The People Xiaomo Xiaomo Y Yao ao Freshman Wei P ei Pan an - PowerPoint PPT Presentation

The People Xiaomo Xiaomo Y Yao ao Freshman
 Wei P ei Pan an Yuw uwei ei Cui Cui Geophysics
 1 st 
Master
 Junior
 Biomedical
 Designer
of
the
GUI
part
from
 Engineering
 Condensed
 an
awesome
‘ab‐ini.o’
design
 Ma6er
Physics
 Overall
construc.on
and
 director
of
the
project,
wiki
 Core
algorithm
–
PSO,
SA
and
 writer,
our
captain
 all
related
Iden.fica.on
 Bo Ding Bo Ding Ph.D
Candidate
 Jiahao Jiahao Li Li Computa@onal
 Sophermore
 Yu He u He Biology
 Electronic
 Junior
 Engineering
 Core
algorithm
–
GA
 Condensed
 Instruc.ons
on
biological
 Ma6er
Physics
 All
about
SBML
and
the
related
 technical
issues
 I/O
issues
 Raw
construc.on
of
database,
 I/O
issues,
logo
and
wiki‐pages


USTC _ S oftware P resents

US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China At
the
sunny
beach……
 Prof
X:
 Hey,
Doc.
I
don’t




 












want
do
experiment.



 












Can
you
give
me

 












some
ideas?
 Dr
Ding:
 I’m
here,
Professor. �

US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China Dr
Ding:
 What
do
you



 















want,

professor?
 Prof
X:
 I
want
……


USTC_Sof US C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China Dr
Ding:
 What
do
you
have

 















in
your
lab,
professor?
 


 Prof
X:

 I
have
all
BioBricks
in


 
















partsregistry.
 Dr
Ding:
 Do
you
have
any

 















special
restric.ons?
 


Prof
X:
 I
have……


US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China Our
soTware
is
running
at
 full
speed:
 Topologies……
 Parameters……
 BioBricks……


USTC_Sof US C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China AGer
the
vaca@on……
 Prof
X:
 Hey,
Dr.
Ding.
 Dr
Ding:
 Nice
to
meet
you.


 















Here
is
your
solu.on.
 Prof
X:
 Only
one
solu.on?
 Dr
Ding:
 No,
several
to


 
















choose.


US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China In
Prof.
X’s
lab……
 Prof
X:
 Wow,
it
works. � Dr
Ding:
 Do
you
have




 

















any
dissa.sfac.on?


Why ABCD? Confronted
with
dazzling
 Biobricks,
ABCD
helps
you
 What
has
Sir
Isaac
Newton
 get
down
to
focus
 brought
to
modern
physics?
 QUANTIFICATION.
 Get
a
control!
 Dynamics
can
help
make
 predic@on,
device
 manipula@on
and
real‐ life
applica@on.
 Last
pic
from
 中国会计网 


1.
Simula@on
and
Iden@fica@on

 
–
an
alterna@ve
approach
to
DEFINE
parameters


Runge‐ Ku6a
 Original
 ODE
 Raw
 Desired
 Model
 Array
 Behavior
 Behavior
 G eneral
 P erformance 
 A verage 
 PSO/SA
 Gene@c
 Algorithm 
 Op@mized
 Parameters
 Experimental

 Op@mized
 Scheme
 Topology
 Database
 LSA
 Robustness
 Quan@fica@on
 Analysis
 And
 GSA
 New
Standard


Prerequisite, Standard and Flow Chart 2.
Prototype
of
two
intertwined
databases
 Reac@on
 Substance


Graphical User Interface Source
code,
soGware
and
demo
available
at:
h6p://ustcabcd.sourceforge.net
 For
further
interests,
see
our
wiki:
h6p://2009.igem.org/Team:USTC_SoGware


Demo decompose
and
dilute
 BBa_K176026


Demo Parameters

 BBa_F2620
 Iden@fied: 
 K 3
 3
 =
0.8
 rA1 rA1
=
0.001

 rmG rmG
=
0.0144

 a
 a
=
0.108
 pG
=
24
 pG d
=
0.00847

 C 1
 =
1.5*10 -10


 C 2
 =
10 10
 
 C 3
 =
8*10 -7 
 C 4
 =
5.8*10 11 Barry
Canton
et
al.
Nature
Biotechnology
26,
787
‐
793
(2008)



Application – Bistable Toggle Switch SA
works
for
parameter
 iden.fica.on
successfully!
 Realize
iden.fica.on
for
 nonlinear
systems
with
MIMO.
 Timothy
S.Gardner.
Ph.
D
Thesis
(2000) �

Application – Tunable Oscillator Target:
 Tunable
Amplitude!
 Realiza@on
of
Par@al
Design!
 What
about
frequency?
 Method:
 Par@cle
Swarm
Op@miza@on � Michael
B.
Elowitz
&
Stanislas
Leibler
Nature

403,
335‐338
(2000) �

Application – Tunable Oscillator Tunable
Frequency
!
 Michael
B.
Elowitz
&
Stanislas
Leibler
Nature

403,
335‐338
(2000) �

Application – Adaptation Nega@ve
 Incoherent
 Target:
 Feedback
 Feed
Forward
 Realiza.on
of
 ab‐ini@o 
Design
!
 Iden.fica.on
of
both
 Topology 
&
 Parameters!
 Global
Sensi@vity
 Topology
 Feed
Back
 Feed
Forward
 Method:
 Two
days
and
two
nights
calcula.on
…… � Gene.c
Algorithm
&
PSO
 Wenzhe
Ma,
et
al.
Cell,
138,
760‐773
(2009) �

Summary In
our
project,
we
successfully
achieve:
  Parameter
Iden@fica@on
for
Specific
Topology
 （ PSO/ SA)
  Topology
Iden@fica@on
&
ab‐ini@o
Design
for
Black
 Box
(GA)
  New
Standard
for
Quan@ta@ve
Characteriza@on
of
 Biobricks
  Friendly
Graphic
User
Interface �

Future Plan - Algorithms • 
Fourier
transforma@on
 • 
Logarithmic
space
 (wavelet)
 • 
 Parallel
compu@ng
 Evolu@on
 Linear
Regime
 Exponen@al
Regime
 Subs
 Subs
 Variables
 X i
 Variables
 X i 
=
 exp( Y i )
 Target
behavior
 Experimental
behavior
 X i :
Lnx min 
to
Ln
x max
 Y i :
Lnx min 
to
Ln
x max
 Score
 Func@on
 Variables
Y i 
 Func@on/ODE
Array
 F i (exp
Y i )
=
F i (X i )
 F i (X i ),
F ix (X i )
=
dF i (X i )/dX i 
 dF i (X i )/dY i 
=
e yi 
F ix (y i ) 
 T
 T
 Fourier
 Fourier
 Trans.
 Trans.
 Sampling
Step
 Sampling
Step
 L x
 L y 
=
Ln
L x
 Subs
 Subs
 Experimental
behavior
 Target
behavior
 Score
 Calcula@on
 Func@on
 Variables
 X i
 Variables
 X i 
=
 exp( Y i )
 Frequency
 Frequency
 X i :
Lnx min 
to
Ln
x max
 Y i :
Lnx min 
to
Ln
x max
 Evolu@on
 move
the
score
func.on
into
frequency
 move
all
sampling
and
ini.aliza.on
 space
aTer
Fourier
Transforma.on � in
logarithmic
space �

Future Plan – Miscellaneous • 
Restric@on
input
 


 standard
&
concision 
 • 
Output
 


 SBML,
SBGN,
SBW
 easy‐drag
interface � • 
Database
 


 data
requirement 
 output
of
.me
course
plot �

Acknowledgements We
thank
Prof.
Lingchong
 You,
Duke
and
Prof.
Pablo
 Iglesias,
JHU
for
 illumina@ve
discussions!
 We
specially
thank
our
 wet
team 
for
 incarna@on
of
our
 Danqian
Liu,
we
owe
you
 DRYasdust
idea
 twenty
seven
cups
of
 tasty
milk
tea
  
 Also
we’d
like
to
express
gra@tude
to
our
 sponsors
–

USTC
Teaching
Affair
Office,
USTC
 Foreign
Affair
Office,
USTC
School
of
Life
 Sciences,
USTC
School
for
the
GiGed
Young,
 USTC
School
of
Informa@on
Sciences
and
 Technology


In
Memory
of
Our
Great
Masters
 � Tsien
Hsue‐shen
( 钱学森 )
 Bei

Shi‐zhang
( 贝时璋 )
 1911.12.11‐2009.10.31 � 
1903.10.10‐2009.10.29 �