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The New Partnering Between Biomedicine and Cyberspace

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.

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The New Partnering Between Biomedicine and Cyberspace

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

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

  3. 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

  4. The Post-Genome Era Genomes Populations& Evolution Structure & Function Gene Products Pathways & Physiology Ecosystems • 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 UCI UCSD The California Institute for Bioengineering, Biotechnology, and Quantitative Biomedical Research The Center for Information Technology Research in the Interest of Society UCD UCB UCM The California NanoSystems Institute UCSF UCSC The California Institute for Telecommunications and Information Technology

  7. Cal-(IT)2A 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

  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 InternetForecast of Internet users worldwide 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 2003 2004 2005 3G Adds Mobility, QoS, and High Speeds Source: Ericsson

  12. The Promise of 3GDriving the Optical Core with Billions of New Internet Sources Video Download Video Steaming Images MMS Text/Mail Text/SMS 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 Source: Ericsson

  13. 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

  14. 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 Eng. / Cal-(IT)2 CS Hosp Med Chem • Wireless LANs ½ Mile SIO Source: Phil Papadopoulos, SDSC

  15. 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

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

  17. Developing the Grid Cyber ArchitectureTo Support Medical Imaging Retrieval Stanford U. Of MN NCRR Imaging and Computing Resources UCSD Harvard Cal Tech SDSC Cal-(IT)2 UCLA Duke Wireless “Pad” Web Interface Proposal-Form a National Scale Testbed for Federating Multi-scale Brain Databases Using NIH High Field NMR Centers Surface Web Deep Web Source: Mark Ellisman, UCSD

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

  19. 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

  20. Immense Computing Power Will Be Required to Lead in Post-Genomic Research • ”We Don’t Need an Evolution in Computing, We Need a Revolution”—CraigVenter • 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

  21. 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

  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 Art Olson, The Scripps Research Institute In Silico Drug Design

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