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biocham
Commits
efcd33ec
Commit
efcd33ec
authored
Nov 20, 2018
by
dcoudrin
Browse files
notebooks and bc files from master
parent
853ed061
Changes
4
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library/examples/MPCE/Qu.ipynb
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efcd33ec
%% Cell type:markdown id: tags:
# Minimal cell cycle model (G2/M transition switch)
after Qu, MacMillan, Weiss 2003
<img
src=
"Qu.png"
width=
500
>
François Fages, Inria Saclay Ile de France,
MPCE course, March 2018.
%% Cell type:code id: tags:
```
load(Qu.bc).
```
%% Cell type:code id: tags:
```
list_model.
```
%%%% Output: execute_result
ksmpf for _=>preMPF.
kdmpfp*preMPF for preMPF=>_.
kdmpfp*MPF for MPF=>_.
kdmpf*APC*MPF for MPF=[APC]=>_.
kdmpf*APC*preMPF for preMPF=[APC]=>_.
kampf*C25P*preMPF for preMPF=[C25P]=>MPF.
kimpf*Wee1*MPF for MPF=[Wee1]=>preMPF.
Viw*Wee1P/(Kiw+Wee1P)for Wee1P=>Wee1.
(Vapw+Vaw*MPF)*Wee1/(Kaw+Wee1)for Wee1=[MPF]=>Wee1P.
Viw*Wee1P/
(Kiw+Wee1P)for Wee1P=>Wee1.
(Vapw+Vaw*MPF)*Wee1/
(Kaw+Wee1)for Wee1=[MPF]=>Wee1P.
ksweemp for _=>Wee1m.
kdweem*Wee1m for Wee1m=>_.
kswee*Wee1m for _=[Wee1m]=>Wee1.
kdwee*Wee1 for Wee1=>_.
kdwee*Wee1P for Wee1P=>_.
Vic*C25P/(Kic25+C25P)for C25P=>C25.
(Vapc+Vac*MPF)*C25/(Kac25+C25)for C25=[MPF]=>C25P.
Vic*C25P/
(Kic25+C25P)for C25P=>C25.
(Vapc+Vac*MPF)*C25/
(Kac25+C25)for C25=[MPF]=>C25P.
ks25 for _=>C25.
kd25*C25 for C25=>_.
kd25*C25P for C25P=>_.
ksiep for _=>IE.
ksie*MPF for _=[MPF]=>IE.
kdie*IE for IE=>_.
(kaapcp+kaapc*IE)*APCi/(Kapc+APCi)for APCi=[IE]=>APC.
kiapc*APC/(Kapc+APC)for APC=>APCi.
(kaapcp+kaapc*IE)*APCi/
(Kapc+APCi)for APCi=[IE]=>APC.
kiapc*APC/
(Kapc+APC)for APC=>APCi.
present(preMPF,0.279939269).
present(MPF,0.747404087).
present(C25,0.629659946).
present(C25P,0.370340054).
present(Wee1,0.00223979517).
present(Wee1P,0.132059534).
present(APC,0.0303504407).
present(IE,0.41856651).
present(Wee1m,0.141190132).
present(APCi,0.973282491).
parameter(
kd25 = 1,
kdmpfp = 0.25,
kampf = 5,
kaapc = 1,
ksweemp = 0.001,
ksweem = 0.5,
kdweem = 1,
Kweem = 0.2,
kwpcn = 5,
Vac = 1,
Kac25 = 0.01,
Kic25 = 0.01,
kdmpf = 2,
Vaw = 1,
Vapc = 0.1,
Kaw = 0.005,
Kiw = 0.005,
Vapw = 0.1,
Kapc = 0.01,
ks25 = 1,
kswee = 0.5,
kimpf = 1.5,
Vic = 0.2,
kiapc = 0.5,
kdwee = 1,
Viw = 0.2,
ksmpf = 0.35,
kdie = 0.1,
ksiep = 0,
ksie = 0.3,
kaapcp = 0
).
%% Cell type:code id: tags:
```
draw_influences.
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
option(time:100). numerical_simulation. plot.
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
plot(show:MPF, against:C25P).
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
plot(show:MPF, against:APC).
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
%slider kdie kampf
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
validity_domain(period(MPF,p)).
```
%%%% Output: execute_result
p=21.00004\/p=21\/p=20
%% Cell type:code id: tags:
```
seed(0). search_parameters(period(MPF,p), [0<=kdie<=1, 0<=kampf<=10], [p -> 24]).
```
%%%% Output: execute_result
Time: 12.635 s
Stopping reason: Fitness: function value 0.00e+00 <= stopFitness (1.00e-04)
Best satisfaction degree: 1.0
[0] parameter(kdie=0.0860196219263221)
[1] parameter(kampf=3.1315611499739138)
%% Cell type:code id: tags:
```
list_parameters.
```
%%%% Output: execute_result
[0] parameter(kd25=1)
[1] parameter(kdmpfp=0.25)
[2] parameter(kaapc=1)
[3] parameter(ksweemp=0.001)
[4] parameter(ksweem=0.5)
[5] parameter(kdweem=1)
[6] parameter(Kweem=0.2)
[7] parameter(kwpcn=5)
[8] parameter(Vac=1)
[9] parameter(Kac25=0.01)
[10] parameter(Kic25=0.01)
[11] parameter(kdmpf=2)
[12] parameter(Vaw=1)
[13] parameter(Vapc=0.1)
[14] parameter(Kaw=0.005)
[15] parameter(Kiw=0.005)
[16] parameter(Vapw=0.1)
[17] parameter(Kapc=0.01)
[18] parameter(ks25=1)
[19] parameter(kswee=0.5)
[20] parameter(kimpf=1.5)
[21] parameter(Vic=0.2)
[22] parameter(kiapc=0.5)
[23] parameter(kdwee=1)
[24] parameter(Viw=0.2)
[25] parameter(ksmpf=0.35)
[26] parameter(ksiep=0)
[27] parameter(ksie=0.3)
[28] parameter(kaapcp=0)
[29] parameter(kdie=0.0860196219263221)
[30] parameter(kampf=3.1315611499739138)
%% Cell type:code id: tags:
```
validity_domain(period(MPF,p)).
```
%%%% Output: execute_result
p=21.00004\/p=21\/p=20
%% Cell type:code id: tags:
```
numerical_simulation. plot.
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
validity_domain(period(MPF,p)).
```
%%%% Output: execute_result
p=24.000019\/p=24\/p=23
%% Cell type:code id: tags:
```
generate_ctl_not.
```
%%%% Output: execute_result
reachable(stable(not'C25P'))
reachable(stable(not'MPF'))
reachable(stable(not'Wee1P'))
reachable(steady('APC'))
reachable(steady('APCi'))
reachable(steady('C25'))
reachable(steady('C25P'))
reachable(steady('IE'))
reachable(steady('MPF'))
reachable(steady('Wee1'))
reachable(steady('Wee1P'))
reachable(steady('Wee1m'))
reachable(steady(preMPF))
reachable(steady(not'APC'))
reachable(steady(not'APCi'))
reachable(steady(not'C25'))
reachable(steady(not'IE'))
reachable(steady(not'Wee1'))
reachable(steady(not'Wee1m'))
reachable(steady(not preMPF))
checkpoint2('APCi',not'APC')
checkpoint2('C25',not'APC')
checkpoint2('C25P',not'APC')
checkpoint2('IE',not'APC')
checkpoint2('MPF',not'APC')
checkpoint2('Wee1',not'APC')
checkpoint2('Wee1P',not'APC')
checkpoint2('Wee1m',not'APC')
checkpoint2(preMPF,not'APC')
checkpoint2('APC',not'APCi')
checkpoint2('C25',not'APCi')
checkpoint2('C25P',not'APCi')
checkpoint2('IE',not'APCi')
checkpoint2('MPF',not'APCi')
checkpoint2('Wee1',not'APCi')
checkpoint2('Wee1P',not'APCi')
checkpoint2('Wee1m',not'APCi')
checkpoint2(preMPF,not'APCi')
checkpoint2('APC',not'C25')
checkpoint2('APCi',not'C25')
checkpoint2('C25P',not'C25')
checkpoint2('IE',not'C25')
checkpoint2('MPF',not'C25')
checkpoint2('Wee1',not'C25')
checkpoint2('Wee1P',not'C25')
checkpoint2('Wee1m',not'C25')
checkpoint2(preMPF,not'C25')
checkpoint2('APC',not'C25P')
checkpoint2('APCi',not'C25P')
checkpoint2('C25',not'C25P')
checkpoint2('IE',not'C25P')
checkpoint2('MPF',not'C25P')
checkpoint2('Wee1',not'C25P')
checkpoint2('Wee1P',not'C25P')
checkpoint2('Wee1m',not'C25P')
checkpoint2(preMPF,not'C25P')
checkpoint2('APC',not'IE')
checkpoint2('APCi',not'IE')
checkpoint2('C25',not'IE')
checkpoint2('C25P',not'IE')
checkpoint2('MPF',not'IE')
checkpoint2('Wee1',not'IE')
checkpoint2('Wee1P',not'IE')
checkpoint2('Wee1m',not'IE')
checkpoint2(preMPF,not'IE')
checkpoint2('APC',not'MPF')
checkpoint2('APCi',not'MPF')
checkpoint2('C25',not'MPF')
checkpoint2('C25P',not'MPF')
checkpoint2('IE',not'MPF')
checkpoint2('Wee1',not'MPF')
checkpoint2('Wee1P',not'MPF')
checkpoint2('Wee1m',not'MPF')
checkpoint2(preMPF,not'MPF')
checkpoint2('APC',not'Wee1')
checkpoint2('APCi',not'Wee1')
checkpoint2('C25',not'Wee1')
checkpoint2('C25P',not'Wee1')
checkpoint2('IE',not'Wee1')
checkpoint2('MPF',not'Wee1')
checkpoint2('Wee1P',not'Wee1')
checkpoint2('Wee1m',not'Wee1')
checkpoint2(preMPF,not'Wee1')
checkpoint2('APC',not'Wee1P')
checkpoint2('APCi',not'Wee1P')
checkpoint2('C25',not'Wee1P')
checkpoint2('C25P',not'Wee1P')
checkpoint2('IE',not'Wee1P')
checkpoint2('MPF',not'Wee1P')
checkpoint2('Wee1',not'Wee1P')
checkpoint2('Wee1m',not'Wee1P')
checkpoint2(preMPF,not'Wee1P')
checkpoint2('APC',not'Wee1m')
checkpoint2('APCi',not'Wee1m')
checkpoint2('C25',not'Wee1m')
checkpoint2('C25P',not'Wee1m')
checkpoint2('IE',not'Wee1m')
checkpoint2('MPF',not'Wee1m')
checkpoint2('Wee1',not'Wee1m')
checkpoint2('Wee1P',not'Wee1m')
checkpoint2(preMPF,not'Wee1m')
checkpoint2('APC',not preMPF)
checkpoint2('APCi',not preMPF)
checkpoint2('C25',not preMPF)
checkpoint2('C25P',not preMPF)
checkpoint2('IE',not preMPF)
checkpoint2('MPF',not preMPF)
checkpoint2('Wee1',not preMPF)
checkpoint2('Wee1P',not preMPF)
checkpoint2('Wee1m',not preMPF)
oscil('APC')
oscil('APCi')
oscil('C25')
oscil('C25P')
oscil('IE')
oscil('MPF')
oscil('Wee1')
oscil('Wee1P')
oscil('Wee1m')
oscil(preMPF)
%% Cell type:code id: tags:
```
reduce_model.
```
%%%% Output: execute_result
removed [ (ksmpf for '_'=>preMPF), (kdmpfp*preMPF for preMPF=>'_'), (kdmpfp*'MPF'for'MPF'=>'_'), (kdmpf*'APC'*'MPF'for'MPF'=['APC']=>'_'), (kdmpf*'APC'*preMPF for preMPF=['APC']=>'_'), ('Viw'*'Wee1P'/ ('Kiw'+'Wee1P')for'Wee1P'=>'Wee1'), (kdwee*'Wee1'for'Wee1'=>'_'), ('Vic'*'C25P'/ ('Kic25'+'C25P')for'C25P'=>'C25'), (kd25*'C25'for'C25'=>'_'), (ksiep for '_'=>'IE')]
%% Cell type:code id: tags:
```
draw_influences.
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
clear_model.
RAF + RAFK <=> RAF-RAFK.
RAF~{p1} + RAFPH <=> RAF~{p1}-RAFPH.
MEK + RAF~{p1} <=> MEK-RAF~{p1}.
MEK~{p1} + RAF~{p1} <=> MEK~{p1}-RAF~{p1}.
MEKPH + MEK~{p1} <=> MEK~{p1}-MEKPH.
MEKPH + MEK~{p1,p2} <=> MEK~{p1,p2}-MEKPH.
MAPK + MEK~{p1,p2} <=> MAPK-MEK~{p1,p2}.
MAPK~{p1} + MEK~{p1,p2} <=> MAPK~{p1}-MEK~{p1,p2}.
MAPKPH + MAPK~{p1} <=> MAPK~{p1}-MAPKPH.
MAPKPH + MAPK~{p1,p2} <=> MAPK~{p1,p2}-MAPKPH.
RAF-RAFK => RAFK + RAF~{p1}.
RAF~{p1}-RAFPH => RAF + RAFPH.
MEK~{p1}-RAF~{p1} => MEK~{p1,p2} + RAF~{p1}.
MEK-RAF~{p1} => MEK~{p1} + RAF~{p1}.
MEK~{p1}-MEKPH => MEK + MEKPH.
MEK~{p1,p2}-MEKPH => MEK~{p1} + MEKPH.
MAPK-MEK~{p1,p2} => MAPK~{p1} + MEK~{p1,p2}.
MAPK~{p1}-MEK~{p1,p2} => MAPK~{p1,p2} + MEK~{p1,p2}.
MAPK~{p1}-MAPKPH => MAPK + MAPKPH.
MAPK~{p1,p2}-MAPKPH => MAPK~{p1} + MAPKPH.
present({
RAFK,
RAF,
MEK,
MAPK,
MAPKPH,
MEKPH,
RAFPH
}).
make_absent_not_present.
```
%%%% Output: execute_result
%% Cell type:code id: tags:
```
%load clock.bc
```
%%%% Output: execute_result
loading clock.bc
%% Cell type:code id: tags:
