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

Driving Cyberinfrastructure with Environmental Metagenomics Samples Collected by Sorcerer II How did Calit2, SIO, and VI Arrive at This Unified Vision? Funded Today! $24. 5 M Over 7 Years J. Craig Venter, et al. Science 2 April 2004: Vol pp

ProchlorococcusMicrobacterium Burkholderia RhodobacterSAR-86 unknown Metagenomics Extreme Assembly Requires Large Amount of Pixel Real Estate Source: Karin Remington J. Craig Venter Institute

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

The OptIPuter – Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data Green: Purkinje Cells Red: Glial Cells Light Blue: Nuclear DNA Source: Mark Ellisman, David Lee, Jason Leigh 300 MPixel Image! Calit2 (UCSD, UCI) and UIC Lead CampusesLarry Smarr PI Partners: SDSC, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST

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

Allows for Interactive Zooming from Cerebellum to Individual Neurons Source: Mark Ellisman, David Lee, Jason Leigh

Why Optical Networks Will Become the 21 st Century Driver Scientific American, January 2001 Number of Years Performance per Dollar Spent Data Storage (bits per square inch) (Doubling time 12 Months) Optical Fiber (bits per second) (Doubling time 9 Months) Silicon Computer Chips (Number of Transistors) (Doubling time 18 Months)

Challenge: Average Throughput of NASA Data Products to End User is Only < 50 Megabits/s Tested from GSFC-ICESAT January

Solution: Individual 1 or 10Gbps Lightpaths -- Lambdas on Demand (WDM) Source: Steve Wallach, Chiaro Networks Lambdas

San Francisco Pittsburgh Cleveland National Lambda Rail (NLR) and TeraGrid Provides Cyberinfrastructure Backbone for U.S. Researchers 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 NLR 4 x 10Gb Lambdas Initially Capable of 40 x 10Gb wavelengths at Buildout NSFs TeraGrid Has 4 x 10Gb Lambda Backbone Links Two Dozen State and Regional Optical Networks DOE, NSF, & NASA Using NLR

Extending Telepresence with Remote Interactive Analysis of Data Over NLR HDTV Over Lambda OptIPuter Visualized Data SIO/UCSD NASA Goddard August 8, Miles Venter Institute

First Trans-Pacific Super High Definition Telepresence Meeting in New Calit2 Digital Cinema Auditorium Keio University President Anzai UCSD Chancellor Fox Sony NTT SGI Lays Technical Basis for Global Scientific Collaboration

September 26-30, 2005 University of California, San Diego California Institute for Telecommunications and Information Technology Is Connected to the World at 10,000 Mbps i Grid 2005 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 Maxine Brown, Tom DeFanti, Co-Chairs 50 Demonstrations, 20 Counties, 10 Gbps/Demo

Calit2 is Partnering with SIO to 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 John Orcutt, Director CEOA Deputy Director, SIO Smarr March 2005 Talk to SIO Council Led to Calit2 Discussions with Craig Venter

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

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

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 YellowProposed Initial Lambda Backbone

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

Marine Microbial Metagenomics From 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 Scripps Genome Center Dr. Terry Gaasterland

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

Comparative Genomics Can Reveal Biological Facts That Are Not Visible Within a Species 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 Co-Authors Pavel Pevzner and Glenn Tesler, UCSD April 1, 2004 December 05, 2002 December 9, 2004

Advanced Algorithmic Techniques Reveal Unexpected Results 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, (09 December 2004)

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): 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. 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

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

Web PortalRich Clients Providing Integrated Grid Software and Infrastructure for Multi-Scale BioModeling Telescience Portal Grid Middleware and Web Services Workflow Middleware PMV ADT Vision Continuity APBSCommand Grid and Cluster Computing ApplicationsInfrastructure Rocks Grid of Clusters APBS Continuity Gtomo2 TxBR Autodock GAMESS QMView National Biomedical Computation Resource an NIH supported resource center Located in Building

Calit2 Intends to Jump Beyond Traditional Web-Accessible Databases Data Backend (DB, Files) W E B PORTAL (pre-filtered, queries metadata) Response Request BIRN PDB NCBI Genbank + many others Source: Phil Papadopoulos, SDSC, Calit2

Flat File Server Farm W E B PORTAL Traditional User Response Request 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 OptIPuter Cluster Cloud Data- Base Farm 10 GigE Fabric Calit2s Direct Access Core Architecture Will Create Next Generation Metagenomics Server Source: Phil Papadopoulos, SDSC, Calit2 + Web Services

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

Looking Back Nearly 4 Billion Years In the Evolution of Microbe Genomics Science Falkowski and Vargas 304 (5667): 58