Living in a World of Nanobioinfotechnology
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Living in a World of Nanobioinfotechnology
Invited Talk
Invitrogen
Carlsbad, CA
September 12, 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
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California’s Institutes for Science and Innovation A Bold Experiment in Collaborative Research
UCSBUCLA
California NanoSystems Institute
UCSF UCB
California Institute for Bioengineering, Biotechnology,
and Quantitative Biomedical Research
UCI
UCSD
California Institute for Telecommunications and Information Technology
Center for Information Technology Research
in the Interest of Society
UCSC
UCDUCM
www.ucop.edu/california-institutes
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UC San Diego
Two New Calit2 Buildings Provide New Laboratories for “Living in the Future”
• “Convergence” Laboratory Facilities– Nanotech, BioMEMS, Chips, Radio, Photonics
– Virtual Reality, Digital Cinema, HDTV, Gaming
• Over 1000 Researchers from 24 Departments– Buildings Linked via Dedicated Optical
Networks
UC Irvinewww.calit2.net
Preparing for a World in Which Distance is Eliminated…
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Federal Agency Source of Funds
Federal Agencies Have Funded $350 Million to Over 300 Calit2 Affiliated Grants
Creating a Rich Ecologyof Basic Research
50 Grants Over $1 Million
Broad Distribution of Medium and Small Grants
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In Spite of the Bubble Bursting, Calit2 Has Partnered with over 130 Companies
Industrial Partners > $1 Million
Over $80 Million From Industry
So Far
1000
10000
100000
1000000
10000000
100000000
0 20 40 60 80
Rank D
olla
rs R
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ved
Per
Co
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any
Broad Range of Companies
More Than 80 Have Provided Funds or In-kind
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Accelerator: The Perfect Storm-- Convergence of Engineering with Bio, Physics, & IT
2 mm
HP MemorySpot
Nanobioinfotechnology
1000x Magnification
2 micron
DNA-Conjugated Microbeads
Human Adenovirus
400x Magnification
IBM Quantum CorralIron Atoms on Copper
5 nanometers
400,000 x !
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Calit2 is Creating a Nano-Bio-Info Innovation Laboratory
Donald Bren School of
Information and
Computer Science
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INRF Supports Researchers in Nano and BioMEMS
Spray atomization of nano powders
New methods of making arrays of nanowires
Boron-based nanowires for novel circuits
Carbon nanotubes for sensor and electronic applications
Micromirror on a catheter for optical biopsy using coherence tomography
Protein crystallization in nanovolumes
0 ms 200 ms
400 ms 600 ms
Microfluidic devices for electrophoretic separations
Microfluidic devices using droplets, CD microfluidics andmagnetohydrodynamics
BioMEMS and Medical Applications
Nanotechnology / Nanofabrication
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INRF Partners Companies with University Researchers: 70 Past and Current Collaborating Companies
• Advanced Customs Sensors Inc.• Agilient• Alpha Industry/Network Device Inc.• AXT/Alpha Photonics Incorporated• Alpine Microsystems Incorporated• Auxora, Inc.• Bethel Material Research• Broadcom• Broadley-James Corp.• Cito Optronics, Inc.• Coherent, Inc.• Conexant• Coventor• DRS Sensors• Endevco
Friends USA• General Monitors• Global Communication Semiconductor• Hewlett Packard• Hitachi Chemical Research• IJ Research• Impco Technology• Intelligent Epitaxy Incorporated• International Technology Works• IOS • Irvine Sensors• Jazz Semiconductor• Linfinity Microelectronics• Maxwell Sensors• Metrolaser Incorporated
Microtek Lab Incorporated• MicroWave Technology• Moog, Inc. • Network Device• Newport Opticom
• NexGen Research Corporation• Northrop Grumman Corporation• Numerical Technologies
Ormet Corp.• Oplink Communications• Optical Crossing• Optinetrics• Optiswitch Technology• Physical Optics Corp.• Printronix• ProComm Enterprises• Rainbow Communications• Raytheon Systems• Rockwell• RF Integrated Corp.• Sabeus Photonics• Saddleback Aerospace• SAIC
Second Sight, LLC• Semco Laser Technology• Sequenom• Silicon Storage Technology, Inc.• Simax• Skyworks Solutions• SVT Associates• Tamarack Scientific, Inc.• Tanner Research, Inc.• Texas Instruments, Inc.• TRW• U Machines• Versa Technology• VSK Photonics• WIN Semiconductors• Xtal Technologies• Y Media Corporation
40 UCI Faculty from
a Dozen Departments
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INRFCalit2BiON
ZeissCenter of
Excellence
Micro/Nano Materials and Devices
Bio-Organic Nano Lab
SEM,Advanced
Characterization
Three centers share a common infrastructure
Photonics,RF,
ChipLabs
Integrate with
Chips, Telecom
Calit2@UCI Nanobioinfotechnology“Innovation Pipeline”
Source: GP Li, Calit2
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Example: Real-Time Electronic Readout from Single Biomolecule Sensors
• 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
Source: Phil Collins & Greg Weiss, Calit2@UCI
1 nm wiring
1 proteinmolecule
… and withoutdevice in buffer with reagents
Schematic & SEM Image of Carbon Nanotube-based Device
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LifeChips: the merging of two major industries, the microelectronic chip industry
with the life science industry
LifeChips medical devices
Lifechips--Merging Two Major Industries: Microelectronic Chips & Life Sciences
65 UCI Faculty
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Calit2@UCSD Building Anchors “Bio-Nano-IT Convergence Quad”
Calit2
Bioengineering
Computer Science and Engineering
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Faculty Leadership Team
Sadik Esener Dept. of Electrical and Computer Engineering
Michael Heller Dept. of Bioengineering
Sungho Jin Dept. of Mechanical and Aerospace Engineering
Jan Talbot Dept. of Mechanical and Aerospace Engineering -
Chemical Engineering Program
Kenneth Vecchio Dept. of Mechanical and
Aerospace Engineering
In the past five years alone, these five faculty filed 51 patent applications and licensed 6 inventions to private companies
Corporate SupportersGMT Ventures ~ Invitrogen ~ Pfizer ~ Illumina ~ QUASAR Federal Systems ~ ResMed ~
Enterprise Partners Venture Capital ~ Varian Medical Systems ~ Sun Microsystems ~ SAIC ~ Intel
UCSD Jacobs School of Engineering NanoEngineering Department Proposal Proponents
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Nano3 FacilityCALIT2.UCSD
10,000 sq. feet State-of-the-Art
Materials and Devices Laboratory
Calit2 Nano3 Clean Rooms Helps “Jump Start”The New Jacobs School Dept. of Nanoengineering
Source: Bernd Fruhberger, Calit2
http://nano3.calit2.net/
45 Faculty with Nano Projects at
Calit2@UCSD
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Yu-Hwa Lo Research GroupElectrical and Computer Engineering
Integrating Photonics and Microfluidics
Microfluidic Flow Cytometry Chip for Portable, Low-cost Blood Analysis. The Chip Contains 12 Lenses and 6 Waveguides to Illuminate a Single Cell and Collect the Light it Scatters
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Treatment, Understanding, and Monitoring of Cancer (UCSD, Burnham Institute, UCSB, UCR, UCI --PI: Sadik Esener)
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Michael J. Sailor Research GroupChemistry and Biochemistry
Nanostructured “Mother Ships” for deliveryof cancer therapeutics.
Nanodevices for In-vivo Detection & Treatment of Cancerous Tumors
Porous Photonic Crystals for Cell-based Biosensor
Human epithelial (HeLa) cells on a photonic crystal.The colors observed can be used to monitor thephysiological status of the cells.
Nano-Structured Porous SiliconApplied to Cancer Treatment
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TEM Images of Hollow Silica Nanospheres for Drug and Gene Delivery Applications
100 nm
100 nm
Silica gel wall 5 nm thick
100 nm cavity
J. Yang, J. U. Lind, W. C. Trogler, Department of Chemistry and Biochemistry and
Calit2 Nanomedicine Laboratory
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Single Cancer Cell Isolated on EngineeredSurface for Phenotyping and Genotyping
Hoechst Nuclear Stain (Blue), Nano-bead Membrane Dye (Green),
Surface AttachmentSite (Red).
Devices for Fast and Automated Detection ofSingle Cancer Cells in Tissue Margins
Advanced Staining Procedures Allows Us to DistinguishEpithelial Cells (Cancerous) From Non-Epithelial Cells
Developing Small Molecule and Quantum Dot Cell Staining Procedures to
Identify Single Cancer Cells in Otherwise Normal Tissue
Green:CancerSpecificStain II
Red:CancerSpecificStain I
Blue:HoechstNucleusStain
Finding the Needle in the Haystack
Cancer NanotechnologyKummel / Trogler / Schuller Cancer Center Project
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Quantum Dot Staining of Filled Cells: Light Microscopy
astro volume (gray); perimeter cx43 (red); internal cx43 (yellow)
Dye Filled Astrocytes in the Brain are Immuno-Labeled
with QDs for Connexin Proteins
(Cell-Borders in Yellow)
Diffraction-Limit Volumes Can Then be Acquired
and the Distribution of the Protein over the Cells
Can be Quantified and Analyzed
Immuno-Labelling of Cx43 with Quantum Dots Allows for Immuno-Labelling of Cx43 with Quantum Dots Allows for Correlated LM and EM of cx43 on the Dye-Filled Astrocyte.Correlated LM and EM of cx43 on the Dye-Filled Astrocyte.
Source: B. Smarr, M. Ellisman, UCSD NCMIR
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Calit2 Brings Computer Scientists and Engineers Together with Biomedical Researchers
• Some Areas of Concentration:– Algorithmic and System Biology
– Bioinformatics
– Metagenomics
– Cancer Genomics
– Human Genomic Variation and Disease
– Proteomics
– Mitochondrial Evolution
– Computational Biology
– Multi-Scale Cellular Imaging
– Information Theory and Biological Systems
– Telemedicine
UC Irvine
UC Irvine
Southern California Telemedicine Learning Center (TLC)
National Biomedical Computation Resource an NIH supported resource center
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Calit2 Facilitated Formation of the Center for Algorithmic and
Systems Biology
http://casb.ucsd.edu/
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UCI’s IGB Develops a Suite of Programs and Servers for Protein Structure and Structural Feature Prediction
www.igb.uci.edu/tools.htm
Source: Pierre Baldi, UCI
Sixty Affiliated IGB Labs at UCI
e.g.:
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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
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PI Larry Smarr
Paul Gilna Ex. Dir.
Announced January 17, 2006$24.5M Over Seven Years
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Marine Genome Sequencing Project – Measuring the Genetic Diversity of Ocean Microbes
Sorcerer II Data Will Double Number of Proteins in GenBank!
Specify Ocean Data
Each Sample ~2000
Microbial Species
Plus 155 Marine
Microbial Genomes
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Enormous Increase in Scale of Known Genes Over Last Decade
1995First Microbe Genome
2007Ocean Microbial Metagenomics
6.3 Billion Bases 5.6 Million Genes
1.8 Million Bases 1749 Genes
~3300x
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CAMERA 1.1 is Up and Running!
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Can We Create a “Facebook” for Science Researchers? Microbial Metagenomics as a Cyber-Community
1300 Registered CAMERA Users From 45 Countries
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From Microbial Genomes To Human Disease
• Microbes Have a Much Simpler Genome Than Humans
• However, Microbes Share Many of the Core Components of the Molecular Signaling Machinery Used by Humans
• Understand Both the Evolution and Regulation of Signaling Systems, First in Microbes and Then in Humans
• We Illustrate This Using the Protein Kinase Superfamily That is Implicated in Numerous Human Diseases
Source: Susan Taylor, SOM, UCSD
Identified 15,000 New Kinases
In Venter Global Ocean Sampling Data
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Medically Relevant Metagenomic Data SetsAre Rapidly Being Accumulated
• “A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms.”
• “We discovered significant inter-subject variability.” • “Characterization of this immensely diverse ecosystem is the first step in
elucidating its role in health and disease.”
“Diversity of the Human Intestinal Microbial Flora” Paul B. Eckburg, et al Science (10 June 2005)
395 Phylotypes
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Full Genome Sequencing is Exploding:Most Sequenced Genomes are Bacterial
www.genomesonline.org
>100Metagenomes
First Genome 1995 6 Genomes/ Year 20001600 Genomes 2007
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Moore Foundation Funded the Venter Institute to Provide the Full Genome Sequence of 155+ Marine Microbes
Phylogenetic Trees Created by Uli Stingl, Oregon State
Blue Means Contains One of the Moore 155 Genomes
www.moore.org/microgenome/trees.aspx
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Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Proteobacteria
Chlorobi
FirmicutesFusobacteria Actinobacteria
Cyanobacteria
Chlamydia
Spriochaetes
Deinococcus-Thermus
Aquificae
Thermotogae
TM6OS-K
Termite GroupOP8
Marine GroupAWS3
OP9
NKB19
OP3
OP10
TM7
OP1OP11
Nitrospira
SynergistesDeferribacteres
Thermudesulfobacteria
Chrysiogenetes
Thermomicrobia
Dictyoglomus
Coprothmermobacter
Well sampled phyla
No cultured taxa
DOE Genomic Encyclopedia of Bacteria and Archaea (GEBA) / Bergey Solution: Deep Sampling Across Phyla
Source: Eddie Rubin, DOE JGI
2007 Goal: Finish ~100 Bacterial and Archaeal Genomes from Culture Collections
Project Lead -- Jonathan Eisen (JGI/UC Davis)
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The Bioinformatics Core of the Joint Center for Structural Genomics is Housed in the Calit2@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
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Interactive Exploration of the Proteins of the Marine Microbe Thermatoga
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Building Genome-Scale Models of Living Organisms
• E. Coli– Has 4300
Genes– Model Has
2000!
Regulatory Actions
Input Signals
Monomers &Energy
Proteins
Genomics
Transcriptomics
Proteomics
Metabolomics
EnvironmentInteractomics
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pgi
pfkA
fba
tpi
fbp
gapA
pgk
gpmA
eno
pykFppsAaceE
zwfpgl gnd
rpiA
rpe
talAtktA1 tktA2
gltA
acnA icdA
sucA
sucC
sdhA1
frdA
fumA
mdh
adhE
AC
ackA
pta
pckA
ppc
cyoA
pnt1A
sdhA2nuoA
atpA
ACxtETHxt
O2O2xt
CO2 CO2xt
Pi Pixt
O2 trx
CO2 trx
Pi trx
EXTRACELLULARMETABOLITE
reaction/gene name
Map Legend
INTRACELLULARMETABOLITE
GROWTH/BIOMASSPRECURSORS
ETH trxAC trx
SUCC trx
acs
FOR
pflA
FORxt
FOR trx
dld
LAC
LACxtLAC trx
PYRxt PYR trx
glpDgpsA
GL3P
GL glpK
GLxt
GL trx
GLCxtGLC trx
glk
RIB
rbsK
RIBxt
RIB trx
FORfdoH
pnt2A
H+ Qh2
GLX
aceA
aceB
maeB
sfcA
G1 + RNAP G1*
v1
nNTP
mRNA1 nNMPb4
b2
v2
v3=k1[mRNA1]
2aGTP
rib
rib1*
protein1b3
v4 (subject to global max.)
v5
aAA-tRNA
b7
2aGDP + 2aPib8
b5
b1 aAAatRNA
aATP
aAMP
+ 2aPi
b6
v6
2nPi
Pi
b9
G1 + RNAP G1*
v1
nNTP
mRNA1 nNMPb4
b2
v2
v3=k1[mRNA1]
2aGTP
rib
rib1*
protein1b3
v4 (subject to global max.)
v5
aAA-tRNA
b7
2aGDP + 2aPib8
b5
b1 aAAatRNA
aATP
aAMP
+ 2aPi
b6
v6
2nPi2nPi
Pi
b9
Pi
b9
G1 + RNAP G1*
v1
nNTP
mRNA1 nNMPb4
b2
v2
v3=k1[mRNA1]
2aGTP
rib
rib1*
protein1b3
v4 (subject to global max.)
v5
aAA-tRNA
b7
2aGDP + 2aPib8
b5
b1 aAAatRNA
aATP
aAMP
+ 2aPi
b6
v6
2nPi
Pi
b9
G1 + RNAP G1*
v1
nNTP
mRNA1 nNMPb4
b2
v2
v3=k1[mRNA1]
2aGTP
rib
rib1*
protein1b3
v4 (subject to global max.)
v5
aAA-tRNA
b7
2aGDP + 2aPib8
b5
b1 aAAatRNA
aATP
aAMP
+ 2aPi
b6
v6
2nPi2nPi
Pi
b9
Pi
b9
Gc2
tc2
Rc2
Pc2 Carbon2A
Oc2
Carbon1
(indirect)
(-)
If [Carbon1] > 0, tc2 = 0
G2a
t2a
R2a
P2a BC + 2 ATP + 3 NADH
O2a
B(+)
G5
t5
R5
P5 C + 4 NADH
O5
(+)
3 E
If R1 = 0, we say [B] is not in surplus, t2a = t5 = 0
G6a
t6a
R6a
P6aH
O6a
(-)
Hext
If Rh> 0, [H] is in surplus, t6a = 0
Gres
tres
Rres
Pres O2 + NADH
ATP
Ores
O2
(+)
G3b
t3b
R3b
P3bG
O3b
(+)
0.8 C + 2 NADH
If Oxygen = 0, we say [O2] = 0, tres= t3b = 0
G + 1 ATP + 2 NADH
Gc2
tc2
Rc2
Pc2 Carbon2A
Oc2
Carbon1
(indirect)
(-)
If [Carbon1] > 0, tc2 = 0
G2a
t2a
R2a
P2a BC + 2 ATP + 3 NADH
O2a
B(+)
G5
t5
R5
P5 C + 4 NADH
O5
(+)
3 E
If R1 = 0, we say [B] is not in surplus, t2a = t5 = 0
G6a
t6a
R6a
P6aH
O6a
(-)
Hext
If Rh> 0, [H] is in surplus, t6a = 0
Gres
tres
Rres
Pres O2 + NADH
ATP
Ores
O2
(+)
G3b
t3b
R3b
P3bG
O3b
(+)
0.8 C + 2 NADH
If Oxygen = 0, we say [O2] = 0, tres= t3b = 0
G + 1 ATP + 2 NADH
E. coli i2K
Source: Bernhard PalssonUCSD Genetic Circuits Research Group
http://gcrg.ucsd.edu
JTB 2002
JBC 2002
in Silico Organisms Now Available
2007:
•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
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Biochemically, Genetically and Genomically (BiGG) Genome-Scale Metabolic Reconstructions
H. influenzae
H. pylori
S. aureus
S. typhimurium
M. barkeri• 619 Reactions• 692 Genes
S. cerevisiae• 1402 Reactions• 910 Genes
E. coli• 2035 Reactions• 1260 Genes
S. aureus• 640 Reactions• 619 Genes Mitoc.
• 218 Rxns
RBC• 39 Rxns
H. sapiens• 3311 Reactions• 1496 Genes
S. typhimurium• 898 Reactions• 826 Genes
H. pylori• 558 Reactions• 341 Genes
H. influenzae• 472 Reactions• 376 Genes
M. tuberculosis• 939 Reactions• 661 Genes
Systems Biology Research Grouphttp://systemsbiology.ucsd.edu
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With Nanobioinfo Devices Everywhere, How Can We Handle the Data Flows?
• Mobile Broadband– 0.1-0.5 Mbps
• Home Broadband– 1-5 Mbps
• University Dorm Room Broadband– 10-100 Mbps
• Calit2 Global Broadband– 1,000-10,000 Mbps
100,000 Fold Range All Here Today!
“The future is already here, it’s just not evenly distributed”
William Gibson, Author of Neuromancer
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The OptIPuter Project: Defining a High Performance Collaboration Infrastructure for Eng-Med
Picture Source:
Mark Ellisman,
David Lee, Jason Leigh
Calit2 (UCSD, UCI) and UIC Lead Campuses—Larry Smarr PIUniv. Partners: SDSC, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST
Industry: IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent
$13.5M Over Five
Years
Scalable Adaptive Graphics
Environment (SAGE)
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My OptIPortalTM – AffordableTermination Device for the OptIPuter Global Backplane
• 20 Dual CPU Nodes, Twenty 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
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OptIPuter Scalable Displays Are Used for Multi-Scale Biomedical Imaging
Green: Purkinje CellsRed: Glial CellsLight Blue: Nuclear DNA
Source: Mark
Ellisman, David Lee,
Jason Leigh
Two-Photon Laser Confocal Microscope Montage of 40x36=1440 Images in 3 Channels of a Mid-Sagittal Section
of Rat Cerebellum Acquired Over an 8-hour Period
200 Megapixels!
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Scalable Displays Allow Both Global Content and Fine Detail
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Allows for Interactive Zooming from Cerebellum to Individual Neurons
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Interactive Exploration of Marine Genomes Using 100 Million Pixels
Ginger Armburst (UW), Terry Gaasterland (UCSD SIO)
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Nearly One Half Billion Pixelsin Calit2 Extreme Visualization Project!
Connected at 2,000 Megabits/s!
UC Irvine
UC San Diego
UCI HIPerWall Analyzing Pre- and Post- Katrina
Falko Kuester, UCSD; Steven Jenks, UCI
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NW!
CICESE
UW
JCVI
MIT
SIO UCSD
SDSU
UIC EVL
UCI
OptIPortals
OptIPortal
An Emerging High Performance Collaboratoryfor Microbial Metagenomics
UC Davis
UMich
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3D OptIPortal Calit2 StarCAVE Telepresence “Holodeck”
60 GB Texture Memory, Renders Images 3,200 Times the Speed of Single PC
Source: Tom DeFanti, Greg Dawe, Calit2Connected at 200 Gb/s
30 HD Projectors!
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www.glif.is
Created in Reykjavik, Iceland 2003
Countries are Aggressively Creating Gigabit Services:Interactive Access to CAMERA Data System
Visualization courtesy of Bob Patterson, NCSA.