 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = cAMP_pathway 
 %  Accession Number = 25 
 %  Transcriber = Upinder S. Bhalla, NCBS 
 %  Developer = Upinder S. Bhalla, NCBS 
 %  Species = Generic mammalian 
 %  Tissue = Brain - Neuronal 
 %  Cell Compartment = Cell membrane + Cytosol 
 %  Notes =  This is a model of the canonical cAMP signaling pathway:<br>Ligand->Receptor->G-protein->Cyclase->cAMP->PKA.<br>It also includes phosphodiesterases to balance out cAMP formation.<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11665614&query_hl=5">Bhalla US Methods Enzymol. 2002;345:3-23</a> 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Wed Feb  2 14:41:16 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 500];
% Molecule names
molnames = {
'1 /kinetics/PKA/R2C2'
'2 /kinetics/PKA/PKA-inhibitor'
'3 /kinetics/PKA/inhibited-PKA'
'4 /kinetics/PKA/cAMP.R2C2'
'5 /kinetics/PKA/cAMP2.R2C2'
'6 /kinetics/PKA/cAMP3.R2C2'
'7 /kinetics/PKA/cAMP4.R2C2'
'8 /kinetics/PKA/cAMP4.R2C'
'9 /kinetics/PKA/cAMP4.R2'
'10 /kinetics/cAMP'
'11 /kinetics/PKA-active'
'12 /kinetics/PKA-active/phosph-PDE/phosph-PDE_cplx'
'13 /kinetics/AC/cAMP-PDE'
'14 /kinetics/AC/cAMP-PDE/PDE/PDE_cplx'
'15 /kinetics/AC/cAMP-PDE*'
'16 /kinetics/AC/cAMP-PDE*/PDE*/PDE*_cplx'
'17 /kinetics/AC/Gs.AC'
'18 /kinetics/AC/AC'
'19 /kinetics/GTP.Ga'
'20 /kinetics/Gs/R'
'21 /kinetics/Gs/L.R'
'22 /kinetics/Gs/GDP.Gabc'
'23 /kinetics/Gs/L.R.GDP.Gabc'
'24 /kinetics/Gs/GDP.Ga'
'25 /kinetics/Gs/Gbg'
'26 /kinetics/Gs/R.GDP.Gabc'
};

bufnames = {
'1 /kinetics/AC/ATP'
'2 /kinetics/AC/AMP'
'3 /kinetics/Gs/L'
};

sumtotnames = {
};

% Initial concs of 26 molecules
y0(1) = 0.5;
y0(2) = 0.25;
y0(3) = 0;
y0(4) = 0;
y0(5) = 0;
y0(6) = 0;
y0(7) = 0;
y0(8) = 0;
y0(9) = 0;
y0(10) = 0;
y0(11) = 0;
y0(12) = 0;
y0(13) = 0.5;
y0(14) = 0;
y0(15) = 0;
y0(16) = 0;
y0(17) = 0;
y0(18) = 0.015;
y0(19) = 0;
y0(20) = 0.0833333;
y0(21) = 0;
y0(22) = 1;
y0(23) = 0;
y0(24) = 0;
y0(25) = 0;
y0(26) = 0;
buff(1) = 5000;
buff(2) = 1000;
buff(3) = 0;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,buff(:,3)*ones(size(t)));
plot(t,y(:,19));
plot(t,y(:,10));
plot(t,y(:,11));
plot(t,y(:,17));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 54 * y(1) * y(10) + 33 * y(4)
 - 60 * y(11) * y(2) + 1 * y(3)
 + 60 * y(11) * y(2) - 1 * y(3)
 + 54 * y(1) * y(10) - 33 * y(4) - 54 * y(4) * y(10) + 33 * y(5)
 + 54 * y(4) * y(10) - 33 * y(5) - 75 * y(5) * y(10) + 110 * y(6)
 + 75 * y(5) * y(10) - 110 * y(6) - 75 * y(10) * y(6) + 32.5 * y(7)
 + 75 * y(10) * y(6) - 32.5 * y(7) - 60 * y(7) + 18 * y(11) * y(8)
 + 60 * y(7) - 18 * y(11) * y(8) - 60 * y(8) + 18 * y(11) * y(9)
 + 60 * y(8) - 18 * y(11) * y(9)
 - 54 * y(1) * y(10) + 33 * y(4) - 54 * y(4) * y(10) + 33 * y(5) - 75 * y(5) * y(10) + 110 * y(6) - 75 * y(10) * y(6) + 32.5 * y(7) + 1.08e+07 * y(17) * buff(1) / ( 1.2e+07 + buff(1) ) - 5.04 * y(10) * y(15) + 80 * y(16) - 2.52 * y(10) * y(13) + 40 * y(14)
 + 60 * y(7) - 18 * y(11) * y(8) + 60 * y(8) - 18 * y(11) * y(9) - 60 * y(11) * y(2) + 1 * y(3) - 6 * y(13) * y(11) + 36 * y(12) + 9 * y(12)
 + 6 * y(13) * y(11) - 36 * y(12) - 9 * y(12)
 - 2.52 * y(10) * y(13) + 40 * y(14) + 10 * y(14) + 0.1 * y(15) - 6 * y(13) * y(11) + 36 * y(12)
 + 2.52 * y(10) * y(13) - 40 * y(14) - 10 * y(14)
 - 5.04 * y(10) * y(15) + 80 * y(16) + 20 * y(16) - 0.1 * y(15) + 9 * y(12)
 + 5.04 * y(10) * y(15) - 80 * y(16) - 20 * y(16)
 + 499.998 * y(18) * y(19) - 1 * y(17)
 - 499.998 * y(18) * y(19) + 1 * y(17)
 - 499.998 * y(18) * y(19) + 1 * y(17) - 0.066667 * y(19) + 0.025 * y(23)
 - 0.100002 * y(20) * buff(3) + 0.1 * y(21) - 0.199998 * y(22) * y(20) + 0.1 * y(26)
 + 0.100002 * y(20) * buff(3) - 0.1 * y(21) - 10.0002 * y(22) * y(21) + 0.1 * y(23) + 0.025 * y(23)
 + 6 * y(24) * y(25) - 10.0002 * y(22) * y(21) + 0.1 * y(23) - 0.199998 * y(22) * y(20) + 0.1 * y(26)
 + 10.0002 * y(22) * y(21) - 0.1 * y(23) + 4.99998 * buff(3) * y(26) - 0.1 * y(23) - 0.025 * y(23)
 + 0.066667 * y(19) - 6 * y(24) * y(25)
 - 6 * y(24) * y(25) + 0.025 * y(23)
 - 4.99998 * buff(3) * y(26) + 0.1 * y(23) + 0.199998 * y(22) * y(20) - 0.1 * y(26)
];

% end of model
