 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = Huang_Ferrell_MAPK 
 %  Accession Number = 30 
 %  Transcriber = Sridhar Hariharaputran, NCBS 
 %  Developer = Huang, C.-Y.F. and Ferrell Jr., J.E. 
 %  Species = Xenopus 
 %  Tissue = Oocytes extract 
 %  Cell Compartment = Cytosol 
 %  Notes = This is the <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8816754>Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83</a> model for the MAPK cascade in Xenopus oocytes extracts. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Wed Feb  2 15:33:08 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 100];
% Molecule names
molnames = {
'1 /kinetics/MAPK/INPUT(E1)'
'2 /kinetics/MAPK/INPUT(E1)/INPUT(E1)/INPUT(E1)_cplx'
'3 /kinetics/MAPK/MAPKKK'
'4 /kinetics/MAPK/MAPKKK*'
'5 /kinetics/MAPK/MAPKKK*/MAPKKK*/MAPKKK*_cplx'
'6 /kinetics/MAPK/MAPKKK*/MAPKKK*[1]/MAPKKK*[1]_cplx'
'7 /kinetics/MAPK/E2'
'8 /kinetics/MAPK/E2/E2/E2_cplx'
'9 /kinetics/MAPK/MAPKK'
'10 /kinetics/MAPK/MAPKK-P'
'11 /kinetics/MAPK/MAPKK-PP'
'12 /kinetics/MAPK/MAPKK-PP/MAPKK-PP/MAPKK-PP_cplx'
'13 /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1]/MAPKK-PP[1]_cplx'
'14 /kinetics/MAPK/MAPKKPase'
'15 /kinetics/MAPK/MAPKKPase/MAPKKPase/MAPKKPase_cplx'
'16 /kinetics/MAPK/MAPKKPase[1]'
'17 /kinetics/MAPK/MAPKKPase[1]/MAPKKPase/MAPKKPase_cplx'
'18 /kinetics/MAPK/MAPK'
'19 /kinetics/MAPK/MAPK-P'
'20 /kinetics/MAPK/MAPK-PP'
'21 /kinetics/MAPK/MAPKPase'
'22 /kinetics/MAPK/MAPKPase/MAPKPase/MAPKPase_cplx'
'23 /kinetics/MAPK/MAPKPase[1]'
'24 /kinetics/MAPK/MAPKPase[1]/MAPKPase/MAPKPase_cplx'
};

bufnames = {
};

sumtotnames = {
};

% Initial concs of 24 molecules
y0(1) = 0.1;
y0(2) = 0;
y0(3) = 0.003;
y0(4) = 0;
y0(5) = 0;
y0(6) = 0;
y0(7) = 0.0003;
y0(8) = 0;
y0(9) = 1.2;
y0(10) = 0;
y0(11) = 0;
y0(12) = 0;
y0(13) = 0;
y0(14) = 0.0003;
y0(15) = 0;
y0(16) = 0.0003;
y0(17) = 0;
y0(18) = 1.2;
y0(19) = 0;
y0(20) = 0;
y0(21) = 0.12;
y0(22) = 0;
y0(23) = 0.12;
y0(24) = 0;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,y(:,4));
plot(t,y(:,11));
plot(t,y(:,20));
plot(t,y(:,10));
plot(t,y(:,11));
plot(t,y(:,19));
plot(t,y(:,20));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 1000 * y(3) * y(1) + 150 * y(2) + 150 * y(2)
 + 1000 * y(3) * y(1) - 150 * y(2) - 150 * y(2)
 - 1000 * y(3) * y(1) + 150 * y(2) + 150 * y(8)
 - 1000 * y(9) * y(4) + 150 * y(5) + 150 * y(5) - 1000 * y(10) * y(4) + 150 * y(6) + 150 * y(6) + 150 * y(2) - 1000 * y(4) * y(7) + 150 * y(8)
 + 1000 * y(9) * y(4) - 150 * y(5) - 150 * y(5)
 + 1000 * y(10) * y(4) - 150 * y(6) - 150 * y(6)
 - 1000 * y(4) * y(7) + 150 * y(8) + 150 * y(8)
 + 1000 * y(4) * y(7) - 150 * y(8) - 150 * y(8)
 - 1000 * y(9) * y(4) + 150 * y(5) + 150 * y(15)
 + 150 * y(5) - 1000 * y(10) * y(4) + 150 * y(6) - 1000 * y(10) * y(14) + 150 * y(15) + 150 * y(17)
 - 1000 * y(18) * y(11) + 150 * y(12) + 150 * y(12) - 1000 * y(19) * y(11) + 150 * y(13) + 150 * y(13) + 150 * y(6) - 1000 * y(11) * y(16) + 150 * y(17)
 + 1000 * y(18) * y(11) - 150 * y(12) - 150 * y(12)
 + 1000 * y(19) * y(11) - 150 * y(13) - 150 * y(13)
 - 1000 * y(10) * y(14) + 150 * y(15) + 150 * y(15)
 + 1000 * y(10) * y(14) - 150 * y(15) - 150 * y(15)
 - 1000 * y(11) * y(16) + 150 * y(17) + 150 * y(17)
 + 1000 * y(11) * y(16) - 150 * y(17) - 150 * y(17)
 - 1000 * y(18) * y(11) + 150 * y(12) + 150 * y(22)
 + 150 * y(12) - 1000 * y(19) * y(11) + 150 * y(13) + 150 * y(24) - 1000 * y(19) * y(21) + 150 * y(22)
 + 150 * y(13) - 1000 * y(20) * y(23) + 150 * y(24)
 - 1000 * y(19) * y(21) + 150 * y(22) + 150 * y(22)
 + 1000 * y(19) * y(21) - 150 * y(22) - 150 * y(22)
 - 1000 * y(20) * y(23) + 150 * y(24) + 150 * y(24)
 + 1000 * y(20) * y(23) - 150 * y(24) - 150 * y(24)
];

% end of model
