 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = MAPK_osc 
 %  Accession Number = 27 
 %  Transcriber = Sridhar Hariharaputran, NCBS 
 %  Developer = Boris N. Kholodenko 
 %  Species = Xenopus 
 %  Tissue = Oocyte extract 
 %  Cell Compartment = Cytosol 
 %  Notes = This MAPK model is based on <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10712587">Boris N. Kholodenko Eur J Biochem. (2000) 267(6):1583-8</a> for data from 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 14:51:29 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 6000];
% Molecule names
molnames = {
'1 /kinetics/MAPK/MAPK'
'2 /kinetics/MAPK/MKKK'
'3 /kinetics/MAPK/MKK'
'4 /kinetics/MAPK/int1'
'5 /kinetics/MAPK/MKKK-P'
'6 /kinetics/MAPK/int3'
'7 /kinetics/MAPK/int5'
'8 /kinetics/MAPK/MKK-P'
'9 /kinetics/MAPK/MAPK-P'
'10 /kinetics/MAPK/int2'
'11 /kinetics/MAPK/int4'
'12 /kinetics/MAPK/Ras-MKKKK'
'13 /kinetics/MAPK/inactiveRas-MKKK'
'14 /kinetics/MAPK/MKK-PP'
'15 /kinetics/MAPK/MAPK-PP'
};

bufnames = {
};

sumtotnames = {
};

% Initial concs of 15 molecules
y0(1) = 0.3;
y0(2) = 0.1;
y0(3) = 0.3;
y0(4) = 0.001;
y0(5) = 0;
y0(6) = 0.001;
y0(7) = 0.001;
y0(8) = 0;
y0(9) = 0;
y0(10) = 0.001;
y0(11) = 0.001;
y0(12) = 0.001;
y0(13) = 0;
y0(14) = 0;
y0(15) = 0;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,y(:,15));
plot(t,y(:,1));
plot(t,y(:,12));
plot(t,y(:,1));
plot(t,y(:,2));
plot(t,y(:,3));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 0.025 * y(14) * y(1) / ( 0.0150001 + y(1) ) + 0.5 * y(7) * y(9) / ( 0.0149997 + y(9) )
 - 2.5 * y(12) * y(2) / ( 0.01 + y(2) ) + 0.25 * y(4) * y(5) / ( 0.008 + y(5) )
 - 0.025 * y(5) * y(3) / ( 0.0150001 + y(3) ) + 0.75 * y(6) * y(8) / ( 0.015 + y(8) )
0
 + 2.5 * y(12) * y(2) / ( 0.01 + y(2) ) - 0.25 * y(4) * y(5) / ( 0.008 + y(5) )
0
0
 - 0.025 * y(5) * y(8) / ( 0.0150001 + y(8) ) + 0.025 * y(5) * y(3) / ( 0.0150001 + y(3) ) - 0.75 * y(6) * y(8) / ( 0.015 + y(8) ) + 0.75 * y(10) * y(14) / ( 0.015 + y(14) )
 - 0.025 * y(14) * y(9) / ( 0.0150001 + y(9) ) + 0.025 * y(14) * y(1) / ( 0.0150001 + y(1) ) - 0.5 * y(7) * y(9) / ( 0.0149997 + y(9) ) + 0.5 * y(11) * y(15) / ( 0.0149997 + y(15) )
0
0
 - 1 * y(15) * y(12) + 0.009 * y(13)
 + 1 * y(15) * y(12) - 0.009 * y(13)
 + 0.025 * y(5) * y(8) / ( 0.0150001 + y(8) ) - 0.75 * y(10) * y(14) / ( 0.015 + y(14) )
 + 0.025 * y(14) * y(9) / ( 0.0150001 + y(9) ) - 0.5 * y(11) * y(15) / ( 0.0149997 + y(15) ) - 1 * y(15) * y(12) + 0.009 * y(13)
];

% end of model
