%KinaseCascade function: will use to return ERK, MEK, and RAF values

%E1 = Ras-GTP
%E2 = RAF Phosphatase
%cx = complex
%P = phosphate (PO4)
%PP = two phosphates
%* = activated
%Pase = phosphatase enzyme (so MEKPase is MEK phosphatase)

function myfun = KinaseCascade(t,y,Km,Vmax);
% y1 = dE2dt
% y2 = dE1dt
% y3 = dERKdt
% y4 = dERKPdt
% y5 = dERKPPdt
% y6 = dMEKdt
% y7 = dMEKPdt
% y8 = dMEKPPdt
% y9 = dRAFdt
% y10 = dRAF*dt
% y11 = dMEKPasedt
% y12 = dMEKPase1dt
% y13 = dERKPasedt
% y14 = dERKPase1dt
% y15 = dE2_cxdt
% y16 = dE1_cxdt
% y17 = dMEKPP_cxdt
% y18 = dMEKPP.MEKPP1_cxdt
% y19 = dRAF*_cxdt
% y20 = dRAF*.RAF*_cxdt
% y21 = dMEKPase_cxdt
% y22 = dMEKPase1.MEKPase_cxdt
% y23 = dERKPase_cxdt
% y24 = dERKPase1.ERKPase_cxdt

myfun(1,:) = - 1000 * y(10) * y(1)+ Km * y(15);
myfun(2,:) = - 1000 * y(9) * y(2)+ Km * y(16);
myfun(3,:) = - 1000 * y(3)* y(8)+ Vmax * y(17)+ Vmax * y(23);
myfun(4,:) = - 1000 * y(4)* y(8)+ Vmax * y(18)- 1000 * y(4)* y(13)+ Vmax * y(23)+ Vmax * y(17)+ Vmax * y(24);
myfun(5,:) = - 1000 * y(5)* y(14)+ Vmax * y(24)+ Vmax * y(18);
myfun(6,:) = - 1000 * y(6)* y(10)+ Vmax * y(19)+ Vmax * y(21);
myfun(7,:) = - 1000 * y(7)* y(10)+ Vmax * y(20)- 1000 * y(7)* y(11)+ Vmax * y(21)+ Vmax * y(19)+ Vmax * y(22);
myfun(8,:) = - 1000 * y(8)* y(12)+ Vmax * y(22)+ Vmax * y(20)- 1000 * y(3) * y(8)+ Km * y(17)- 1000 * y(4) * y(8)+ Km * y(18);
myfun(9,:) = - 1000 * y(9)* y(2)+ Vmax * y(16)+ Vmax * y(15);
myfun(10,:) = - 1000 * y(10)* y(1)+ Vmax * y(15)+ Vmax * y(16)- 1000 * y(6) * y(10)+ Km * y(19)- 1000 * y(7) * y(10)+ Km * y(20);
myfun(11,:) = - 1000 * y(7) * y(11)+ Km * y(21);
myfun(12,:) = - 1000 * y(8) * y(12)+ Km * y(22);
myfun(13,:) = - 1000 * y(4) * y(13)+ Km * y(23);
myfun(14,:) = - 1000 * y(5) * y(14)+ Km * y(24);
myfun(15,:) = 1000 * y(10) * y(1)- Km * y(15);
myfun(16,:) = 1000 * y(9) * y(2)- Km * y(16);
myfun(17,:) = 1000 * y(3) * y(8)- Km * y(17);
myfun(18,:) = 1000 * y(4) * y(8)- Km * y(18);
myfun(19,:) = 1000 * y(6) * y(10)- Km * y(19);
myfun(20,:) = 1000 * y(7) * y(10)- Km * y(20);
myfun(21,:) = 1000 * y(7) * y(11)- Km * y(21);
myfun(22,:) = 1000 * y(8) * y(12)- Km * y(22);
myfun(23,:) = 1000 * y(4) * y(13)- Km * y(23);
myfun(24,:) = 1000 * y(5) * y(14)- Km * y(24);