Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =22;
end
% There are a total of 11 entries in each of the rate and state variable arrays.
% There are a total of 25 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_CONSTANTS(:,1) = strpad('kappa_R_1a_cGMP in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,2) = strpad('kappa_R_1b_cGMP in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,3) = strpad('kappa_R_2a_cGMP in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,4) = strpad('kappa_R_2b_cGMP in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,5) = strpad('kappa_R_1_sGC in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,6) = strpad('kappa_R_2_sGC in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,7) = strpad('kappa_R_3_sGC in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,8) = strpad('kappa_R_4_sGC in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,9) = strpad('kappa_R_DNO_sGC in component BG_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,10) = strpad('K_GTP in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,11) = strpad('K_E5c in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,12) = strpad('K_cGMP in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,13) = strpad('K_PDE in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,14) = strpad('K_GTP_E5c in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,15) = strpad('K_cGMP_PDE in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,16) = strpad('K_GMP in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,17) = strpad('K_Eb in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,18) = strpad('K_NO in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,19) = strpad('K_E6c in component BG_parameters (per_fmol)');
LEGEND_CONSTANTS(:,20) = strpad('K_NO_product in component BG_parameters (per_fmol)');
LEGEND_VOI = strpad('t in component environment (second)');
LEGEND_CONSTANTS(:,21) = strpad('vol_myo in component environment (pL)');
LEGEND_STATES(:,1) = strpad('q_cGMP in component environment (fmol)');
LEGEND_STATES(:,2) = strpad('q_GTP in component environment (fmol)');
LEGEND_STATES(:,3) = strpad('q_E5c in component environment (fmol)');
LEGEND_STATES(:,4) = strpad('q_PDE in component environment (fmol)');
LEGEND_STATES(:,5) = strpad('q_GTP_E5c in component environment (fmol)');
LEGEND_STATES(:,6) = strpad('q_cGMP_PDE in component environment (fmol)');
LEGEND_STATES(:,7) = strpad('q_GMP in component environment (fmol)');
LEGEND_STATES(:,8) = strpad('q_Eb in component environment (fmol)');
LEGEND_STATES(:,9) = strpad('q_NO in component environment (fmol)');
LEGEND_STATES(:,10) = strpad('q_E6c in component environment (fmol)');
LEGEND_STATES(:,11) = strpad('q_NO_product in component environment (fmol)');
LEGEND_ALGEBRAIC(:,8) = strpad('v_R_1a_cGMP in component cGMP (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,9) = strpad('v_R_1b_cGMP in component cGMP (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,10) = strpad('v_R_2a_cGMP in component cGMP (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,11) = strpad('v_R_2b_cGMP in component cGMP (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,18) = strpad('v_R_1_sGC in component sGC (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,19) = strpad('v_R_2_sGC in component sGC (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,20) = strpad('v_R_3_sGC in component sGC (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,21) = strpad('v_R_4_sGC in component sGC (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,22) = strpad('v_R_DNO_sGC in component sGC (fmol_per_sec)');
LEGEND_CONSTANTS(:,22) = strpad('v_NO_generation in component environment (fmol_per_sec)');
LEGEND_CONSTANTS(:,23) = strpad('R in component constants (J_per_K_per_mol)');
LEGEND_CONSTANTS(:,24) = strpad('T in component constants (kelvin)');
LEGEND_CONSTANTS(:,25) = strpad('F in component constants (C_per_mol)');
LEGEND_ALGEBRAIC(:,1) = strpad('mu_GTP in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,2) = strpad('mu_E5c in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,3) = strpad('mu_cGMP in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,4) = strpad('mu_PDE in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,5) = strpad('mu_GTP_E5c in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,6) = strpad('mu_cGMP_PDE in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('mu_GMP in component cGMP (J_per_mol)');
LEGEND_ALGEBRAIC(:,12) = strpad('mu_Eb in component sGC (J_per_mol)');
LEGEND_ALGEBRAIC(:,13) = strpad('mu_NO in component sGC (J_per_mol)');
LEGEND_ALGEBRAIC(:,14) = strpad('mu_E6c in component sGC (J_per_mol)');
LEGEND_ALGEBRAIC(:,15) = strpad('mu_E5c in component sGC (J_per_mol)');
LEGEND_ALGEBRAIC(:,16) = strpad('mu_cGMP in component sGC (J_per_mol)');
LEGEND_ALGEBRAIC(:,17) = strpad('mu_NO_product in component sGC (J_per_mol)');
LEGEND_RATES(:,1) = strpad('d/dt q_cGMP in component environment (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_GTP in component environment (fmol)');
LEGEND_RATES(:,3) = strpad('d/dt q_E5c in component environment (fmol)');
LEGEND_RATES(:,4) = strpad('d/dt q_PDE in component environment (fmol)');
LEGEND_RATES(:,5) = strpad('d/dt q_GTP_E5c in component environment (fmol)');
LEGEND_RATES(:,6) = strpad('d/dt q_cGMP_PDE in component environment (fmol)');
LEGEND_RATES(:,7) = strpad('d/dt q_GMP in component environment (fmol)');
LEGEND_RATES(:,8) = strpad('d/dt q_Eb in component environment (fmol)');
LEGEND_RATES(:,9) = strpad('d/dt q_NO in component environment (fmol)');
LEGEND_RATES(:,10) = strpad('d/dt q_E6c in component environment (fmol)');
LEGEND_RATES(:,11) = strpad('d/dt q_NO_product in component environment (fmol)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
CONSTANTS(:,1) = 192.663;
CONSTANTS(:,2) = 0.00328297;
CONSTANTS(:,3) = 56591.2;
CONSTANTS(:,4) = 0.0110353;
CONSTANTS(:,5) = 3.61127e+06;
CONSTANTS(:,6) = 0.00328297;
CONSTANTS(:,7) = 4.92446;
CONSTANTS(:,8) = 0.0361127;
CONSTANTS(:,9) = 0.01;
CONSTANTS(:,10) = 17040;
CONSTANTS(:,11) = 0.304602;
CONSTANTS(:,12) = 1;
CONSTANTS(:,13) = 17.6706;
CONSTANTS(:,14) = 5190.42;
CONSTANTS(:,15) = 35.3412;
CONSTANTS(:,16) = 0.0051282;
CONSTANTS(:,17) = 0.0276911;
CONSTANTS(:,18) = 1;
CONSTANTS(:,19) = 30.4602;
CONSTANTS(:,20) = 0.1;
CONSTANTS(:,21) = 1;
STATES(:,1) = 1e-6;
STATES(:,2) = 0.0005;
STATES(:,3) = 1e-16;
STATES(:,4) = 1e-10;
STATES(:,5) = 1e-16;
STATES(:,6) = 1e-16;
STATES(:,7) = 1e-16;
STATES(:,8) = 1e-6;
STATES(:,9) = 0.00836;
STATES(:,10) = 1e-16;
STATES(:,11) = 1e-16;
CONSTANTS(:,22) = 0.000114;
CONSTANTS(:,23) = 8.31;
CONSTANTS(:,24) = 310;
CONSTANTS(:,25) = 96485;
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,1) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,10).*STATES(:,2));
ALGEBRAIC(:,2) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3));
ALGEBRAIC(:,5) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,14).*STATES(:,5));
ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
RATES(:,2) = - ALGEBRAIC(:,8);
ALGEBRAIC(:,3) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1));
ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
RATES(:,5) = ALGEBRAIC(:,8) - ALGEBRAIC(:,9);
ALGEBRAIC(:,4) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,13).*STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,15).*STATES(:,6));
ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,7) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,16).*STATES(:,7));
ALGEBRAIC(:,11) = CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
RATES(:,4) = - ALGEBRAIC(:,10)+ALGEBRAIC(:,11);
RATES(:,6) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
RATES(:,7) = ALGEBRAIC(:,11);
ALGEBRAIC(:,12) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,17).*STATES(:,8));
ALGEBRAIC(:,13) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,18).*STATES(:,9));
ALGEBRAIC(:,14) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,19).*STATES(:,10));
ALGEBRAIC(:,18) = CONSTANTS(:,5).*(exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,15) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3));
ALGEBRAIC(:,19) = CONSTANTS(:,6).*(exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,15)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,20) = CONSTANTS(:,7).*(exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
RATES(:,10) = (ALGEBRAIC(:,18) - ALGEBRAIC(:,19)) - ALGEBRAIC(:,20);
ALGEBRAIC(:,16) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1));
ALGEBRAIC(:,21) = CONSTANTS(:,8).*(exp((ALGEBRAIC(:,15)+ ALGEBRAIC(:,16).*2.00000)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
RATES(:,1) = ((ALGEBRAIC(:,9) - ALGEBRAIC(:,10)) - ALGEBRAIC(:,11)) - 2.00000.*ALGEBRAIC(:,21);
RATES(:,3) = ( - ALGEBRAIC(:,8)+ALGEBRAIC(:,9)+ALGEBRAIC(:,19)+ALGEBRAIC(:,20)) - ALGEBRAIC(:,21);
RATES(:,8) = - ALGEBRAIC(:,18)+ALGEBRAIC(:,21);
ALGEBRAIC(:,17) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,20).*STATES(:,11));
ALGEBRAIC(:,22) = CONSTANTS(:,9).*(exp(ALGEBRAIC(:,13)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
RATES(:,9) = (( - ALGEBRAIC(:,18)+ALGEBRAIC(:,21)) - ALGEBRAIC(:,22))+CONSTANTS(:,22);
RATES(:,11) = ALGEBRAIC(:,22);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,1) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,10).*STATES(:,2));
ALGEBRAIC(:,2) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3));
ALGEBRAIC(:,5) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,14).*STATES(:,5));
ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,3) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1));
ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,4) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,13).*STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,15).*STATES(:,6));
ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,7) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,16).*STATES(:,7));
ALGEBRAIC(:,11) = CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,12) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,17).*STATES(:,8));
ALGEBRAIC(:,13) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,18).*STATES(:,9));
ALGEBRAIC(:,14) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,19).*STATES(:,10));
ALGEBRAIC(:,18) = CONSTANTS(:,5).*(exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,15) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3));
ALGEBRAIC(:,19) = CONSTANTS(:,6).*(exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,15)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,20) = CONSTANTS(:,7).*(exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,16) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1));
ALGEBRAIC(:,21) = CONSTANTS(:,8).*(exp((ALGEBRAIC(:,15)+ ALGEBRAIC(:,16).*2.00000)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))));
ALGEBRAIC(:,17) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,20).*STATES(:,11));
ALGEBRAIC(:,22) = CONSTANTS(:,9).*(exp(ALGEBRAIC(:,13)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,23).*CONSTANTS(:,24))));
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end