Transcript PPT - Larry Smarr

Emerging Trends
IEEE Spectrum Editorial Board
New York, NY
June 29, 2007
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
Accelerator: The Perfect Storm--
Convergence of Engineering with Bio, Physics, & IT
1000x
Magnification
HP
MemorySpot
400,000 x !
2 mm
2 micron
DNA-Conjugated Microbeads
400x
Magnification
IBM Quantum Corral
Iron Atoms on Copper
5 nanometers
Human Adenovirus
Nanobioinfotechnology
The Intersection of Solid State and
Biological Information Systems
Snail neuron grown on a CMOS chip with 128x128 Transistors.
The electrical activity of the neuron is recorded by the chip.
(Chip fabricated by Infineon Technologies)
www.biochem.mpg.de/en/research/rd/fromherz/publications/03eve/index.html
Lifechips--Merging Two Major Industries:
Microelectronic Chips & Life Sciences
65 UCI Faculty
LifeChips: the merging of two major industries, the
microelectronic chip industry with the life science
industry
LifeChips medical devices
Nano-Structured Porous Silicon
Applied to Cancer Treatment
Nanodevices for In-vivo Detection & Treatment of Cancerous Tumors
Nanostructured “Mother Ships”
for Delivery of Cancer Therapeutics
Michael J. Sailor Research Group
Chemistry and Biochemistry
A World of Distributed Sensors Starts
with Integrated Nanosensors
Developing Multiple Nanosensors
on a Single Chip,
Integrated with Local Processing
and Wireless Communications
2006
45 Faculty with
Nano Projects at
Calit2@UCSD
Fluidic circuit
Guided wave Free space
optics
optics
Aqueous
Physical
bio/chem
sensors
sensors
Gas/chemical
sensors
Electronics (communication, powering)
Ivan Schuller holding the first prototype in 2004
Technology Transfer:
RedX (Explosive Sensors), RheVision (Fauvation Optics)
I. K. Schuller, A. Kummel, M. Sailor, W. Trogler, Y-H Lo
Real-Time Electronic Readout from
Single Biomolecule Sensors
40 Nano Projects
at Calit2@UCI
• Carbon Nanotube Circuits
Provide Nanoscale Connectivity
• New Techniques Integrate
Single-Molecule Attachments
• Dynamics and Interactions
With the Environment Can be
Directly Measured
• Electronic Readout Compatible
With Hand-held, Low-power
Devices
1 nm
wiring
1 protein
molecule
Schematic & SEM Image of Carbon Nanotube-based Device
device in buffer with reagents
… and without
Source: Phil Collins & Greg Weiss, Calit2@UCI
Building a Genome-Scale Model
of E. Coli in Silico
JTB 2002
E. coli i2K
Transcription &Translation
b8
v1
G1 + RNAP
G1 *
2aGDP + 2aPi
v2
Genomics
b3
protein1
b5
b1
2nPi
aAA
Transcriptomics
Regulatory Actions
v5
rib
v4 (subject to
global max.)
aAMP
+ 2aPi
aAA-tRNA
Regulation
rib1*
2aGTP
Pi
If [Carbon1] > 0, tc2 = 0
Monomers &
Energy
Proteins
Pc2
A
Metabolism
GLC trx
zwf
G6P
6PGA
6PG
pgl
H+
ATP
2PG
aceE
PYR trx
pflA
LAC trx
ETH
FORxt
ackA
ETHxt
AC
(+)
P5
3E
G6a
O6a
(+)
(-)
t2a
R5
C+
4 NADH
C + 2 ATP +
3 NADH
P2a
t6a
R2a
B
Hext
H
P6a
R6a
G + 1 ATP +
2 NADH
SUCC
SUCCxt
SuccCoA
Map Legend
sucA
aceA
CIT
acs
ETH trx
G2a
aceB
ACTP
FOR trx
t5
FOR
FADH
GLX
gltA
pta
adhE
FOR
dld
LAC
LACxt
fdoH
sdhA2
SUCC trx
OAA
pckA
AcCoA
pykF
O2a
O5
sucC
ppc
ppsA
AC trx
acnA
icdA
ICIT
ACxt
AKG
in Silico Organisms
Now Available
2007:
If Rh > 0, [H] is in surplus, t6a = 0
mdh
sfcA
PYR
PYRxt
frdA
eno
pts
NADH
maeB
PEP
GLxt
O2 +
NADH
sdhA1
fumA
MAL
gpmA
Rres
B
pnt1A
FUM
3PG
GL trx
Qh2
nuoA
RIBxt
pgk
glpK
cyoA
NADPH
RIB trx
gapA
DPG
GL3P
G5
O2xt
atpA
pnt2A
tpi
gpsA
Pres
ATP
R3b
O2 trx
rbsK
RIB
GA3P
GL
CO 2xt
CO2 trx
O2
FDP
glpD
tktA2
R5P
fba
Metabolomics
CO 2
talA
tktA1
rpiA
pfkA
fbp
O2
G
Pi trx
Ru5P
F6P
DHAP
tres
(+)
Pixt
Pi
gnd
pgi
Rc2
Gres
P3b
0.8 C +
2 NADH
Carbon2
If R1 = 0, we say [B] is not in surplus, t 2a = t5 = 0
E4P
rpe
glk
pts
S7P
X5P
GLC
Ores
O3b
t3b (+)
tc2
(-)
Carbon1
(indirect)
G3b
Gc2
Oc2
GLCxt
If Oxygen = 0, we say [O2] = 0, tres= t3b = 0
– Has 4300
Genes
– Model Has
2000!
b9
b7
Proteomics
JBC 2002
b4
mRNA1v3=k1[mRNA1] nNMP
atRNA
v6
b6
b2
nNTP
aATP
• E. Coli
GROWTH/BIOMASS
PRECURSORS
Input Signals
EXTRACELLULAR
METABOLITE
INTRACELLULAR
METABOLITE
reaction/gene name
Interactomics
Environment
Source: Bernhard Palsson
UCSD Genetic Circuits Research Group
http://gcrg.ucsd.edu
•Escherichia coli
•Haemophilus influenzae
•Helicobacter pylori
•Homo sapiens Build 1
•Human red blood cell
•Human cardiac mitochondria
•Methanosarcina barkeri
•Mouse Cardiomyocyte
•Mycobacterium tuberculosis
•Saccharomyces cerevisiae
•Staphylococcus aureus
Information Theorists Working with Bio, IT, and Nano Researchers
Will Radically Transform Our View of Living Systems
"Through the strong loupe of
information theory,
we will be able to watch
how such [living] beings
do what nonliving systems
cannot do:
extract information from
their surrounds,
store it in a stable molecular form,
and eventually parcel it out
for their creative endeavors.
... So viewed, the information
circle becomes the unit of life.”
--Werner Loewenstein
The Touchstone of Life (1999)
Calit2’s
Information Theory
and Applications Center
http://ita.ucsd.edu
President Kalam of India Believes Nanobioinfotech
is the Future for 600,000 Villages
•
•
•
•
Interactive Knowledge System
Convergence of Info- Nano - Bio
Make the Bandwidth Available with No Limits
PURA--Societal Grid With Electronic Connection of a Billion People
Photo: Alan Decker, UCSD
The University Research World Is Connecting
with Dedicated 10Gbps Light Paths
Maxine Brown, Tom DeFanti, Co-Chairs
iGrid
2005
THE GLOBAL LAMBDA INTEGRATED FACILITY
www.igrid2005.org
September 26-30, 2005
Calit2 @ University of California, San Diego
California Institute for Telecommunications and Information Technology
50 Demonstrations, 20 Counties, 10 Gbps/Demo
First Trans-Pacific Super High Definition Telepresence
Meeting Using Digital Cinema 4k Streams
100 Times
the Resolution
of YouTube!
Streaming 4k Talk by
with JPEG 2000 Laurin
Compression
Herr
½ gigabit/sec
Lays
Technical
Basis for
Global
Digital
Keio University
President Anzai Cinema
UCSD
Chancellor Fox
Sony
NTT
SGI
Beyond 4k –
From 8 Megapixels Towards a Billion Megapixels
HDTV
Calit2@UCI Apple Tiled Display Wall
Driven by 25 Dual-Processor G5s
50 Apple 30” Cinema Displays
Digital Cameras
Digital Cinema
Data—One Foot Resolution
USGS Images of La Jolla, CA
Source: Falko Kuester, Calit2@UCI
NSF Infrastructure Grant
The OptIPuter Project: Creating High Resolution Portals
Over Dedicated Optical Channels to Global Science Data
Scalable
Adaptive
Graphics
Environment
(SAGE)
$13.5M
Over
Five
Years
Picture
Source:
Mark
Ellisman,
David Lee,
Jason Leigh
Calit2 (UCSD, UCI) and UIC Lead Campuses—Larry Smarr PI
Univ. Partners: SDSC, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST
Industry: IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent
Broadband Depends on Where You Are
• Mobile Broadband
– 0.1-0.5 Mbps
100,000 Fold Range
All Here Today!
• Home Broadband
– 1-5 Mbps
“The future is already here,
it’s just not evenly distributed”
William Gibson, Author of Neuromancer
• University Dorm Room Broadband
– 10-100 Mbps
• Calit2 Global Broadband
– 1,000-10,000 Mbps
Marine Genome Sequencing Project –
Measuring the Genetic Diversity of Ocean Microbes
Each Sample
~2000
Microbial
Species
Specify
Ocean Data
Sorcerer II Data Will Double
Number of Proteins in GenBank!
Use of OptIPortal
to Interactively View Microbial Genome
15,000 x 15,000 Pixels
Acidobacteria bacterium Ellin345 (NCBI)
Soil Bacterium 5.6 Mb
Source: Raj Singh, UCSD
Use of OptIPortal
to Interactively View Microbial Genome
15,000 x 15,000 Pixels
Acidobacteria bacterium Ellin345 (NCBI)
Source: Raj Singh, UCSD
Soil Bacterium 5.6 Mb
Use of OptIPortal
to Interactively View Microbial Genome
15,000 x 15,000 Pixels
Acidobacteria bacterium Ellin345 (NCBI)
Source: Raj Singh, UCSD
Soil Bacterium 5.6 Mb
An Emerging High Performance Collaboratory
for Microbial Metagenomics
OptIPortals
UW
UMich
NW!
UIC EVL
MIT
UC Davis
JCVI
UCI
SIO
UCSD
SDSU
CICESE
OptIPortal
e-Science Collaboratory Without Walls
Enabled by Uncompressed HD Telepresence
1500 Mbits/sec Calit2 to UW Research Channel Over NLR
May 23, 2007
John Delaney, PI LOOKING, Neptune
Photo: Harry Ammons, SDSC
3D OptIPortal Calit2 StarCAVE
Telepresence “Holodeck”
Connected at 200 Gb/s
Source: Tom DeFanti, Greg Dawe, Calit2
30 HD
Projectors!
60 GB Texture Memory,
Renders Images 3,200 Times the Speed of Single PC
Can We Create a “My Space” for Science Researchers?
Microbial Metagenomics as a Cyber Community
Over 1000 Registered Users From 45 Countries
USA
United Kingdom
Canada
France
Germany
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