% Bree Aldridge, 2/15/2006
% ode file specifying the caspase-3 activation model with caspase-3 and
% regulated by caspase-8 and XIAP.  See Table 1 and equations 1-8 of the
% manuscript for more details.


function dydt = casp3modelodes(t,y)

%network species
c8=y(1);    %casp-8
c8a=y(2);   %casp-8*
c3=y(3);    %casp-3
c3a=y(4);   %casp-3*
c8c3a=y(5); %casp-8:casp-3*
c8ac3=y(6); %casp-8*:casp-3
xiap=y(7);  %XIAP
c3ax=y(8);  %casp-3*:XIAP

%parameters
kd2=.008;
kd4=1e-3;
k1=2.667e-9;
kd1=.01;
k3=6.8e-8;
kd3=.05;
k5=7e-5;
kd5=1e7/6e11;
kd6=1/6000;

%odes
dc8 = -k1*c3a*c8 + kd1*c8c3a;
dc8a =  kd2*c8c3a -k3*c8a*c3 +kd3*c8ac3 +kd4*c8ac3;
dc3 = -k3*c8a*c3 +kd3*c8ac3;
dc3a = kd4*c8ac3 -k1*c3a*c8 + kd1*c8c3a - k5*xiap*c3a +kd5*c3ax +kd2*c8c3a;
dc8c3a = -kd2*c8c3a + k1*c3a*c8 - kd1*c8c3a;
dc8ac3 = -kd4*c8ac3 +k3*c8a*c3 -kd3*c8ac3;
dxiap = -k5*xiap*c3a +kd5*c3ax +kd6*c3ax;
dc3ax = k5*xiap*c3a -kd5*c3ax -kd6*c3ax;

dydt=[dc8;dc8a;dc3;dc3a;dc8c3a;dc8ac3;dxiap;dc3ax];