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 =11;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 14 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_VOI = strpad('time in component environment (second)');
LEGEND_STATES(:,1) = strpad('q_GTP in component environment (fmol)');
LEGEND_STATES(:,2) = strpad('q_E5c in component environment (fmol)');
LEGEND_STATES(:,3) = strpad('q_cGMP 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_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_CONSTANTS(:,1) = strpad('kappa_R_1a_cGMP in component cGMP_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,2) = strpad('kappa_R_1b_cGMP in component cGMP_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,3) = strpad('kappa_R_2a_cGMP in component cGMP_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,4) = strpad('kappa_R_2b_cGMP in component cGMP_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,5) = strpad('K_GTP in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,6) = strpad('K_E5c in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,7) = strpad('K_cGMP in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,8) = strpad('K_PDE in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,9) = strpad('K_GTP_E5c in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,10) = strpad('K_cGMP_PDE in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,11) = strpad('K_GMP in component cGMP_parameters (per_fmol)');
LEGEND_CONSTANTS(:,12) = strpad('R in component constants (J_per_K_per_mol)');
LEGEND_CONSTANTS(:,13) = strpad('T in component constants (kelvin)');
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_CONSTANTS(:,14) = strpad('F in component constants (C_per_mol)');
LEGEND_RATES(:,1) = strpad('d/dt q_GTP in component environment (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_E5c in component environment (fmol)');
LEGEND_RATES(:,3) = strpad('d/dt q_cGMP 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_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 = [];
STATES(:,1) = 1e-18;
STATES(:,2) = 1e-18;
STATES(:,3) = 1e-18;
STATES(:,4) = 1e-18;
STATES(:,5) = 1e-18;
STATES(:,6) = 1e-18;
STATES(:,7) = 1e-18;
CONSTANTS(:,1) = 1772.99;
CONSTANTS(:,2) = 0.0302117;
CONSTANTS(:,3) = 73652.7;
CONSTANTS(:,4) = 0.0143623;
CONSTANTS(:,5) = 1600.8;
CONSTANTS(:,6) = 0.0255983;
CONSTANTS(:,7) = 0.0939434;
CONSTANTS(:,8) = 10.5002;
CONSTANTS(:,9) = 152.027;
CONSTANTS(:,10) = 7.31926;
CONSTANTS(:,11) = 0.000481761;
CONSTANTS(:,12) = 8.31;
CONSTANTS(:,13) = 310;
CONSTANTS(:,14) = 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(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,5).*STATES(:,1));
ALGEBRAIC(:,2) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,6).*STATES(:,2));
ALGEBRAIC(:,5) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,9).*STATES(:,5));
ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
RATES(:,1) = - ALGEBRAIC(:,8);
ALGEBRAIC(:,3) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,7).*STATES(:,3));
ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
RATES(:,2) = - ALGEBRAIC(:,8)+ALGEBRAIC(:,9);
RATES(:,5) = ALGEBRAIC(:,8) - ALGEBRAIC(:,9);
ALGEBRAIC(:,4) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,8).*STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,10).*STATES(:,6));
ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
ALGEBRAIC(:,7) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,11).*STATES(:,7));
ALGEBRAIC(:,11) = CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
RATES(:,3) = (ALGEBRAIC(:,9) - ALGEBRAIC(:,10)) - ALGEBRAIC(:,11);
RATES(:,4) = - ALGEBRAIC(:,10)+ALGEBRAIC(:,11);
RATES(:,6) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
RATES(:,7) = ALGEBRAIC(:,11);
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(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,5).*STATES(:,1));
ALGEBRAIC(:,2) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,6).*STATES(:,2));
ALGEBRAIC(:,5) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,9).*STATES(:,5));
ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
ALGEBRAIC(:,3) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,7).*STATES(:,3));
ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
ALGEBRAIC(:,4) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,8).*STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,10).*STATES(:,6));
ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
ALGEBRAIC(:,7) = CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,11).*STATES(:,7));
ALGEBRAIC(:,11) = CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
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