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% Text S5. Function definition for the full model.
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% File name: mdmx_p53_mdm2_model_full.m
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% This is function definition file. Please rename this file as above.
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% function definition file for a full model.
% Sohyoung Kim. Jul 2009
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function dxdt=f(t, x, flag, params)

% set parameter values
% the description of the each parameter can be found in the paper.
k1=params(1); % Basal production of p53
k2=params(2); % Basal degradation of p53
k3=params(3); % Phosphorylation of p53
k4=params(4); % Dephosphorylation of p53P
k5=params(5); % Degradation of p53P
k6=params(6); % Basal production of Mdm2
k7=params(7); % Basal degradation of Mdm2
k8=params(8); % Phosphorylation of Mdm2
k9=params(9); % Dephosphorylation of Mdm2P
k10=params(10); % Degradation of Mdm2P
k11=params(11); % Association between p53 (x1) and Mdm2 (x3)
k12=params(12); % Dissociation of p53:Mdm2 (x7)
k13=params(13); % Mdm2 dependent degradation of p53 (x1)
k14=params(14); % p53 dependent degradation of Mdm2 (x3)
k15=params(15); % Basal production of MdmX (x5)
k16=params(16); % Basal degradation of MdmX (x5)
k17=params(17); % Phosphorylation of MdmX (x5)
k18=params(18); % Dephosphorylation of MdmXP (x6)
k19=params(19); % Degradation of MdmXP (x6)
k20=params(20); % Association between Mdm2(x3) and MdmXP(x6)
k21=params(21); % Dissociation of Mdm2:MdmXP(x8)
k22=params(22); % Mdm2 (x3) dependent degradation of MdmXP
k23=params(23); % Association between Mdm2(x3) and MdmX(x5)
k24=params(24); % Dissociation of Mdm2:MdmX(x9)
k25=params(25); % Association between p53 (x1) and MdmX (x5)
k26=params(26); % Dissociation of p53:MdmX (x10)
k27=params(27); % Dimerization of p53P (x2)
k28=params(28); % Dissociation of p53P dimer, p53P:p53P (x11) 
k29=params(29); % Dimerization of p53P:p53P (x11)
k30=params(30); % Dissociation of p53P tetramer, (p53P:p53P):(p53P:p53P) (x12)
k31=params(31); % Association between p53P tetramer (x12) and promoter (x13)
k32=params(32); % Dissociation of p53P tetramer and promoter complex (x14)
k33=params(33); % Production rate constant of mRNA
k34=params(34); % Association rate constant between p53 and promoter
k35=params(35); % Dissociation rate constant between p53 and promoter
k36=params(36); % Basal transcription rate constant by p53 bound promoter
k37=params(37); % Degradation rate constant of mRNA
k38=params(38); % Production rate constant of Mdm2 from mRNA

% set initial values
x1=x(1); % p53
x2=x(2); % p53p
x3=x(3); % Mdm2
x4=x(4); % Mdm2p
x5=x(5); % MdmX
x6=x(6); % MdmXp
x7=x(7); % p53:Mdm2
x8=x(8); % Mdm2:MdmXp
x9=x(9); % Mdm2:MdmX
x10=x(10); % p53:MdmX
x11=x(11); % p53p:p53p
x12=x(12); % (p53p:p53p):(p53p:p53p)
x13=x(13); % Promoter
x14=x(14); % Promoter:[(p53p:p53p):(p53p:p53p)]
x15=x(15); % mRNA
x16=x(16); % p53:Promoter

dxdt=zeros(16,1);
 
% ODE
dxdt(1)=k1-k2*x1-k3*x1+k4*x2-k11*x1*x3+k12*x7+k14*x7-k25*x1*x5+k26*x10-k34*x1*x13+k35*x16;
dxdt(2)=k3*x1-k4*x2-k5*x2-2*k27*x2*x2+2*k28*x11;
dxdt(3)=k6-k7*x3-k8*x3+k9*x4-k11*x1*x3+k12*x7+k13*x7-k20*x3*x6+k21*x8+k22*x8-k23*x3*x5+k24*x9+k38*x15;
dxdt(4)=k8*x3-k9*x4-k10*x4;
dxdt(5)=k15-k16*x5-k17*x5+k18*x6-k23*x3*x5+k24*x9-k25*x1*x5+k26*x10;
dxdt(6)=k17*x5-k18*x6-k19*x6-k20*x3*x6+k21*x8;
dxdt(7)=k11*x1*x3-k12*x7-k13*x7-k14*x7;
dxdt(8)=k20*x3*x6-k21*x8-k22*x8;
dxdt(9)=k23*x3*x5-k24*x9;
dxdt(10)=k25*x1*x5-k26*x10;
dxdt(11)=k27*x2*x2-k28*x11-2*k29*x11*x11+2*k30*x12;
dxdt(12)=k29*x11*x11-k30*x12-k31*x12*x13+k32*x14;
dxdt(13)=-k31*x12*x13+k32*x14-k34*x1*x13+k35*x16;
dxdt(14)=k31*x12*x13-k32*x14;
dxdt(15)=k33*x14-k37*x15+k36*x16;
dxdt(16)=k34*x1*x13-k35*x16;