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The New Partnering Between Biomedicine and Cyberspace Luncheon Speech to BioParks 2001 University of California, San Diego June 23, 2001.

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Presentation on theme: "The New Partnering Between Biomedicine and Cyberspace Luncheon Speech to BioParks 2001 University of California, San Diego June 23, 2001."— Presentation transcript:

1 The New Partnering Between Biomedicine and Cyberspace Luncheon Speech to BioParks 2001 University of California, San Diego June 23, 2001

2 Biology & Medicine Engineering Information Technology The Convergence: A Challenge for the 21st Century

3 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 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

4 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

5 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

6 California Has Undertaken a Grand Experiment in Partnering UCSB UCLA The California NanoSystems Institute UCSF UCB 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

7 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 States $100 M Creates Unique Buildings, Equipment, and Laboratories

8 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 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 Computers Communications Software Sensors Biomedical Startups Venture Firms $140 M Match From Industry

9 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.

10 Cellular Signaling Pathway Database, Analysis Tools and User Interface Shankar Subramaniam, UCSD, Director, Data Coordination & Bioinformatics Lab, Alliance for Cell Signaling

11 Dynamic Growth in Mobile Internet Forecast of Internet users worldwide ,000 1,200 1,400 1,600 1,800 2, Mobile Internet Fixed Internet Subscribers (millions) 3G Adds Mobility, QoS, and High Speeds Source: Ericsson

12 Text/SMS Text/Mail ImagesMMS VideoDownload VideoSteaming The Promise of 3G Driving 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

13 Broadband Wireless Internet is Here Today Local Area Wireless Internet Watering Holes –Ad Hoc IEEE 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

14 ½ Mile Commodity Internet, Internet2 CENICs ONI, Cal-REN2, Dig. Cal. PACI Distributed Terascale Facility Wireless LANs The UCSD Living Grid Laboratory Fiber, Wireless, Compute, Data, Software SIO SDSC CS Chem Med Eng. / Cal-(IT) 2 Hosp High-speed optical core Source: Phil Papadopoulos, SDSC Wireless WAN

15 As Our Bodies Move On-Line Bioengineering and Bioinformatics Merge New SensorsIsraeli Video Pill –Battery, Light, & Video Camera –Images Stored on Hip Device Next StepPutting 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

16 Vast Data Sets Will Require High Resolution Data Analysis Facilities SDSC SIO Newsday Photo Ira Schwarz Celera Control Room Cal-(IT) 2 Control Room Cox Communications Teraburst Networks Panoram Technologies

17 Wireless Pad Web Interface Developing the Grid Cyber Architecture To 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 Duke UCLA Cal Tech Stanford U. Of MN Harvard NCRR Imaging and Computing Resources UCSD Cal-(IT) 2 SDSC

18 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?

19 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

20 Immense Computing Power Will Be Required to Lead in Post-Genomic Research We Dont Need an Evolution in Computing, We Need a RevolutionCraig 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 4s! Prototype by 2004

21 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 sites! –226 Countries Contributing Cycles (US is 57%) Sophisticated Data & Signal Processing Analysis Arecibo Radio Telescope

22 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

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