Commit d2048102 authored by FAGES Francois's avatar FAGES Francois
Browse files

MPCE

parent be881fef
% Cell cycle adapted from Qu et al, Biophysical journal
% 04/05/05
% kdweem=1, ksweem=0.5 to avoid high levels of Wee1m
% kwpcn=5, Kweem=0.2 instead of 2 and 1 because of Cry-deficient mice
% ksmpf=0.35 (instead of 0.3) for shorter cell cycle in autonomous cell cycle model.
parameter(kd25=1).
parameter(kdmpfp=0.25).
parameter(kampf=5).
parameter(kaapc=1).
parameter(ksweemp=0.001).
parameter(ksweem=0.5).
parameter(kdweem=1).
parameter(Kweem=0.2).
parameter(kwpcn=5).
parameter(Vac=1).
parameter(Kac25=0.01).
parameter(Kic25=0.01).
parameter(kdmpf=2).
parameter(Vaw=1).
parameter(Vapc=0.1).
parameter(Kaw=0.005).
parameter(Kiw=0.005).
parameter(Vapw=0.1).
parameter(Kapc=0.01).
parameter(ks25=1).
parameter(kswee=0.5).
parameter(kimpf=1.5).
parameter(Vic=0.2).
parameter(kiapc=0.5).
parameter(kdwee=1).
parameter(Viw=0.2).
parameter(ksmpf=0.35).
parameter(kdie=0.1).
parameter(ksiep=0).
parameter(ksie=0.3).
parameter(kaapcp=0).
% Reaction rules
% MPF - preMPF
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.
%function(ratio=kampf/kimpf).
% Wee1
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=>_.
% Cdc25
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=>_.
% APC
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.
% Initial state
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).
This diff is collapsed.
%%% Circadian clock model from:
%%% J. Leloup and A.Goldbeter. Toward a detailedcomputational model for the mammalian circadian clock.
%%% Proceedings of the National Academy of Sciences, 100, pp. 7051-7056, 2003.
%%% Version od the model incorporating REV-ERBalpha
% mRNA
present(mPER,mperinit).
parameter(mperinit,0.63).
present(mCRY,mcryinit).
parameter(mcryinit,0.5).
present(mBmal1,mbmal1init).
parameter(mbmal1init,0.4).
present(mREVERB,mreverbinit).
parameter(mreverbinit,0.14).
vsP*Bmal1_nucl^n/(KAP^n+Bmal1_nucl^n)
for _=[Bmal1_nucl]=>mPER.
vmP*mPER/(KmP+mPER)+kdmp*mPER for mPER=>_.
vsC*Bmal1_nucl^n/(KAC^n+Bmal1_nucl^n)
for _=[Bmal1_nucl]=>mCRY.
vmC*mCRY/(KmC+mCRY)+kdmc*mCRY for mCRY=>_.
vsB*KIB^m/(KIB^m+REVERB_nucl^m) for _=[REVERB_nucl]=>mBmal1.
vmB*mBmal1/(KmB+mBmal1)+kdmb*mBmal1 for mBmal1=>_.
vsR*Bmal1_nucl^h/(KAR^h+Bmal1_nucl^h)
for _=[Bmal1_nucl]=>mREVERB.
vmR*mREVERB/(KmR+mREVERB)+kdmr*mREVERB for mREVERB=>_.
%Proteins
present(PER_cyto,percytoinit).
parameter(percytoinit,0.841323888).
present(PER_cyto~{p},percytopinit).
parameter(percytopinit,0.117599215).
present(CRY_cyto,crycytoinit).
parameter(crycytoinit,8.03578267).
present(CRY_cyto~{p},crycytopinit).
parameter(crycytopinit,0.715418129).
present(PER_cyto-CRY_cyto,percytocrycytoinit).
parameter(percytocrycytoinit,5.4251231).
present(PER_nucl-CRY_nucl,pernuclcrynucl).
parameter(pernuclcrynucl,3.50345817).
present((PER_cyto-CRY_cyto)~{p},percytocrycytopinit).
parameter(percytocrycytopinit,0.250178481).
present((PER_nucl-CRY_nucl)~{p},pernuclcrynuclpinit).
parameter(pernuclcrynuclpinit,0.239897171).
ksP*mPER for _=[mPER]=>PER_cyto.
V2P*PER_cyto~{p}/(Kdp+PER_cyto~{p})
for PER_cyto~{p}=>PER_cyto.
ka4*PER_cyto-CRY_cyto
for PER_cyto-CRY_cyto=>PER_cyto+CRY_cyto.
V1P*PER_cyto/(Kp+PER_cyto) for PER_cyto=>PER_cyto~{p}.
kdn*PER_cyto for PER_cyto=>_.
ka3*PER_cyto*CRY_cyto
for PER_cyto+CRY_cyto=>PER_cyto-CRY_cyto.
kdn*PER_cyto~{p}+vdPC*PER_cyto~{p}/(Kd+PER_cyto~{p})
for PER_cyto~{p}=>_.
ksC*mCRY for _=[mCRY]=>CRY_cyto.
V2C*CRY_cyto~{p}/(Kdp+CRY_cyto~{p})
for CRY_cyto~{p}=>CRY_cyto.
V1C*CRY_cyto/(Kp+CRY_cyto)
for CRY_cyto=>CRY_cyto~{p}.
kdnc*CRY_cyto for CRY_cyto=>_.
vdCC*CRY_cyto~{p}/(Kd+CRY_cyto~{p})+kdn*CRY_cyto~{p}
for CRY_cyto~{p}=>_.
V2PC*(PER_cyto-CRY_cyto)~{p}/(Kdp+(PER_cyto-CRY_cyto)~{p})
for (PER_cyto-CRY_cyto)~{p}=>PER_cyto-CRY_cyto.
V1PC*PER_cyto-CRY_cyto/(Kp+PER_cyto-CRY_cyto)
for PER_cyto-CRY_cyto=>(PER_cyto-CRY_cyto)~{p}.
ka2*PER_nucl-CRY_nucl
for PER_nucl-CRY_nucl=>PER_cyto-CRY_cyto.
ka1*PER_cyto-CRY_cyto
for PER_cyto-CRY_cyto=>PER_nucl-CRY_nucl.
kdn*PER_cyto-CRY_cyto for PER_cyto-CRY_cyto=>_.
V4PC*(PER_nucl-CRY_nucl)~{p}/(Kdp+(PER_nucl-CRY_nucl)~{p})
for (PER_nucl-CRY_nucl)~{p}=>PER_nucl-CRY_nucl.
V3PC*PER_nucl-CRY_nucl/(Kp+PER_nucl-CRY_nucl)
for PER_nucl-CRY_nucl=>(PER_nucl-CRY_nucl)~{p}.
ka8*In for In=>Bmal1_nucl+PER_nucl-CRY_nucl.
ka7*Bmal1_nucl*PER_nucl-CRY_nucl
for Bmal1_nucl+PER_nucl-CRY_nucl=>In.
kdn*PER_nucl-CRY_nucl for PER_nucl-CRY_nucl=>_.
vdPCC*(PER_cyto-CRY_cyto)~{p}
/(Kd+(PER_cyto-CRY_cyto)~{p})+kdn*(PER_cyto-CRY_cyto)~{p}
for (PER_cyto-CRY_cyto)~{p}=>_.
vdPCN*(PER_nucl-CRY_nucl)~{p}
/(Kd+(PER_nucl-CRY_nucl)~{p})+kdn*(PER_nucl-CRY_nucl)~{p}
for (PER_nucl-CRY_nucl)~{p}=>_.
present(Bmal1_cyto,bmal1cytoinit).
parameter(bmal1cytoinit,1.71314172).
present(Bmal1_cyto~{p},bmal1cytopinit).
parameter(bmal1cytopinit,0.91889792).
present(Bmal1_nucl,bmal1nuclinit).
parameter(bmal1nuclinit,0.308181747).
present(Bmal1_nucl~{p},bmal1nuclpinit).
parameter(bmal1nuclpinit,243137076).
present(In,ininit).
parameter(ininit,0.637094766).
ksB*mBmal1 for _=[mBmal1]=>Bmal1_cyto.
V2B*Bmal1_cyto~{p}/(Kdp+Bmal1_cyto~{p})
for Bmal1_cyto~{p}=>Bmal1_cyto.
V1B*Bmal1_cyto/(Kp+Bmal1_cyto)
for Bmal1_cyto=>Bmal1_cyto~{p}.
ka6*Bmal1_nucl for Bmal1_nucl=>Bmal1_cyto.
ka5*Bmal1_cyto for Bmal1_cyto=>Bmal1_nucl.
kdn*Bmal1_cyto for Bmal1_cyto=>_.
vdBC*Bmal1_cyto~{p}/(Kd+Bmal1_cyto~{p})+kdn*Bmal1_cyto~{p}
for Bmal1_cyto~{p}=>_.
V4B*Bmal1_nucl~{p}/(Kdp+Bmal1_nucl~{p})
for Bmal1_nucl~{p}=>Bmal1_nucl.
V3B*Bmal1_nucl/(Kp+Bmal1_nucl)
for Bmal1_nucl=>Bmal1_nucl~{p}.
kdn*Bmal1_nucl for Bmal1_nucl=>_.
vdBN*Bmal1_nucl~{p}/(Kd+Bmal1_nucl~{p})+kdn*Bmal1_nucl~{p}
for Bmal1_nucl~{p}=>_.
vdIN*In/(Kd+In)+kdn*In
for In=>_.
present(REVERB_nucl,reverbnuclinit).
parameter(reverbnuclinit,1).
present(REVERB_cyto,reverbcytoinit).
parameter(reverbcytoinit,1).
ksR*mREVERB for _=[mREVERB]=>REVERB_cyto.
ka10*REVERB_nucl for _=[REVERB_nucl]=>REVERB_cyto.
(ka9+kdn)*REVERB_cyto+vdRC*REVERB_cyto/(Kd+REVERB_cyto)
for REVERB_cyto=>_.
ka9*REVERB_cyto for _=[REVERB_cyto]=> REVERB_nucl.
(ka10+kdn)*REVERB_nucl+vdRN*REVERB_nucl/(Kd+REVERB_nucl)
for REVERB_nucl=>_.
% Light-dark entrainment
parameter(vsP_dark,2.31).
parameter(vsP_light,2.36).
function(vsP=sq_wave(vsP_light,10,vsP_dark,10)).
function(PER_total=PER_cyto+PER_cyto-CRY_cyto+PER_nucl-CRY_nucl
+PER_cyto~{p}+(PER_cyto-CRY_cyto)~{p}+(PER_nucl-CRY_nucl)~{p}+In).
function(CRY_total=CRY_cyto+PER_cyto-CRY_cyto+PER_nucl-CRY_nucl
+CRY_cyto~{p}+(PER_cyto-CRY_cyto)~{p}+(PER_nucl-CRY_nucl)~{p}+In).
function(Bmal1_total=Bmal1_cyto+Bmal1_cyto~{p}+Bmal1_nucl
+Bmal1_nucl~{p}+In).
parameter(KAP=0.6). parameter(ka4=0.4). parameter(V2B=0.2).
parameter(vmP=2.2). parameter(V1P=9.6). parameter(ka6=0.4).
parameter(KmP=0.3). parameter(Kp=1.006). parameter(V1B=1.4).
parameter(kdmp=0.02). parameter(ka3=0.8). parameter(ka5=0.8).
parameter(vsC=1.8). parameter(vdPC=3.4). parameter(vdBC=3).
parameter(KAC=0.6). parameter(ksC=3.2). parameter(V4B=0.4).
parameter(vmC=2). parameter(V2C=0.2). parameter(V3B=1.4).
parameter(KmC=0.4). parameter(V1C=1.2). parameter(vdBN=3).
parameter(kdmc=0.02). parameter(kdnc=0.02). parameter(vdIN=1.6).
parameter(vsB=1.8). parameter(vdCC=1.4). parameter(vsR=1.6).
parameter(KIB=0.35). parameter(V2PC=0.2). parameter(KAR=0.6).
parameter(vmB=1.3). parameter(ka2=0.4). parameter(h=2).
parameter(KmB=0.4). parameter(V1PC=2.4). parameter(vmR=1.67).
parameter(kdmb=0.02). parameter(ka1=0.8). parameter(KmR=0.4).
parameter(n=2). parameter(V4PC=0.2). parameter(kdmr=0.02).
parameter(m=2). parameter(ka8=0.2). parameter(ksR=1.7).
parameter(Kd=0.3). parameter(V3PC=2.4). parameter(ka10=0.4).
parameter(kdn=0.02). parameter(ka7=1). parameter(ka9=0.8).
parameter(ksP=1.2). parameter(vdPCC=1.4). parameter(vdRC=4.4).
parameter(V2P=0.6). parameter(vdPCN=1.4). parameter(vdRN=0.8).
parameter(Kdp=0.1). parameter(ksB=0.32).
This diff is collapsed.
% Minimal mitotic oscillator after Albert Goldbeter 1991 PNAS
% in Biocham v4 by F. Fages
parameter(VM1=3, VM3=1, Kc=0.5, vi=0.025,
kd=0.01, vd=0.25, Kd=0.02, K1=0.005,
V2=1.5, K2=0.005, K3=0.0051, K4=0.005, V4=0.5).
vi for _=>Cyclin.
kd*Cyclin for Cyclin=>_.
Kinase*V2/(K2+Kinase) for Kinase=>KinaseP.
VM1*(KinaseP/(K1+KinaseP))*Cyclin/(Kc+Cyclin) for KinaseP=[Cyclin]=>Kinase.
Kinase*Protease*VM3/(K3+Protease) for Protease=[Kinase]=>ProteaseP.
ProteaseP*V4/(K4+ProteaseP) for ProteaseP=>Protease.
vd*Cyclin/(Kd+Cyclin)*ProteaseP for Cyclin=[ProteaseP]=>_.
present(Cyclin,0.01). present(Kinase,0.01). present(ProteaseP,0.01). present(KinaseP,0.99). present(Protease,0.99).
option(time:100).
This diff is collapsed.
This diff is collapsed.
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