Commit c718c372 authored by SOLIMAN Sylvain's avatar SOLIMAN Sylvain

example with kinetics

parent 722dfe91
%% Cell cycle Qu et al. 2003 Biophysical journal
%% Cyclin
k1 for _=>CycB.
k2*[CycB] for CycB=>_.
k2u*[APC]*[CycB] for CycB=[APC]=>_.
(k3*[CDK]*[CycB],k4*[CycB-CDK~{p1,p2}])
for CDK+CycB<=>CycB-CDK~{p1,p2}.
k5*[CycB-CDK~{p1,p2}] for CycB-CDK~{p1,p2}=>CycB-CDK~{p1}.
k5u*[C25~{p1,p2}]*[CycB-CDK~{p1,p2}]
for CycB-CDK~{p1,p2}=[C25~{p1,p2}]=>CycB-CDK~{p1}.
k6*[CycB-CDK~{p1}] for CycB-CDK~{p1}=>CycB-CDK~{p1,p2}.
[Wee1]*[CycB-CDK~{p1}] for CycB-CDK~{p1}=[Wee1]=>CycB-CDK~{p1,p2}.
k7*[CycB-CDK~{p1}] for CycB-CDK~{p1}=>CDK.
k7u*[APC]*[CycB-CDK~{p1}] for CycB-CDK~{p1}=[APC]=>CDK.
%% Cdc25
k8 for _=>C25.
k9*[C25] for C25=>_.
k9*[C25~{p1}] for C25~{p1}=>_.
k9*[C25~{p1,p2}] for C25~{p1,p2}=>_.
bz*[C25] for C25=>C25~{p1}.
cz*[CycB-CDK~{p1}]*[C25] for C25=[CycB-CDK~{p1}]=>C25~{p1}.
az*[C25~{p1}] for C25~{p1}=>C25.
bz*[C25~{p1}] for C25~{p1}=>C25~{p1,p2}.
cz*[CycB-CDK~{p1}]*[C25~{p1}] for C25~{p1}=[CycB-CDK~{p1}]=>C25~{p1,p2}.
az*[C25~{p1,p2}] for C25~{p1,p2}=>C25~{p1}.
%% Wee1
k10 for _=>Wee1.
k11*[Wee1] for Wee1=>_.
k11*[Wee1~{p1}] for Wee1~{p1}=>_.
bw*[Wee1] for Wee1=>Wee1~{p1}.
cw*[CycB-CDK~{p1}]*[Wee1] for Wee1=[CycB-CDK~{p1}]=>Wee1~{p1}.
aw*[Wee1~{p1}] for Wee1~{p1}=>Wee1.
%% APC
(([CycB-CDK~{p1}]^2)/(a^2+([CycB-CDK~{p1}]^2)))/tho
for _=[CycB-CDK~{p1}]=>APC.
[APC]/tho for APC=>_.
%% CKI
k12 for _=>CKI.
k13*[CKI] for CKI=>_.
(k14*[CKI]*[CycB-CDK~{p1}],k15*[CKI-CycB-CDK~{p1}])
for CKI+CycB-CDK~{p1}<=>CKI-CycB-CDK~{p1}.
bi*[CKI-CycB-CDK~{p1}] for CKI-CycB-CDK~{p1}=>(CKI-CycB-CDK~{p1})~{p2}.
ci*[CycB-CDK~{p1}]*[CKI-CycB-CDK~{p1}]
for CKI-CycB-CDK~{p1}=[CycB-CDK~{p1}]=>(CKI-CycB-CDK~{p1})~{p2}.
ai*[(CKI-CycB-CDK~{p1})~{p2}] for (CKI-CycB-CDK~{p1})~{p2}=>CKI-CycB-CDK~{p1}.
k16*[(CKI-CycB-CDK~{p1})~{p2}]
for (CKI-CycB-CDK~{p1})~{p2}=>CDK.
k16u*[APC]*[(CKI-CycB-CDK~{p1})~{p2}]
for (CKI-CycB-CDK~{p1})~{p2}=[APC]=>CDK.
% k3=30 in initial model but after addition of CDK as a molecule
% and not a macro, the value has been adapted : 30/200=0.15
set_parameter(k1 = 300). set_parameter(k2 = 5). set_parameter(k3 = 0.15).
set_parameter(k4 = 30). set_parameter(k5 = 0.1). set_parameter(k6 = 1).
set_parameter(k7 = 10). set_parameter(k8 = 100). set_parameter(k9 = 1).
set_parameter(k10 = 10). set_parameter(k11 = 1). set_parameter(k12 = 0).
set_parameter(k13 = 1). set_parameter(k14 = 1). set_parameter(k15 = 1).
set_parameter(k16 = 2). set_parameter(k2u = 50). set_parameter(k7u = 0).
set_parameter(k16u = 25). set_parameter(c0 = 200). set_parameter(a = 4).
set_parameter(tho = 25). set_parameter(az = 10). set_parameter(aw = 10).
set_parameter(ai = 10). set_parameter(bz = 0.1). set_parameter(bw = 0.1).
set_parameter(bi = 0.1). set_parameter(cz = 1). set_parameter(cw = 1).
set_parameter(ci = 1). set_parameter(k5u = 1).
% Initial state
present(CDK, 200).
present(Wee1, 1).
present(CKI, 1).
make_absent_not_present.
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment