Opportunities for Collaboration
Presentation to Visiting Team from
Sandia National Laboratory
Meeting Held at UCSD
La Jolla, CA
April 16, 2001
Governor Davis Created New Institutes for
Science, Innovation, and Tech Transfer
The California Institute for Bioengineering,
Biotechnology,
and Quantitative Biomedical Research
The Center for
Information Technology Research
in the Interest of Society
(Proposed-UCB, UCD, UCSC, UCM)
UCB
UCSF
UCSC
The California
NanoSystems Institute
UCSB
UCLA
UCI
UCSD
The California Institute
for Telecommunications
and Information Technology
The Next Wave of the Internet Will
Extend IP Throughout the Physical World
This is the Research Context for the
California Institute for Telecommunications
and Information Technology
Materials and Devices Team, UCSD
The Institute is Built on
Existing UCSD/UCI Faculty Strengths
Center for
Wireless Communications
Broadband Wireless
LOW-POWERED
CIRCUITRY
RF
Mixed A/D
ASIC
Materials
ANTENNAS AND
PROPAGATION
COMMUNICATION
THEORY
COMMUNICATION
NETWORKS
MULTIMEDIA
APPLICATIONS
Architecture
Changing
Modulation
Media Access
Smart Antennas
Environment
Channel
Coding
Scheduling
Adaptive Arrays
Protocols
Multiple Access End-to-End QoS Multi-Resolution
Compression
Hand-Off
Source: UCSD CWC
San Diego Supercomputer Center
Cal(IT)2 Research & Infrastructure Partner
• Areas of Strength & Leadership for Initial Interactions between
Cal(IT)2 and
Clusters
Networking and Wireless
Phil Papadopoulos
Phil Papadopoulos, Frank Dwyer, Ronn Ritke,
kc claffy, Hans-Werner Braun
Data Mining/Metadata/AI
Chaitan Baru, Reagan Moore, Tony Fountain
Enviroinformatics/Observing Systems
Alison Withey
Visualization/GIS/Augmented Reality
Mike Bailey, John Moreland
Computing and Portals
Jay Boisseau, Mary Thomas, Allan Snavely
Core IT Infrastructure and Integration
Mike Vildibill, Frank Dwyer, Phil Andrews, Phil P.
Computer Security Infrastructure
Tom Perrine
Education/Outreach
Ann Redelfs, Kim Baldridge, Theresa Boisseau
Bioinformatics/Digitally Enabled Med./
Comp. Chemistry/Biology
Management
John Wooley, Phil Bourne, Shankar Subramaniam,
Mark Ellisman, Mike Gribskov, Kim Baldridge
Peter Arzberger, Anke Kamrath, Phil Papadopoulos,
Chaitan Baru, Alison Withey
Complex Problems Require
a New Research and Education Framework
220 UCSD & UCI Faculty
Working in Multidisciplinary Teams
With Students, Industry, and the Community
The State Provides $100 M
For New Buildings and Equipment
www.calit2.net
The UCSD Cal-(IT)2 Building
Preliminary Design
Occupancy 2004
220,000 Gross SF
• New Media Arts Spaces
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Research Lab
Visualization Labs
Audiovisual Editing Facilities
Gallery Space
Helping Design Auditorium
A Broad Partnership Response
from the Private Sector
Akamai
Boeing
Broadcom
AMCC
CAIMIS
Compaq
Conexant
Copper Mountain
Emulex
Enterprise Partners VC
Entropia
Ericsson
Global Photon
IBM
IdeaEdge Ventures
Intersil
Irvine Sensors
Leap Wireless
Litton Industries
MedExpert
Merck
Microsoft
Computers
Communications
Software
Sensors
Biomedical
Startups
Venture Firms
Large Partners
>$10M Over 4 Years
Mission Ventures
NCR
Newport Corporation
Orincon
Panoram Technologies
Printronix
QUALCOMM
Quantum
R.W. Johnson Pharmaceutical RI
SAIC
SciFrame
Seagate Storage
Silicon Wave
Sony
STMicroelectronics
Sun Microsystems
TeraBurst Networks
Texas Instruments
UCSD Healthcare
The Unwired Fund
WebEx
$140 M Match From Industry
Elements of the
Cal -(IT)2 Industrial Partnerships
• Endowed Chairs for Professors
• Start-Up Support for Young Faculty
• Graduate Student Fellowships
• Research and Academic Professionals
• Sponsored Research Programs
• Equipment Donations for Cal-(IT)2 and Campus
• Named Laboratories in new Institute Buildings
• Pro Bono Services and Software
The Southern High Tech Coast
Is Well Organized for Partnering
• From Bandwidth Bay to Wireless Valley
– 70,000 Fiber Strand-Miles Under Downtown SD
– Nation’s Center for Wireless Companies
• San Diego Telecom Council
– www.sdtelecomcouncil.org
– 200 Member Companies
– SIGs on Optical, Wireless, Satellite, etc.
• UCSD CONNECT
– www.connect.org
– UCSD Program in Technology and Entrepreneurship
• Many Others
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BIOCOM
Mayor’s Science and Technology Commission
UCI Chief Executive Roundtable
…
Near Term Goal:
Build an International Lambda Grid
• Establish PACI High Performance Network
– SDSC to NCSA to PSC LambdaNet
• Link to:
– State Dark Fiber
– Metropolitan Optical Switched Networks
– Campus Optical Grids
– International Optical Research Networks
• NSF Fund Missing Dark Fiber Links For:
– Scientific Applications
– Network Research
Nanotechnology Is Becoming
Essential for Photonics
Source: UCSD Ultrafast
and Nanoscale Optics Group,
Shaya Fainman
The UCSD “Living Grid Laboratory”—
Fiber, Wireless, Compute, Data, Software
•Commodity Internet, Internet2
•Link UCSD and UCI
SDSC
• High-speed optical core
CS
Eng. / Cal-(IT)2
Hosp
Med
Chem
• Campus Wireless
SIO
½ Mile
Source: Phil Papadopoulos, SDSC
Broadband Wireless Internet is Here Today
• Create Wireless Internet “Watering Holes”
– Ad Hoc IEEE 802.11 Domains
– Real Broadband--11 mbps Going to 54 mbps
– Home, Neighborhoods, Office
– MobileStar--Admiral Clubs, Major Hotels, Restaurants, …
– UCSD—Key Campus Buildings, Dorms, Coffee Shops…
• Upsides
– Ease of Use
– Unlicensed so Anyone can Be a Wireless ISP
– Will Accelerate Innovation—”Living in the Future”
• Downsides
– Not Secure
– Shared Bandwidth
– Short Range Coverage
“The future is already here, it’s just not evenly distributed”
William Gibson, Author of Neuromancer
Web Interface to Grid Computing
The NPACI GridPort Architecture
802.11b Wireless
Interactive Access to:
• State of Computer
• Job Status
• Application Codes
Cal -(IT)2 Researchers Will Focus on
Semiconductor “System Chips”
• Two Trends:
– Increasing Use of “Embedded Intelligence”
– Networking of Embedded Intelligence
• In Ten Years:
– The Big: eg., Terabit Optical Core, Gigabit Wireless, ...
– The Small: eg., Pervasive Self-powered Sensor “Motes”
– The Cheap: eg., One-Cent Radios
– Short-range (10-100m), Low Power (10nJ/bit), Low Bit
Rate (1-100kbps)
• The Consequence:
– Smart Spaces, Intelligent Interfaces, Ad Hoc Networks
Source: Rajesh Gupta, UCI Center for
Embedded Computer Systems
Goal: Design of Configurable Wireless Embedded
Sensing/Computing/Communicating Appliances
Wireless
RTOS
Applications
sensors Reconf.
Logic
Processors
Memory
Protocol
Processors
Protocol
Stacks
Network
Transport
Data Link
Physical
RF
Protocols
Sw/Hw/Sensor/RF
Co-design
Reconfiguration
DSP
SoC Design
Methodologies
Sw/Silicon/MEMS
Implementation
Source: Sujit Dey, UCSD ECE
Internet
The Wireless Internet will Transform
Computational Science and Engineering
• Teraflop Supercomputers Simulate in Dynamic 3D
• Evolving a System Requires Knowing the Initial State
• Add Wireless Sensors and Embedded Processors
– Give Detailed State Information
– Allows for Comparison of Simulation with Reality
• Critical Software Research Required
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Security
Robust Scalable Middleware
Effervescent Architectures
Mobile Code
Resource Discovery
Ad Hoc Networking
SensorNet Simulations
The High Performance
Wireless Research and Education Network
NSF Funded
PI, Hans-Werner Braun, SDSC
Co-PI, Frank Vernon, SIO
45mbps Duplex Backbone
http://hpwren.ucsd.edu/Presentations/HPWREN
Wireless Antennas Anchor
Network High Speed Backbone
http://hpwren.ucsd.edu/Presentations/HPWREN
Source: Hans-Werner Braun, SDSC
The Wireless Internet Adds
Bio-Chemical-Physical Sensors to the Grid
•
From Experiments
to Wireless
Infrastructure
•
Scripps Institution
of Oceanography
San Diego
Supercomputer
Center
Cal-(IT)2
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Source: John Orcutt, SIO
Building on
Pioneering Work of
Hans-Werner Braun
& Frank Vernon
The Wireless Internet Will Improve
the Safety of California’s 25,000 Bridges
New Bay Bridge Tower
with Lateral Shear Links
Cal-(IT)2 Will
Develop and Install
Wireless Sensor Arrays
Linked to
Crisis Management
Control Rooms
Source: UCSD Structural Engineering Dept.
Can Use of These Technologies Help Us
Avoid the Downsides of Prolonged Growth?
• Add Wireless
Sensor Array
• Build GIS Data
• Focus on:
UCI
Huntington
Beach
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High Tech Coast
UCSD
Mission Bay
San Diego Bay
Pollution
Water Cycle
Earthquakes
Bridges
Traffic
Policy
• Work with the
Community to
Adapt to Growth
High Resolution Data Analysis Facility
Linked by Optical Networks to PACI TeraGrid
Panoram Technologies,
SGI, Sun, TeraBurst Networks,
Cox Communications, Global Photon
Institute Industrial Partners
Planned for Fall 2001 at SIO
Support from SDSC and SDSU
From Telephone Conference Calls to
Access Grid International Video Meetings
Creating a Virtual Global Research Lab
Access Grid Lead-Argonne
NSF STARTAP Lead-UIC’s Elec. Vis. Lab
Bridging Internet Data Collection and
Theoretical Scaling Analysis
• Network Graph Theory
100,000 nodes Colored by Node IP Address
Bill Cheswick, Lucent Bell Labs and Hal Burch, CMU
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Sparse
Clustered
Hierarchical
Power Laws
• Goal
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IT First Principles
Quantitative Laws
Verify Against Reality
Use for Optimal Design
Fan Chung Graham, UCSD
www.caida.org/projects/internetatlas/gallery/
Possible Multiple Qubit Quantum Computer
•
500 nm
SEM picture of posts fabricated at the
Cornell Nanofabrication Facility
– PI John Goodkind (UCSD Physics) &
Roberto Panepucci of the CNF
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Electrons Floating over Liquid He
One Electron per Gold Post
g round p al ne
ni su al to r
vo ltage el ad s
ni su al to r
NSF ITR PROGRAM CASE WESTERN RESERVE UNIVERSITY/
UCSD/MICHIGAN STATE
The Institute Facilitates Faculty Teams to
Compete for Large Federal Grants
Proposal-Form a National Scale Testbed
for Federating Multi-scale Brain Databases
Using NIH High Field NMR Centers
Stanford
U. Of MN
NCRR Imaging
and Computing
Resources UCSD
Harvard
Cal Tech
SDSC
Surface Web
Cal-(IT)2
Deep Web
UCLA
Duke
Source: Mark Ellisman, UCSD
Wireless “Pad”
Web Interface
Why Not Constantly Compute
on Federated Repositories?
•
Currently
– Instrument Coordinates
– Virtual Human NLM Project
– Transformations to Organ Coordinates
– Surgical View of Body
– Define Differences in Organs
– Eg. UCLA Human Brain Mapping
Project—Art Toga
– Fly Through Organs
– Virtual Colonoscopy
(www.vitalimaging.com)
•
Future
– Train AI Software on
– Millions of Human Image DataSets
– Define Distribution Functions
– Thresholds for Medical Attention
– Life Cycle of Single Individuals
– Automatic Early Warnings
As Our Bodies Move On-Line
Bioengineering and Bioinformatics Merge
• New Sensors—Israeli Video Pill
– Battery, Light, & Video Camera
– Images Stored on Hip Device
• Next Step—Putting You On-Line!
– Key Metabolic and Physical Variables
– Wireless Internet Transmission
– Model -- Dozens of 25 Processors and 60
Sensors / Actuators Inside of our Cars
• Post-Genomic Individualized Medicine
– Combine Your Genetic Code & Imaging,
with Your Body’s Data Flow
– Use Powerful AI Data Mining Techniques
www.givenimaging.com
What Data is Needed to Specify
a Single Eukaryotic Cell?
•
Organelles
– 4 Million Ribosomes
– 30,000 Proteasomes
– Dozens of Mitochondria
•
Macromolecules
– 5 Billion Proteins
– 5,000 to 10,000
different species
– 1 meter of DNA with
Several Billion bases
– 60 Million tRNAs
– 700,000 mRNAs
•
Chemical Pathways
– Vast numbers
– Tightly coupled
www.people.virginia.edu/~rjh9u/cell1.html
•
Is a Virtual Cell Possible?
Cellular Signaling Pathway Database,
Analysis Tools and User Interface
Genes
(Proteins)
Sequence
Annotation
Interactions
Motif
Libraries
Signaling
Pathways
Organism
Data Structure
Database
Query Tools
Temporary
Storage
Interaction
Modules
Pathway
GUI
Editing
Tool
Data Store
Signaling
Networks
Bulletin
Board
Annotations
System
Molecular
Diseases
Proteomics
Profiles
Interaction
Profiles
Comparison
Tool
Alliance for Cell Signaling
PI: Alfred Gilman, UT-SW MED
UCSF, Caltech, Stanford, UCSD
NIH and Industrial Funding
Analysis Tools
Legacy
Pathways
Expression
Profiles
Cell & Tissue
Specificity
Other
Analysis
Tools
Shankar Subramaniam, UCSD, Director,
Data Coordination & Bioinformatics Lab,
Alliance for Cell Signaling
Monte Carlo Cellular Microphysiology
From IBM Blue Horizon to the Grid
•
PROJECT LEADERS
– Francine D. Berman
Rendered by Tom Bartol of the Salk Institute for Biological Studies &
Joel Stiles of Cornell University
using Pixar PhotoRealistic RenderMan
– UC San Diego
– Terrence J. Sejnowski
– Salk Institute for
Biological Studies
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PARTICIPANTS
– Dorian Arnold
Jack Dongarra
Richard Wolski
– University of
Tennessee
Neurotransmitter Activity
Leading to Muscle Contraction
• MCell Simulated:
• The Transmission of 6,000 Molecules of the
Neurotransmitter Acetylcholine (Cyan Specks)
• In a Reconstructed Mouse Sternomastoid
Neuromuscular Junction
• Containing Acetylcholinesterase (White Spheres).
www.npaci.edu/envision/v16.4/mcell.html
– Thomas M. Bartol
Lin-Wei Wu
– Salk Institute for
Biological Studies
– Henri Casanova
Mark H. Ellisman
Maryann Martone
– UC San Diego
The Institute Will Focus on the Use of Highly
Parallel and Distributed Systems
• PACI Distributed Terascale Linux Clusters
– Multi-Teraflop
– Thousands of Processors
• High Performance Grids
– Lambda Connected
– Heterogeneous Compute and Storage
• DoE Labs
– Highest End Machines
– Experimental Architectures (Blue Light)
• Peer-to-Peer Computing
– Millions of Processors
– NT/Intel Homogenous PCs
The Drive toward Commodity Processors
in Parallel Computing
100x Processors
Cray X-MP
TMC CM-5
IBM SP
RISC
Processors
Changes in Architecture Induce Changes in Algorithms
PC Clusters
ASCI Red
Internet Computing
Intel
Processors
100x Processors?
Entropia’s Planetary Computer
Grew to a Teraflop in Only Two Years
The Great Mersenne Prime (2P-1) Search (GIMPS)
Found the First Million Digit Prime
www.entropia.com
Eight 1000p IBM Blue Horizons
Deployed in Over 80 Countries
SETI@home Demonstrated that PC Internet
Computing Could Grow to Megacomputers
•
Running on 500,000 PCs, ~1000 CPU Years per Day
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Over Half a Million CPU Years so far!
22 Teraflops sustained 24x7
Sophisticated Data & Signal Processing Analysis
Distributes Datasets from Arecibo Radio Telescope
Arecibo
Radio Telescope
Next StepAllen Telescope Array
Extending the Grid to Planetary Dimensions
Using Distributed Computing and Storage
AutoDock Application Software Has Been Downloaded to Over 20,000 PCs
Nearly 3 Million CPU-Hours Computed
In Silico
Drug Design
Art Olson,
TSRI
From Software as Engineering
to Software as Biology
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Stanford Professor John Koza
Uses Genetic Programming to Create a Working Computer Program From a
High-Level Problem Statement of a Problem
Starting With a Primordial Ooze of Thousands of Randomly Created
Computer Programs, a Population of Programs Is Progressively Evolved
Over a Series of Generations
Has Produced 21 Human-Competitive Results
1,000-Pentium Beowulf-Style Cluster
Computer for Genetic Programming
www.genetic-programming.com/
A Mobile Internet
Powered by a Planetary Scale Computer