 %  DOQCS :http://doqcs.ncbs.res.in/ 
 %  Accession Name = MAPK_network_2003 
 %  Accession Number = 50 
 %  Pathway Name = PP1 
 %  Pathway Number = 218 
 %  Transcriber = Upinder S. Bhalla, NCBS 
 %  Developer = Upinder S. Bhalla, NCBS 
 %  Species = Generic mammalian 
 %  Tissue =  Brain - Neuronal 
 %  Cell Compartment = Synapse 
 %  Notes =  This is a network model of many pathways present at the neuronal synapse. The network has properties of temporal tuning as well as steady-state computational properties. In its default form the network is bistable.<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15298883&query_hl=11">Bhalla US Biophys J. 2004 Aug;87(2):745-53</a>
 
  % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Mon Feb 14 12:32:13 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 600];
% Molecule names
molnames = {
'1 /kinetics/sGC/cGMP'
'2 /kinetics/sGC/sGC'
'3 /kinetics/sGC/Heme'
'4 /kinetics/sGC/CO'
'5 /kinetics/sGC/Hemeoxyg2'
'6 /kinetics/sGC/Hemeoxyg2/HOXY/HOXY_cplx'
'7 /kinetics/sGC/GC6-CO'
'8 /kinetics/sGC/GC5_CO'
'9 /kinetics/sGC/PDE'
'10 /kinetics/sGC/PDE/kenz/kenz_cplx'
'11 /kinetics/sGC/5prime_GMP'
'12 /kinetics/sGC/Ery_HbO2'
'13 /kinetics/sGC/COHb'
};

bufnames = {
'1 /kinetics/sGC/GTP'
'2 /kinetics/sGC/dissoCO'
};

sumtotnames = {
};

% Initial concs of 13 molecules
y0(1) = 0;
y0(2) = 3;
y0(3) = 11.3;
y0(4) = 0;
y0(5) = 2;
y0(6) = 0;
y0(7) = 0;
y0(8) = 0;
y0(9) = 5;
y0(10) = 0;
y0(11) = 0;
y0(12) = 5;
y0(13) = 0;
buff(1) = 1000;
buff(2) = 0.1142;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
%plot(t,y(:,1));
% plot(t,y(:,4));
% plot(t,y(:,8));
 plot(t,y(:,7));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 + 54.54 * y(8) * buff(1) / ( 0.5 + buff(1) ) - 9.675 * y(1) * y(9) + 15.48 * y(10)
 - 0.12 * y(2) * y(4) + 28 * y(7)
 - 0.46789 * y(3) * y(5) + 1.4224 * y(6)
 + 0.3556 * y(6) - 0.12 * y(2) * y(4) + 28 * y(7)
 - 0.46789 * y(3) * y(5) + 1.4224 * y(6) + 0.3556 * y(6)
 + 0.46789 * y(3) * y(5) - 1.4224 * y(6) - 0.3556 * y(6)
 + 0.12 * y(2) * y(4) - 28 * y(7) - 0.95 * y(7)
 + 0.95 * y(7) - 1000 * y(8)
 - 9.675 * y(1) * y(9) + 15.48 * y(10) + 3.87 * y(10)
 + 9.675 * y(1) * y(9) - 15.48 * y(10) - 3.87 * y(10)
 + 3.87 * y(10)
 - 0.17 * buff(2) * y(12) + 0.0078 * y(13)
 + 0.17 * buff(2) * y(12) - 0.0078 * y(13)
];

% end of model
