1
Collaborations Between Calit2, SIO, and the
Venter Institutea Beginning"

• Talk to the
• Venter Institute Board
• La Jolla, CA
• December 5, 2005

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
Driving Cyberinfrastructure with Environmental
Metagenomics
Samples Collected by Sorcerer II
Funded Today! 24. 5 M Over 7 Years
J. Craig Venter, et al. Science 2 April
2004 Vol. 304. pp. 66 - 74
How did Calit2, SIO, and VI Arrive at This
Unified Vision?
3
Metagenomics Extreme Assembly Requires Large
Amount of Pixel Real Estate
Source Karin Remington J. Craig Venter Institute
4
Metagenomics Requires a Global View of Data and
the Ability to Zoom Into Detail Interactively
Overlay of Metagenomics Data onto Sequenced
Reference Genomes(This Image Prochloroccocus
marinus MED4)
Source Karin Remington J. Craig Venter Institute
5
The OptIPuter Creating High Resolution Portals
Over Dedicated Optical Channels to Global
Science Data
300 MPixel Image!
Source Mark Ellisman, David Lee, Jason Leigh
Green Purkinje Cells Red Glial Cells Light
Blue Nuclear DNA
Calit2 (UCSD, UCI) and UIC Lead CampusesLarry
Smarr PI Partners SDSC, USC, SDSU, NW, TAM,
UvA, SARA, KISTI, AIST
6
Scalable Displays Allow Both Global Content and
Fine Detail
Source Mark Ellisman, David Lee, Jason Leigh
30 MPixel SunScreen Display Driven by a 20-node
Sun Opteron Visualization Cluster
7
Allows for Interactive Zooming from Cerebellum
to Individual Neurons
Source Mark Ellisman, David Lee, Jason Leigh
8
Why Optical NetworksWill Become the 21st Century
Driver
Performance per Dollar Spent
0
1
2
3
4
5
Number of Years
Scientific American, January 2001
9
Challenge Average Throughput of NASA Data
Products to End User is Only lt 50 Megabits/s
Tested from GSFC-ICESAT January 2005
http//ensight.eos.nasa.gov/Missions/icesat/index.
shtml
10
Solution Individual 1 or 10Gbps Lightpaths --
Lambdas on Demand
(WDM)
Source Steve Wallach, Chiaro Networks
11
National Lambda Rail (NLR) and TeraGrid Provides
Cyberinfrastructure Backbone for U.S. Researchers
NSFs TeraGrid Has 4 x 10Gb Lambda Backbone
International Collaborators
Seattle
Portland
Boise
UC-TeraGrid UIC/NW-Starlight
Ogden/ Salt Lake City
Cleveland
Chicago
New York City
Denver
Pittsburgh
San Francisco
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
Houston
San Antonio
NLR 4 x 10Gb Lambdas Initially Capable of 40 x
10Gb wavelengths at Buildout
12
Extending Telepresence with Remote Interactive
Analysis of Data Over NLR
www.calit2.net/articles/article.php?id660
August 8, 2005
SIO/UCSD
NASA Goddard
13
First Trans-Pacific Super High Definition
Telepresence Meeting in New Calit2 Digital Cinema
Auditorium
Lays Technical Basis for Global Scientific
Collaboration
Sony NTT SGI
14
Calit2_at_UCSD Is Connected to the World at 10,000
Mbps
Maxine Brown, Tom DeFanti, Co-Chairs
T H E G L O B A L L A M B D A I N T E G R A T
E D F A C I L I T Y
www.igrid2005.org

• September 26-30, 2005
• Calit2 _at_ University of California, San Diego
• California Institute for Telecommunications and
  Information Technology

50 Demonstrations, 20 Counties, 10 Gbps/Demo
15
Calit2 is Partnering with SIOto Prototype a
Digital Environment Research Systems

• Viewing and Analyzing Earth Satellite Data Sets
• Earth Topography
• Atmospheric Brown Clouds
• Climate Modeling
• Surface, Subsurface, and Ocean Floor
  Observatories
• Coastal Zone Data Assimilation
• Ocean Environmental Metagenomics

Smarr March 2005 Talk to SIO Council Led to
Calit2 Discussions with Craig Venter
John Orcutt, Director CEOA Deputy Director, SIO
16
First Remote Interactive High Definition Video
Exploration of Deep Sea Vents
Canadian-U.S. Collaboration
Source John Delaney Deborah Kelley, UWash
17
A Near Future Metagenomics Fiber Optic-Enabled
Data Generator
Source John Delaney, UWash
18
Use SCCOOS As Prototype for Coastal Zone Data
Assimilation Testbed
Goal Link SCCOOS Sites with LambdaGrid to
Prototype Future Ocean and Earth Sciences
Observing System
www.sccoos.org
19
Use 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)
http//ourocean.jpl.nasa.gov/
20
Marine Microbial MetagenomicsFrom Species
Genomes to Ecological Genomes

• Each Sequence is a Part of an Entire Biological
  Community
• Sequences, Genes and Gene Families, Coupled With
  Environmental Metadata
• Tremendous Potential to Better Understand the
  Functioning of Natural Ecosystems
• Challenge
• Much More Powerful Information Infrastructure
  Required to Support Metagenomics

Dr. Terry Gaasterland
Scripps Genome Center
21
Evolution is the Principle of Biological
SystemsMost of Evolutionary Time Was in the
Microbial World
Source Carl Woese, et al
22
Comparative Genomics Can Reveal Biological
FactsThat Are Not Visible Within a Species
Co-Authors Pavel Pevzner and Glenn Tesler, UCSD
December 05, 2002
April 1, 2004
December 9, 2004
After sequencing these three genomes, it is
clear that substantial rearrangements in the
human genome happen only once in a million years,
while the rate of rearrangements in the rat and
mouse is much faster. --Glenn Tesler, UCSD Dept.
of Mathematics
www.calit2.net/culture/features/2004/4-1_pevzner.h
tml
23
Advanced Algorithmic Techniques Reveal
Unexpected Results
Many of the chickenhuman 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)
24
Calit2 Researcher Eskin Collaborates with
Perlegen Sciences on Map of Human Genetic
Variation Across Populations
We have characterized whole-genome patterns of
common human DNA variation by genotyping
1,586,383 single-nucleotide polymorphisms (SNPs)
in 71 Americans of European, African, and Asian
ancestry.
David A. Hinds, Laura L. Stuve, Geoffrey B.
Nilsen, Eran Halperin, Eleazar Eskin, Dennis G.
Ballinger, Kelly A. Frazer, David R. Cox.
Whole-Genome Patterns of Common DNA Variation
in Three Human Populations Science 18 February,
2005 307(5712)1072-1079.
Although knowledge of a single genetic risk
factor can seldom be used to predict the
treatment outcome of a common disease, knowledge
of a large fraction of all the major genetic risk
factors contributing to a treatment response or
common disease could have immediate utility,
allowing existing treatment options to be matched
to individual patients without requiring
additional knowledge of the mechanisms by which
the genetic differences lead to different
outcomes .
More detailed haplotype analysis results are
available at http//research.calit2.net/hap/wgha/

25
The Bioinformatics Core of the Joint Center for
Structural Genomics will be Housed in the
Calit2_at_UCSD 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
26
Providing Integrated Grid Software and
Infrastructure for Multi-Scale BioModeling
Located in Calit2_at_UCSD Building
Web Portal
Rich Clients
Grid Middleware and Web Services
Workflow
APBSCommand
Middleware
PMV ADT Vision
Telescience Portal
Continuity
27
Calit2 Intends to Jump BeyondTraditional
Web-Accessible Databases
W E B PORTAL (pre-filtered, queries metadata)
Data Backend (DB, Files)
Request
Response
many others
Source Phil Papadopoulos, SDSC, Calit2
28
Calit2s Direct Access Core Architecture Will
Create Next Generation Metagenomics Server
Traditional User
Request
Response
Web Services
Source Phil Papadopoulos, SDSC, Calit2
29
What Will Our Core Data Sets Be?

• Metagenomic
• Sargasso Sea Sorcerer II Expedition (GOS)
• JGI Community Sequencing Project
• Microbial Genomes
• Moore Marine Microbial Project
• JGI Community Sequencing Project
• Other Relevant genomes (e.g., from Genbank)
• Standard
• Non-Redundant Nucleotide and AA Databases
• Environmental and Satellite data
• NOAA Oceans and NASA Goddard Satellite Date

Source Saul Kravitz Director of Software
Engineering J. Craig Venter Institute
30
Looking Back Nearly 4 Billion YearsIn the
Evolution of Microbe Genomics
Science Falkowski and Vargas 304 (5667) 58