Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) Invited Talk  CONNECT Investment ...
Two New Calit2 Buildings Provide ~340,000 GSF  and New Laboratories for “Living in the Future” <ul><li>Over 1000 Researche...
Calit2 Brings Computer Scientists and Engineers  Together with Biomedical Researchers <ul><li>Some Areas of Concentration:...
The OptIPuter Project – Creating High Resolution Portals  Over Dedicated Optical Channels to Global Science Data <ul><li>N...
Dedicated Optical Channels Makes  High Performance Cyberinfrastructure Possible Parallel Lambdas are Driving Optical Netwo...
National LambdaRail (NLR) and TeraGrid Provides  Cyberinfrastructure Backbone for U.S. Researchers NLR 4 x 10Gb Lambdas In...
PI Larry Smarr Announced January 17, 2006 $24.5M Over Seven Years
Paul Gilna Has Just Been Recruited from Los Alamos  to Become Executive Director of CAMERA <ul><li>Formerly </li></ul><ul>...
Calit2’s Direct Access Core Architecture  Will Create Next Generation Metagenomics Server Traditional User Response Reques...
The Future Home of the Moore Foundation Funded Marine Microbial Ecology Metagenomics Complex First Implementation of  the ...
CAMERA  Tools and Workflows <ul><li>Initial set </li></ul><ul><ul><li>BLAST Server </li></ul></ul><ul><ul><li>Clustering <...
The Bioinformatics Core of the Joint Center for Structural Genomics will be Housed in the Calit2@UCSD Building Extremely T...
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 Cen...
Countries are Aggressively Creating Gigabit Services: Interactive Access to CAMERA and LOOKING Systems www.glif.is Created...
OptIPortal–  Termination Device for the OptIPuter Global Backplane <ul><li>20 Dual CPU Nodes, 20 24” Monitors, ~$50,000 </...
UIC/UCSD 10GE  CAVEWave o n the National LambdaRail Emerging OptIPortal Sites   CAVEWave Connects Chicago to Seattle to Sa...
First Remote Interactive High Definition Video  Exploration of Deep Sea Vents Source John Delaney & Deborah Kelley, UWash ...
High Definition Still Frame  of Hydrothermal Vent Ecology 2.3 Km Deep  White Filamentous Bacteria on 'Pill Bug' Outer Cara...
A Near Future Metagenomics  Fiber Optic-Enabled Data Generator Source John Delaney, UWash
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Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)

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06.07.31
Invited Talk
CONNECT Investment Community Meeting
Calit2@UCSD
Title: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)
La Jolla, CA

Published in: Education, Technology
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Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)

  1. 1. Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) Invited Talk CONNECT Investment Community Meeting [email_address] La Jolla, CA July 31, 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. 2. Two New Calit2 Buildings Provide ~340,000 GSF and New Laboratories for “Living in the Future” <ul><li>Over 1000 Researchers in Two Buildings </li></ul><ul><ul><li>Linked via Dedicated Optical Networks </li></ul></ul><ul><ul><li>International Conferences and Testbeds </li></ul></ul><ul><li>New Laboratories </li></ul><ul><ul><li>Nanotechnology </li></ul></ul><ul><ul><li>Virtual Reality, Digital Cinema </li></ul></ul>UC Irvine www.calit2.net State Funded $100M in Capital for Calit2 Buildings UC San Diego Richard C. Atkinson Hall Dedication Oct. 28, 2005
  3. 3. Calit2 Brings Computer Scientists and Engineers Together with Biomedical Researchers <ul><li>Some Areas of Concentration: </li></ul><ul><ul><li>Metagenomics </li></ul></ul><ul><ul><li>Genomic Analysis of Organisms </li></ul></ul><ul><ul><li>Evolution of Genomes </li></ul></ul><ul><ul><li>Cancer Genomics </li></ul></ul><ul><ul><li>Human Genomic Variation and Disease </li></ul></ul><ul><ul><li>Proteomics </li></ul></ul><ul><ul><li>Mitochondrial Evolution </li></ul></ul><ul><ul><li>Computational Biology </li></ul></ul><ul><ul><li>Information Theory and Biological Systems </li></ul></ul>UC San Diego UC Irvine
  4. 4. The OptIPuter Project – Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data <ul><li>NSF Large Information Technology Research Proposal </li></ul><ul><ul><li>Calit2 (UCSD, UCI) and UIC Lead Campuses—Larry Smarr PI </li></ul></ul><ul><ul><li>Partnering Campuses: SDSC, USC, SDSU, NCSA, NW, TA&M, UvA, SARA, NASA Goddard, KISTI, AIST, CRC(Canada), CICESE (Mexico) </li></ul></ul><ul><li>Industrial Partners </li></ul><ul><ul><li>IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent </li></ul></ul><ul><li>$13.5 Million Over Five Years—Now In the Fourth Year </li></ul>NIH Biomedical Informatics NSF EarthScope and ORION Research Network
  5. 5. Dedicated Optical Channels Makes High Performance Cyberinfrastructure Possible Parallel Lambdas are Driving Optical Networking The Way Parallel Processors Drove 1990s Computing ( WDM) Source: Steve Wallach, Chiaro Networks “ Lambdas”
  6. 6. National LambdaRail (NLR) and TeraGrid Provides Cyberinfrastructure Backbone for U.S. Researchers NLR 4 x 10Gb Lambdas Initially Capable of 40 x 10Gb wavelengths at Buildout Links Two Dozen State and Regional Optical Networks DOE, NSF, & NASA Using NLR San Francisco Pittsburgh Cleveland San Diego Los Angeles Portland Seattle Pensacola Baton Rouge Houston San Antonio Las Cruces / El Paso Phoenix New York City Washington, DC Raleigh Jacksonville Dallas Tulsa Atlanta Kansas City Denver Ogden/ Salt Lake City Boise Albuquerque UC-TeraGrid UIC/NW-Starlight Chicago International Collaborators NSF’s TeraGrid Has 4 x 10Gb Lambda Backbone
  7. 7. PI Larry Smarr Announced January 17, 2006 $24.5M Over Seven Years
  8. 8. Paul Gilna Has Just Been Recruited from Los Alamos to Become Executive Director of CAMERA <ul><li>Formerly </li></ul><ul><ul><li>Former Director of the Department of Energy’s Joint Genome Institute (JGI) Operations at Los Alamos National Laboratory (LANL) </li></ul></ul><ul><ul><li>Group Leader of Genomic Science and Computational Biology in LANL’s Bioscience Division </li></ul></ul><ul><li>JGI </li></ul><ul><ul><li>A $70-million-per-Year Collaboration: </li></ul></ul><ul><ul><ul><li>Lawrence Berkeley, </li></ul></ul></ul><ul><ul><ul><li>Lawrence Livermore, </li></ul></ul></ul><ul><ul><ul><li>Los Alamos, </li></ul></ul></ul><ul><ul><ul><li>Oak Ridge, and </li></ul></ul></ul><ul><ul><ul><li>Pacific Northwest </li></ul></ul></ul><ul><ul><ul><li>and the Stanford Human Genome Center </li></ul></ul></ul><ul><ul><li>Working at The Frontiers of Genome Sequencing and Biosciences </li></ul></ul>
  9. 9. Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server Traditional User Response Request Source: Phil Papadopoulos, SDSC, Calit2 + Web Services <ul><ul><li>Sargasso Sea Data </li></ul></ul><ul><ul><li>Sorcerer II Expedition (GOS) </li></ul></ul><ul><ul><li>JGI Community Sequencing Project </li></ul></ul><ul><ul><li>Moore Marine Microbial Project </li></ul></ul><ul><ul><li>NASA Goddard Satellite Data </li></ul></ul><ul><ul><li>Community Microbial Metagenomics Data </li></ul></ul>Flat File Server Farm W E B PORTAL Dedicated Compute Farm (1000 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 ~100s TB 10 GigE Fabric
  10. 10. The Future Home of the Moore Foundation Funded Marine Microbial Ecology Metagenomics Complex First Implementation of the CAMERA Complex Photo Courtesy Joe Keefe, Calit2 Major Buildout of Calit2 Server Room Underway
  11. 11. CAMERA Tools and Workflows <ul><li>Initial set </li></ul><ul><ul><li>BLAST Server </li></ul></ul><ul><ul><li>Clustering </li></ul></ul><ul><ul><li>HMM/Profile </li></ul></ul><ul><ul><li>Neighborhood Analysis </li></ul></ul><ul><ul><li>Multiple Sequence Alignments </li></ul></ul><ul><ul><li>Assembly </li></ul></ul><ul><li>Proposed New Tools </li></ul><ul><ul><li>Multiple Auto Annotation Pipelines </li></ul></ul><ul><ul><li>Fast Sequence Lookup </li></ul></ul><ul><ul><li>Customized Assembly </li></ul></ul><ul><ul><li>Phylogenetic Analysis </li></ul></ul><ul><ul><li>Clustering Tools </li></ul></ul>
  12. 12. 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) <ul><ul><li>Determining the Protein Structures of the Thermotoga Maritima Genome </li></ul></ul><ul><ul><li>122 T.M. Structures Solved by JCSG (75 Unique In The PDB) </li></ul></ul><ul><ul><li>Direct Structural Coverage of 25% of the Expressed Soluble Proteins </li></ul></ul><ul><ul><li>Probably Represents the Highest Structural Coverage of Any Organism </li></ul></ul>Source: John Wooley, UCSD
  13. 13. Interactive Visualization of Thermatoga Proteins at Calit2 Source: John Wooley, Jurgen Schulze, Calit2
  14. 14. OptIPuter Scalable Adaptive Graphics Environment (SAGE) Allows Integration of HD Streams Source: David Lee, NCMIR, UCSD
  15. 15. 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
  16. 16. Countries are Aggressively Creating Gigabit Services: Interactive Access to CAMERA and LOOKING Systems www.glif.is Created in Reykjavik, Iceland 2003 Visualization courtesy of Bob Patterson, NCSA.
  17. 17. OptIPortal– Termination Device for the OptIPuter Global Backplane <ul><li>20 Dual CPU Nodes, 20 24” Monitors, ~$50,000 </li></ul><ul><li>1/4 Teraflop, 5 Terabyte Storage, 45 Mega Pixels--Nice PC! </li></ul><ul><li>Scalable Adaptive Graphics Environment ( SAGE) Jason Leigh, EVL-UIC </li></ul>Source: Phil Papadopoulos SDSC, Calit2
  18. 18. UIC/UCSD 10GE CAVEWave o n the National LambdaRail Emerging OptIPortal Sites CAVEWave Connects Chicago to Seattle to San Diego…and Washington D.C. as of 4/1/06 and JCVI as of 5/15/06 NEW! NEW! SunLight CICESE UW JCVI MIT SIO UCSD SDSU UIC EVL UCI OptIPortals
  19. 19. First Remote Interactive High Definition Video Exploration of Deep Sea Vents Source John Delaney & Deborah Kelley, UWash Canadian-U.S. Collaboration
  20. 20. High Definition Still Frame of Hydrothermal Vent Ecology 2.3 Km Deep White Filamentous Bacteria on 'Pill Bug' Outer Carapace Source: John Delaney and Research Channel, U Washington 1 cm.
  21. 21. A Near Future Metagenomics Fiber Optic-Enabled Data Generator Source John Delaney, UWash
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