The New Internet andBiomedical Research

Briefing to the

Dean’s Advisory Board

School of Medicine, UCSD

San Diego, CA

March 1, 2001

www.soe.uiuc.edu/~lsmarr

• 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

The Emerging Global Information GridA Mobile Internet Powered by a Planetary Computer

Complex Problems Require a New Research and Education Framework

www.calit2.net

220 UCSD & UCI FacultyWorking in Multidisciplinary Teams

With Students, Industry, and the Community

A Broad Partnership Response from the Private Sector

Akamai Boeing

BroadcomAMCC CAIMISCompaq

Conexant Copper Mountain

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

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

Wireless “Pad” Web Interface

Developing the Grid Cyber ArchitectureTo Support Medical Imaging Retrieval

DukeUCLA

Cal Tech

StanfordU. Of MN

Harvard

NCRR Imaging and Computing Resources UCSD

Cal-(IT)2SDSC

Deep Web

Surface Web

Method-Form a National Scale Testbed for Federating Large DatabasesUsing NIH High Field NMR Centers

Source: Mark Ellisman, UCSD

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

The Perfect Storm: Convergence of Engineering with BioMed, Physics, & IT

5 nanometersHuman Rhinovirus

IBM Quantum CorralIron Atoms on Copper400x

Magnification

From MEMS to Nanotech

VCSELaser

500x Magnification 2 mm

Nanogen MicroArray

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!– 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 BuildingThe Capstone of the Engineering Quad

Occupancy 2004220,000 Gross SF

Integrate Cross-Cutting TeamsSDSC / Faculty Joint ProjectsNanofabrication Clean Rooms Telecommunications LaboratoriesAdvanced VisualizationAntenna Farm

From Telephone Conference Calls to Access Grid International Video Meetings

Access Grid Lead-ArgonneNSF STARTAP Lead-UIC’s Elec. Vis. Lab

Linking Researchers with IP Multicast

½ Mile

•Commodity Internet, Internet2•High-speed WAN (OC48+)•Remote Wireless Data Ingestion

• Campus Wireless

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

SIO

SDSC

CS

ChemMed

Eng. / Cal-(IT)2

Hosp

• High-speed optical core• 8 Gigabit now• 80 Gigabit in 18 months• 1 Terabit in 36 Months

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 PCsNearly 1.5 Million CPU-Hours Computed

In SilicoDrug Design

Art Olson, TSRI