1. Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Invited Talk
Metagenomics 2006
UCSD
La Jolla, CA
October 4, 2006
Dr. Larry Smarr
Director, California Institute for Telecommunications and Information Technology
Harry E. Gruber Professor,
Dept. of Computer Science and Engineering
Jacobs School of Engineering, UCSD

2. Internet2 Backbone is 10,000 Mbps! Throughput is < 0.5% to End User
Challenge: Average Throughput of NASA Data Products to End User is < 50 Mbps
Tested
October 2005
Internet2 Backbone is 10,000 Mbps!
Throughput is < 0.5% to End User

3. Source: Steve Wallach, Chiaro Networks
Dedicated Optical Channels Makes High Performance Cyberinfrastructure Possible
(WDM)
Source: Steve Wallach, Chiaro Networks
“Lambdas”
Parallel Lambdas are Driving Optical Networking The Way Parallel Processors Drove 1990s Computing

4. National Lambda Rail (NLR) and TeraGrid Provides Cyberinfrastructure Backbone for U.S. Researchers
NSF’s TeraGrid Has 4 x 10Gb
Lambda Backbone
Seattle
International
Collaborators
Portland
Boise
UC-TeraGrid
UIC/NW-Starlight
Ogden/
Salt Lake City
Cleveland
Chicago
New York City
San Francisco
Denver
Pittsburgh
Washington, DC
Kansas City
Raleigh
Albuquerque
Tulsa
Los Angeles
Atlanta
San Diego
Phoenix
Dallas
Baton Rouge
Las Cruces /
El Paso
Links Two Dozen State and Regional Optical Networks
Jacksonville
Pensacola
DOE, NSF, & NASA
Using NLR
San Antonio
Houston
NLR 4 x 10Gb Lambdas Initially
Capable of 40 x 10Gb wavelengths at Buildout

5. NSF EarthScope and ORION
The OptIPuter Project – Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data
NSF Large Information Technology Research Proposal
Calit2 (UCSD, UCI) and UIC Lead Campuses—Larry Smarr PI
Partnering Campuses: SDSC, USC, SDSU, NCSA, NW, TA&M, UvA, SARA, NASA Goddard, KISTI, AIST, CRC(Canada), CICESE (Mexico)
Engaged Industrial Partners:
IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent
$13.5 Million Over Five Years—Now In the Fifth Year
NIH Biomedical Informatics
NSF EarthScope and ORION
Research Network

6. OptIPuter Software Architecture--a Service-Oriented Architecture Integrating Lambdas Into the Grid
Distributed Applications/ Web Services
Telescience
Vol-a-Tile
SAGE
JuxtaView
Visualization
Data Services
LambdaRAM
Source: Andrew Chien, UCSD
DVC Configuration
Distributed Virtual Computer (DVC) API
DVC Runtime Library
DVC Services
DVC Core Services
DVC Job Scheduling
DVC
Communication
Resource
Identify/Acquire
Namespace
Management
Security Management
High Speed
Storage Services IP
Lambdas
Discovery
and Control
PIN/PDC
RobuStore
Globus
GRAM
GSI
XIO
GTP
XCP
UDT
CEP
LambdaStream
RBUDP

7. Source: Harry Dent, The Great Boom Ahead
Calit2 “Lives in the Future” By Building Systems of Emerging Disruptive Technologies
Co-Evolution of Personal Automobile and Highway/Petroleum Infrastructure
Technologies Diffuse Into Society Following an S-Curve
Calit2
Works Here {
Source: Harry Dent, The Great Boom Ahead

8. Calit2--A Systems Approach to the Future of the Internet and its Transformation of Our Society
Calit2 Has Assembled a Complex Social Network of Over 350 UC San Diego & UC Irvine Faculty
Working in Multidisciplinary Teams
With Staff, Students, Industry, and the Community
Integrating Technology Consumers and Producers
Into “Living Laboratories”

9. Some Areas of Concentration:
Calit2 Brings Computer Scientists and Engineers Together with Biomedical Researchers
Some Areas of Concentration:
Metagenomics
Genomic Analysis of Organisms
Evolution of Genomes
Cancer Genomics
Human Genomic Variation and Disease
Proteomics
Mitochondrial Evolution
Computational Biology
Information Theory and Biological Systems
UC Irvine
UC San Diego

10. Much of Genome Work Has Occurred in Animals
Evolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial World
You Are Here
Much of Genome Work Has Occurred in Animals
Source: Carl Woese, et al

11. Calit2 is Now Attracting Private Foundation Grants
Paul Gilna Ex. Dir.
PI Larry Smarr
Calit2 is Now Attracting Private Foundation Grants
Announced January 17, $24.5M Over Seven Years

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

13. Current Universe of Medium/ Large Protein Families
17,067 Protein Family Clusters
Protein Families Unique to GOS
Protein Families Conserved Across Tree of Life
Source: Shibu Yooseph, et al. (PLOS Biology in press 2006)

15. Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server
Sargasso Sea Data
Sorcerer II Expedition (GOS)
JGI Community Sequencing Project
Moore Marine Microbial Project
NASA Goddard Satellite Data
Community Microbial Metagenomics Data
Traditional
User
Dedicated
Compute Farm
(1000 CPUs)
Flat File
Server
Farm
W E B PORTAL
Request
Data-
Base
Farm
10 GigE
Fabric
Response
+ Web Services
Web
(other service)
Local
Cluster
Environment
Direct
Access
Lambda
Cnxns
TeraGrid: Cyberinfrastructure Backplane
(scheduled activities, e.g. all by all comparison)
(10000s of CPUs)
Source: Phil Papadopoulos, SDSC, Calit2

16. The Bioinformatics Core of the Joint Center for Structural Genomics will be Housed in the Building
Extremely Thermostable -- Useful for Many
Industrial Processes (e.g. Chemical and Food)
173 Structures (122 from JCSG)
Determining the Protein Structures of the Thermotoga Maritima Genome
122 T.M. Structures Solved by JCSG (75 Unique In The PDB)
Direct Structural Coverage of 25% of the Expressed Soluble Proteins
Probably Represents the Highest Structural Coverage of Any Organism
Source: John Wooley, UCSD

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

18. OptIPortal– Termination Device for the OptIPuter Global Backplane
20 Dual CPU Nodes, 20 24” Monitors, ~$50,000
1/4 Teraflop, 5 Terabyte Storage, 45 Mega Pixels--Nice PC!
Scalable Adaptive Graphics Environment ( SAGE) Jason Leigh, EVL-UIC
Source: Phil Papadopoulos SDSC, Calit2

19. Calit2 is Now OptIPuter Connecting Remote Moore-Funded Microbial Researchers
OptIPortals UW
NW!
UIC EVL
MIT
JCVI
UCI
SIO
UCSD
OptIPortal
SDSU
CICESE

20. Live Demonstration of 21st Century National-Scale Team Science
Calit2 and the Venter Institute Will Combine Telepresence with Remote Interactive Analysis
Live Demonstration of 21st Century National-Scale Team Science
25 Miles
Venter Institute
OptIPuter
Visualized Data
HDTV Over
Lambda

21. Countries are Aggressively Creating Gigabit Services: Interactive Access to CAMERA and LOOKING Systems
Visualization courtesy of Bob Patterson, NCSA.
Created in Reykjavik, Iceland 2003

22. NEPTUNE CI Requirements of Gigabit Flows Routine
New OptIPuter Driver: Gigabit Fibers on the Ocean Floor -- Controlling Sensors and HDTV Cameras Remotely
National Science Foundation Is Planning a New Generation of Ocean Observatories
Ocean Research Interactive Observatory Networks (ORION)
Fibered Observatories Linked to Land Fiber Infrastructure
Laboratory for the Ocean Observatory Knowledge Integration Grid (LOOKING)
Building a Prototype Based on OptIPuter Technologies Plus Web/Grid Services
HDTV Streams Over IP Will be a Major Driver
LOOKING is Driven By
NEPTUNE CI Requirements
(Funded by NSF ITR-
John Delaney, UWash, PI)
Making Management
of Gigabit Flows Routine

23. Using the OptIPuter to Couple Data Assimilation Models to Remote Data Sources Including Biology
NASA MODIS Mean Primary Productivity
for April 2001 in California Current System
Regional Ocean Modeling System (ROMS)

24. Canadian-U.S. Collaboration
Deploying Novel Infrastructure Enables New Science: Gigabit Fibers on the Ocean Floor
Canadian-U.S. Collaboration
An Experiment in the NSF Laboratory for the Ocean Observatory Knowledge Integration Grid (LOOKING) ITR
Prototype of CI for NSF’s ORION
Source: John Delaney & Deborah Kelley, UWash

25. High Definition Still Frame of Hydrothermal Vent Ecology 2.3 Km Deep
1 cm.
Source: John Delaney and Research Channel, U Washington
White Filamentous Bacteria on 'Pill Bug' Outer Carapace

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