The New Partnering Between Biomedicine and Cyberspace

Luncheon Speech to

BioParks 2001

University of California, San Diego

June 23, 2001

Biology &Medicine

Engineering

Information Technology

The Convergence: A Challenge for the 21st Century

National Institutes of HealthBiomedical 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 High-

Performance 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

Structure & Function

Pathways & Physiology

Populations& Evolution

Ecosystems

Genomes

Gene Products

The Post-Genome Era

• 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

UCSBUCLA

The California NanoSystems Institute

UCSFUCB

The California Institute for Bioengineering, Biotechnology,

and Quantitative Biomedical Research

UCI

UCSD

The California Institute for Telecommunications

and Information Technology

The Center for Information Technology Research

in the Interest of Society

UCSC

UCD

UCM

Cal-(IT)2

A Integrated Approach to the New Internet

www.calit2.net

220 UCSD & UCI FacultyWorking in Multidisciplinary Teams

With Students, Industry, and the Community

The State’s $100 M Creates Unique Buildings, Equipment, and Laboratories

A Broad Partnership Response from the Private Sector

Akamai Boeing

BroadcomAMCC CAIMISCompaq

Conexant Cox Communications

EmulexEnterprise Partners VC

EntropiaEricsson

Global PhotonIBM

IdeaEdge VenturesIntersil

Irvine SensorsLeap Wireless

Litton IndustriesMedExpert

Merck Microsoft

Mission VenturesNCR

Newport CorporationOrincon

Panoram Technologies Printronix

QUALCOMMQuantum

R.W. Johnson Pharmaceutical RISAIC

SciFrameSeagate Storage

Silicon Wave Sony

STMicroelectronicsSun Microsystems

TeraBurst Networks Texas InstrumentsUCSD Healthcare The Unwired Fund

WebEx

ComputersCommunications

SoftwareSensors

BiomedicalStartups

Venture Firms

$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

Shankar Subramaniam, UCSD, Director, Data Coordination & Bioinformatics Lab,

Alliance for Cell Signaling

M o tifL ib r a r ie s

S equenceA n n o ta t io nI n te r a c t io n s

Q u e r y T o o ls A n a ly s is T o o ls

D a ta b a s e T e m p o r a r yS to r a g e

D a ta S tr u c tu r e

E d it in gT o o l

C o m p a r is o nT o o l

P a th w a yG U I

L e g a c yP a th w a y s

S ig n a lin gN e tw o r k s

D a ta S to r e B u lle t inB o a r d

A n n o ta t io n sS y s te m

O th e rA n a ly s is

T o o ls

S ig n a lin gP a th w a y s

O r g a n is m

E x p r e s s io nP r o f ile s

P r o te o m ic sP r o f ile s

I n te r a c t io nP r o f ile s

C e ll & T is s u eS p e c if ic it y

M o le c u la rD is e a s e s

G e n e s(P r o te in s )

I n te r a c t io nM o d u le s

Dynamic Growth in Mobile InternetForecast of Internet users worldwide

0

200

400

600

800

1,000

1,200

1,400

1,600

1,800

2,000

1999 2000 2001 2002 2003 2004 2005

Mobile Internet

Fixed Internet

Subscribers (millions)

3G Adds Mobility, QoS, and High Speeds

Source: Ericsson

Text/SMSText/SMS

Text/MailText/Mail

ImagesImagesMMSMMS

VideoVideoDownloadDownload

VideoVideoSteamingSteaming

The Promise of 3GDriving the Optical Core with Billions of New Internet Sources

Source: Ericsson

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

to 23% in 2007

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

½ Mile

•Commodity Internet, Internet2•CENIC’s ONI, Cal-REN2, Dig. Cal.•PACI Distributed Terascale Facility

• Wireless LANs

The UCSD “Living Grid Laboratory”—Fiber, Wireless, Compute, Data, Software

SIO

SDSC

CS

ChemMed

Eng. / Cal-(IT)2

Hosp

• High-speed optical core

Source: Phil Papadopoulos, SDSC

Wireless WAN

As Our Bodies Move On-LineBioengineering 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 RequireHigh Resolution Data Analysis Facilities

SDSCSIO

Newsday PhotoIra Schwarz

Celera Control Room

Cal-(IT)2 Control Room

Cox CommunicationsTeraburst Networks

Panoram Technologies

Wireless “Pad” Web Interface

Developing the Grid Cyber ArchitectureTo Support Medical Imaging Retrieval

Deep Web

Surface Web

Proposal-Form a National Scale Testbed for Federating Multi-scale Brain Databases

Using NIH High Field NMR Centers

Source: Mark Ellisman, UCSD

DukeUCLA

Cal Tech

StanfordU. Of MN

Harvard

NCRR Imaging and Computing Resources UCSD

Cal-(IT)2SDSC

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

• Is a Virtual Cell Possible?

www.people.virginia.edu/~rjh9u/cell1.html

Exploding Demand for Computational Powerin 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

AreciboRadio Telescope

Biology is at the Leading Edge of Using the Emerging Planetary Computer

Application Software Has Been Downloaded to Over 28,000 PCsOver 500 CPU-Years Computed

Total Storage 50 Terabytes, Peak Speed 13 Teraflops

In SilicoDrug Design

Art Olson, The Scripps

Research Institute