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Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)

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Larry Smarr
Larry Smarr

06.04.26 Invited Talk CONNECT Board Meeting Title: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) La Jolla, CA

Technology
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Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) Invited Talk CONNECT Board Meeting La Jolla, CA April 26, 2006 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technologies Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD
Genomes Range Over Orders of Magnitude in Length Russell Dolittle, Nature v.419, p. 494 (2002) Microbes
Evolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial World Source: Carl Woese, et al You Are Here Much of Genome Work Has Occurred in Animals
Microbial Genomics Let’s Us Look Back Nearly 4 Billion Years In the Evolution of Life Science Falkowski and Vargas 304 (5667): 58
The Sargasso Sea Experiment The Power of Environmental Metagenomics ,[object Object],[object Object],[object Object],[object Object],MODIS-Aqua satellite image of ocean chlorophyll in the Sargasso Sea grid about the BATS site from 22 February 2003 J. Craig Venter, et al. Science 2 April 2004: Vol. 304. pp. 66 - 74
Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes Sorcerer II Data Will Double Number of Proteins in GenBank!
PI Larry Smarr Announced January 17, 2006 $24.5M Over Seven Years
Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server Traditional User Response Request Source: Phil Papadopoulos, SDSC, Calit2 + Web Services ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Flat File Server Farm W E B PORTAL Dedicated Compute Farm (100s of CPUs) TeraGrid: Cyberinfrastructure Backplane (scheduled activities, e.g. all by all comparison) (10000s of CPUs) Web (other service) Local Cluster Local Environment Direct Access Lambda Cnxns Data- Base Farm 10 GigE Fabric
First Implementation of the CAMERA Complex Compute Database & Storage
CAMERA Timeline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The Bioinformatics Core of the Joint Center for Structural Genomics will be Housed in the Calit2@UCSD Building Extremely Thermostable -- Useful for Many Industrial Processes (e.g. Chemical and Food) 173 Structures (122 from JCSG) ,[object Object],[object Object],[object Object],[object Object],Source: John Wooley, UCSD
Interactive Visualization of Thermatoga Proteins at Calit2 Source: John Wooley, Jurgen Schulze, Calit2
OptIPuter Scalable Adaptive Graphics Environment (SAGE) Allows Integration of HD Streams Source: David Lee, NCMIR, UCSD
Calit2 and the Venter Institute Will Combine Telepresence with Remote Interactive Analysis Live Demonstration of 21st Century National-Scale Team Science OptIPuter Visualized Data HDTV Over Lambda 25 Miles Venter Institute
Paul Gilna Has Just Been Recruited from Los Alamos to Become Executive Director of CAMERA ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Embargoed till Press Announcement This Week!

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Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)

  • 1. Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) Invited Talk CONNECT Board Meeting La Jolla, CA April 26, 2006 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technologies Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD
  • 2. Genomes Range Over Orders of Magnitude in Length Russell Dolittle, Nature v.419, p. 494 (2002) Microbes
  • 3. Evolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial World Source: Carl Woese, et al You Are Here Much of Genome Work Has Occurred in Animals
  • 4. Microbial Genomics Let’s Us Look Back Nearly 4 Billion Years In the Evolution of Life Science Falkowski and Vargas 304 (5667): 58
  • 5.
  • 6. Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes Sorcerer II Data Will Double Number of Proteins in GenBank!
  • 7. PI Larry Smarr Announced January 17, 2006 $24.5M Over Seven Years
  • 8.
  • 9. First Implementation of the CAMERA Complex Compute Database & Storage
  • 10.
  • 11.
  • 12. Interactive Visualization of Thermatoga Proteins at Calit2 Source: John Wooley, Jurgen Schulze, Calit2
  • 13. OptIPuter Scalable Adaptive Graphics Environment (SAGE) Allows Integration of HD Streams Source: David Lee, NCMIR, UCSD
  • 14. Calit2 and the Venter Institute Will Combine Telepresence with Remote Interactive Analysis Live Demonstration of 21st Century National-Scale Team Science OptIPuter Visualized Data HDTV Over Lambda 25 Miles Venter Institute
  • 15.