06.07.12 Invited Talk JASON Summer Program Title: Genomics at the Speed of Light: Understanding the Living Ocean La Jolla, CA

1. Genomics at the Speed of Light: Understanding the Living Ocean Invited Talk JASON Summer Program La Jolla, CA July 12, 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. Calit2 -- Research and Living Laboratories on the Future of the Internet www.calit2.net UC San Diego & UC Irvine Faculty Working in Multidisciplinary Teams With Students, Industry, and the Community

5. Comparative Genomics Can Reveal Biological Facts That Are Not Visible Within a Species “ Many of the chicken–human aligned, non-coding sequences occur far from genes, frequently in clusters that seem to be under selection for functions that are not yet understood.” Nature 432, 695 - 716 (09 December 2004)

6. Genomes Range Over Orders of Magnitude in Length Russell Dolittle, Nature v.419, p. 494 (2002) Microbes

7. 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

8. Microbial Genomics Let’s Us Look Back Nearly 4 Billion Years In the Evolution of Life Science Falkowski and Vargas 304 (5667): 58

10. Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes Sorcerer II Data Will Double Number of Proteins in GenBank!

11. Moore Foundation Funded the Venter Institute to Provide the Full Genome Sequence of 150 Marine Microbes www.moore.org/microgenome/trees_main.asp

12. Moore Microbial Genome Sequencing Project: Cyanobacteria Being Sequenced by Venter Institute

13. 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”

14. From “Supercomputer–Centric” to “Supernetwork-Centric” Cyberinfrastructure Megabit/s Gigabit/s Terabit/s Network Data Source: Timothy Lance, President, NYSERNet 32x10Gb “Lambdas” 1 GFLOP Cray2 60 TFLOP Altix Bandwidth of NYSERNet Research Network Backbones T1 Optical WAN Research Bandwidth Has Grown Much Faster Than Supercomputer Speed! Computing Speed (GFLOPS)

16. OptIPuter Scalable Adaptive Graphics Environment (SAGE) Allows Integration of HD Streams OptIPortal– Termination Device for the OptIPuter Global Backplane

17. National Lambda Rail (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

18. Using the OptIPuter to Couple Data Assimilation Models to Remote Data Sources Including Biology Regional Ocean Modeling System (ROMS) http://ourocean.jpl.nasa.gov/ NASA MODIS Mean Primary Productivity for April 2001 in California Current System

19. PI Larry Smarr Announced January 17, 2006 $24.5M Over Seven Years

21. Announced January 17, 2006

23. 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

25. Interactive Visualization of Thermatoga Proteins at Calit2 Source: John Wooley, Jurgen Schulze, Calit2

26. 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

27. 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

29. NSF’s Ocean Observatories Initiative (OOI) Envisions Global, Regional, and Coastal Scales LEO15 Inset Courtesy of Rutgers University, Institute of Marine and Coastal Sciences

31. First Remote Interactive High Definition Video Exploration of Deep Sea Vents Source John Delaney & Deborah Kelley, UWash Canadian-U.S. Collaboration

32. High Definition Video - 2.5 km Below the Ocean Surface

33. MARS Cable Observatory Testbed – LOOKING “Living Laboratory” Tele-Operated Crawlers Central Lander MARS Installation Oct 2005 -Jan 2006 Source: Jim Bellingham, MBARI

34. A Near Future Metagenomics Fiber Optic-Enabled Data Generator Source John Delaney, UWash

35. 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.