Students, Industry, and the Community
The State’s $100 M
Creates Unique Buildings, Equipment, and Laboratories
www.calit2.net
A Broad Partnership Response
from the Private Sector
Akamai
Boeing
Broadcom
AMCC
CAIMIS
Compaq
Conexant
Cox Communications
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
The Alliance For Cellular Signaling (AfCS)
An Academic / Industrial / Government Partnership
• Principal Investigator: Alfred Gilman, UT-SWMED
– Academic Partners: UCSF, Caltech, Stanford, UCSD
• Federal Sponsors
– The National Institute of General Medical sciences
– The National Institute of Allergy and Infectious Diseases
– The National Cancer Institute
• Industrial Sponsors
–
–
–
–
–
–
–
Eli Lilly and Company
Johnson & Johnson
Merck Genome Research Institute
Novartis AG
Chiron Corporation
Aventis
The Agouron Research Institute
• Scientific Collaborations With:
– Isis Pharmaceuticals
– Myriad Genetics, Inc.
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
Dynamic Growth in Mobile Internet
Forecast of Internet users worldwide
3G Adds Mobility, QoS, and High Speeds
Subscribers (millions)
2,000
1,800
1,600
1,400
1,200
1,000
Mobile Internet
800
600
400
Fixed Internet
200
0
1999
2000
2001
2002
Source: Ericsson
2003
2004
2005
The Promise of 3G
Driving the Optical Core with Billions of New Internet Sources
Consumers are 80% of 2G Usage
Corporations are Supposed to be 80% of Early 3G
3G Is Estimated to Grow From
1.3% of the Wireless Market in 2002
Images
to 23% in 2007
MMS
Text/Mail
Text/SMS
Source: Ericsson
Video
Steaming
Video
Download
Broadband Wireless Internet is Here Today
• Local Area Wireless Internet “Watering Holes”
– Ad Hoc IEEE 802.11 Domains
– Real Broadband--11 mbps Going to 54 mbps
– Security and Authentication can be Added
– But, it is Shared and Local
– MobileStar--Admiral Clubs, Starbucks, Major Hotels, …
• Doctors Are Experimenting with Wireless and PDAs
– Medical Record in the Hand
– Avoiding Medical Errors
– Link to Literature and Real Time Patient Readouts
The UCSD “Living Grid Laboratory”—
Fiber, Wireless, Compute, Data, Software
•Commodity Internet, Internet2
•CENIC’s ONI, Cal-REN2, Dig. Cal.
•PACI Distributed Terascale Facility
Wireless WAN
SDSC
• High-speed optical core
CS
Eng. / Cal-(IT)2
Hosp
Med
Chem
• Wireless LANs
SIO
½ Mile
Source: Phil Papadopoulos, SDSC
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!
– Wireless Internet Transmission
– Key Metabolic and Physical Variables
– Model -- Dozens of 25 Processors and 60
Sensors / Actuators Inside of our Cars
• Post-Genomic Individualized Medicine
– Combine
– Genetic Code
– Body Data Flow
– Use Powerful AI Data Mining Techniques
www.givenimaging.com
Vast Data Sets Will Require
High Resolution Data Analysis Facilities
Celera
Control Room
SDSC
SIO
Cal-(IT)2
Control Room
Cox Communications
Teraburst Networks
Panoram Technologies
Newsday Photo
Ira Schwarz
Developing the Grid Cyber Architecture
To Support Medical Imaging Retrieval
Proposal-Form a National Scale Testbed
for Federating Multi-scale Brain 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
What Data is Needed to Specify
a Single Eukaryotic Cell?
•
Organelles
– 4 Million Ribosomes
– 30,000 Proteasomes
– Dozens of Mitochondria
•
Macromolecules
– 5 Billion Proteins
– 5,000 to 10,000
different species
– 1 meter of DNA with
Several Billion bases
– 60 Million tRNAs
– 700,000 mRNAs
•
Chemical Pathways
– Vast numbers
– Tightly coupled
www.people.virginia.edu/~rjh9u/cell1.html
•
Is a Virtual Cell Possible?
Exploding Demand for Computational Power
in the Life Sciences
• Life Sciences
– $9 billion in IT by 2003 – IBM
– Bioinformatics: $3.8 billion in IT – UBS Warburg
– IBM, Compaq, Sun, HP targeting
• Life Sciences
– Drug screening
– DNA sequencing
– Genomics
– Proteomics
– Computational chemistry
Immense Computing Power Will Be Required
to Lead in Post-Genomic Research
• ”We Don’t Need an Evolution in Computing,
We Need a Revolution”—Craig Venter
• Sandia and Celera Will Collaborate On:
– Advanced Algorithms
– Visualization Technologies for Analyzing
Massive Quantities of Experimental Data From
High-Throughput Instruments
• Equivalent to 100,000 Pentium 4’s!
• Prototype by 2004
SETI@home Demonstrated that PC Internet
Computing Could Grow to Megacomputers
• Running on 670,000 PCs, ~1000 CPU Years per Day
– Over Half a Million CPU Years so far!
– 22 Teraflops sustained 24x7
– Windows Outnumbers Mac, or Linux + Solaris 10:1
– 64% of Cycles from .com or .net sites!
– 226 Countries Contributing Cycles (US is 57%)
• Sophisticated Data & Signal Processing Analysis
Arecibo
Radio Telescope
Biology is at the Leading Edge of Using the
Emerging Planetary Computer
Application Software Has Been Downloaded to Over 28,000 PCs
Over 500 CPU-Years Computed
Total Storage 50 Terabytes, Peak Speed 13 Teraflops
In Silico
Drug Design
Art Olson,
The Scripps
Research
Institute