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

The People

Overall
construc.on
and
 director
of
the
project,
wiki
 writer,
our
captain


Wei P ei Pan an 1st
Master
 Biomedical
 Engineering


Core
algorithm
–
PSO,
SA
and
 all
related
Iden.fica.on


Yuw uwei ei Cui Cui Junior
 Condensed
 Ma6er
Physics


Designer
of
the
GUI
part
from
 an
awesome
‘ab‐ini.o’
design


Xiaomo Xiaomo Y Yao ao Freshman
 Geophysics


All
about
SBML
and
the
related
 I/O
issues


Jiahao Jiahao Li Li Sophermore
 Electronic
 Engineering


Raw
construc.on
of
database,
 I/O
issues,
logo
and
wiki‐pages


Yu He u He Junior
 Condensed
 Ma6er
Physics


Core
algorithm
–
GA
 Instruc.ons
on
biological
 technical
issues


Bo Ding Bo Ding Ph.D
Candidate
 Computa@onal
 Biology


USTC _Software Presents

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

Prof
X:
Hey,
Doc.
I
don’t




 












want
do
experiment.



 












Can
you
give
me

 












some
ideas?
 Dr
Ding:
I’m
here,
Professor. At
the
sunny
beach……


Dr
Ding:
What
do
you



 















want,

professor?
 Prof
X:
I
want
……


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




Prof
X:
I
have……
 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?


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:
 Parameters……
 Topologies……
 BioBricks……


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:
No,
several
to


 
















choose.
 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?


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:
Do
you
have




 

















any
dissa.sfac.on?
 In
Prof.
X’s
lab……
 Prof
X:
Wow,
it
works.

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

Why ABCD?

Get
a
control!
 Dynamics
can
help
make
 predic@on,
device
 manipula@on
and
real‐ life
applica@on.
 Confronted
with
dazzling
 Biobricks,
ABCD
helps
you
 get
down
to
focus


What
has
Sir
Isaac
Newton
 brought
to
modern
physics?
 QUANTIFICATION.


Last
pic
from
中国会计网


1.
Simula@on
and
Iden@fica@on

 
–
an
alterna@ve
approach
to
DEFINE
parameters


Original
 Model
 ODE
 Array
 LSA
 GSA
 Robustness
 Analysis
 Runge‐ Ku6a
 Raw
 Behavior
 Op@mized
 Parameters
 Gene@c
 Algorithm
 Op@mized
 Topology
 Database
 Experimental

 Scheme
 Quan@fica@on
 And
 New
Standard
 Desired
 Behavior
 General
 Performance
 Average
 PSO/SA


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


Parameters

 Iden@fied:


K3


3
=
0.8


rA1 rA1
=
0.001

 rmG rmG
=
0.0144

 a
 a
=
0.108
 pG pG
=
24
 d
=
0.00847

 C1
=
1.5*10-10


 C2
=
1010

 C3
=
8*10-7
 C4
=
5.8*1011 Barry
Canton
et
al.
Nature
Biotechnology
26,
787
‐
793
(2008)



BBa_F2620


Demo

Application – Bistable Toggle Switch

Timothy
S.Gardner.
Ph.
D
Thesis
(2000)

SA
works
for
parameter
 iden.fica.on
successfully!
 Realize
iden.fica.on
for
 nonlinear
systems
with
MIMO.


Application – Tunable Oscillator

Michael
B.
Elowitz
&
Stanislas
Leibler
Nature

403,
335‐338
(2000)

Tunable
Amplitude!
 What
about
frequency?


Target:
 Realiza@on
of
Par@al
Design!
 Method:
 Par@cle
Swarm
Op@miza@on

Application – Tunable Oscillator

Michael
B.
Elowitz
&
Stanislas
Leibler
Nature

403,
335‐338
(2000)

Tunable
Frequency
!


Wenzhe
Ma,
et
al.
Cell,
138,
760‐773
(2009)

Application – Adaptation Target:
 Realiza.on
of
ab‐ini@o
Design
!
 Iden.fica.on
of
both
Topology
&
Parameters!
 Method:
 Gene.c
Algorithm
&
PSO


Feed
Back
 Feed
Forward
 Global
Sensi@vity
 Topology


Nega@ve
 Feedback
 Incoherent
 Feed
Forward


Two
days
and
two
nights
calcula.on
……

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


(wavelet)


move
the
score
func.on
into
frequency
 space
aTer
Fourier
Transforma.on

T
 Subs


Fourier
 Trans.


T
 Subs


Fourier
 Trans.
 Experimental
behavior
 Target
behavior


Score
 Func@on


Frequency
 Subs


Experimental
behavior


Frequency
 Subs


Target
behavior


Score
 Func@on


Evolu@on


Evolu@on


move
all
sampling
and
ini.aliza.on
 in
logarithmic
space

Linear
Regime
 Exponen@al
Regime
 Variables
Xi
 Xi:
Lnxmin
to
Ln
xmax
 Variables
Xi
=
exp(Yi)
 Yi:
Lnxmin
to
Ln
xmax
 Func@on/ODE
Array
 Fi(Xi),
Fix(Xi)
=
dFi(Xi)/dXi
 Variables
Yi
 Fi(exp
Yi)
=
Fi(Xi)
 dFi(Xi)/dYi
=
eyi
Fix(yi)
 Sampling
Step
 Lx
 Sampling
Step
 Ly
=
Ln
Lx
 Variables
Xi
 Xi:
Lnxmin
to
Ln
xmax
 Variables
Xi
=
exp(Yi)
 Yi:
Lnxmin
to
Ln
xmax
 Calcula@on


• Parallel
compu@ng

• Logarithmic
space


Future Plan – Miscellaneous

• Restric@on
input





standard
&
concision


easy‐drag
interface

• utput
of
.me
course
plot
• Output





SBML,
SBGN,
SBW


• Database





data
requirement


Acknowledgements

We
specially
thank
our


wet
team
for


incarna@on
of
our
 DRYasdust
idea
 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
 Danqian
Liu,
we
owe
you
 twenty
seven
cups
of
 tasty
milk
tea

 We
thank
Prof.
Lingchong
 You,
Duke
and
Prof.
Pablo
 Iglesias,
JHU
for
 illumina@ve
discussions!


In
Memory
of
Our
Great
Masters


Tsien
Hsue‐shen
(钱学森)
 1911.12.11‐2009.10.31 Bei

Shi‐zhang
(贝时璋)
 
1903.10.10‐2009.10.29