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 =16;
end
% There are a total of 6 entries in each of the rate and state variable arrays.
% There are a total of 19 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_CONSTANTS(:,1) = strpad('q_PKACI_init in component environment (fmol)');
LEGEND_CONSTANTS(:,2) = strpad('q_Ip_init in component environment (fmol)');
LEGEND_CONSTANTS(:,3) = strpad('q_Ip_PKACI_init in component environment (fmol)');
LEGEND_CONSTANTS(:,4) = strpad('q_PP2a_init in component environment (fmol)');
LEGEND_CONSTANTS(:,5) = strpad('q_Ip_PP2a_init in component environment (fmol)');
LEGEND_CONSTANTS(:,6) = strpad('q_I_init in component environment (fmol)');
LEGEND_ALGEBRAIC(:,1) = strpad('q_PKACI in component environment (fmol)');
LEGEND_ALGEBRAIC(:,2) = strpad('q_Ip in component environment (fmol)');
LEGEND_ALGEBRAIC(:,3) = strpad('q_Ip_PKACI in component environment (fmol)');
LEGEND_ALGEBRAIC(:,4) = strpad('q_PP2a in component environment (fmol)');
LEGEND_ALGEBRAIC(:,5) = strpad('q_Ip_PP2a in component environment (fmol)');
LEGEND_ALGEBRAIC(:,6) = strpad('q_I in component environment (fmol)');
LEGEND_STATES(:,1) = strpad('q_PKACI in component Inhib1 (fmol)');
LEGEND_STATES(:,2) = strpad('q_Ip in component Inhib1 (fmol)');
LEGEND_STATES(:,3) = strpad('q_Ip_PKACI in component Inhib1 (fmol)');
LEGEND_STATES(:,4) = strpad('q_PP2a in component Inhib1 (fmol)');
LEGEND_STATES(:,5) = strpad('q_Ip_PP2a in component Inhib1 (fmol)');
LEGEND_STATES(:,6) = strpad('q_I in component Inhib1 (fmol)');
LEGEND_CONSTANTS(:,7) = strpad('kappa_PKAi1 in component Inhib1_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,8) = strpad('kappa_PKAi2 in component Inhib1_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,9) = strpad('kappa_PP2ai1 in component Inhib1_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,10) = strpad('kappa_PP2ai2 in component Inhib1_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,11) = strpad('K_PKACI in component Inhib1_parameters (per_fmol)');
LEGEND_CONSTANTS(:,12) = strpad('K_Ip in component Inhib1_parameters (per_fmol)');
LEGEND_CONSTANTS(:,13) = strpad('K_Ip_PKACI in component Inhib1_parameters (per_fmol)');
LEGEND_CONSTANTS(:,14) = strpad('K_PP2a in component Inhib1_parameters (per_fmol)');
LEGEND_CONSTANTS(:,15) = strpad('K_Ip_PP2a in component Inhib1_parameters (per_fmol)');
LEGEND_CONSTANTS(:,16) = strpad('K_I in component Inhib1_parameters (per_fmol)');
LEGEND_CONSTANTS(:,17) = strpad('R in component constants (J_per_K_per_mol)');
LEGEND_CONSTANTS(:,18) = strpad('T in component constants (kelvin)');
LEGEND_ALGEBRAIC(:,13) = strpad('vPKAi1 in component Inhib1 (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,14) = strpad('vPKAi2 in component Inhib1 (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,15) = strpad('vPP2ai1 in component Inhib1 (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,16) = strpad('vPP2ai2 in component Inhib1 (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,7) = strpad('mu_PKACI in component Inhib1 (J_per_mol)');
LEGEND_ALGEBRAIC(:,8) = strpad('mu_Ip in component Inhib1 (J_per_mol)');
LEGEND_ALGEBRAIC(:,9) = strpad('mu_Ip_PKACI in component Inhib1 (J_per_mol)');
LEGEND_ALGEBRAIC(:,10) = strpad('mu_PP2a in component Inhib1 (J_per_mol)');
LEGEND_ALGEBRAIC(:,11) = strpad('mu_Ip_PP2a in component Inhib1 (J_per_mol)');
LEGEND_ALGEBRAIC(:,12) = strpad('mu_I in component Inhib1 (J_per_mol)');
LEGEND_CONSTANTS(:,19) = strpad('F in component constants (C_per_mol)');
LEGEND_RATES(:,1) = strpad('d/dt q_PKACI in component Inhib1 (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_Ip in component Inhib1 (fmol)');
LEGEND_RATES(:,3) = strpad('d/dt q_Ip_PKACI in component Inhib1 (fmol)');
LEGEND_RATES(:,4) = strpad('d/dt q_PP2a in component Inhib1 (fmol)');
LEGEND_RATES(:,5) = strpad('d/dt q_Ip_PP2a in component Inhib1 (fmol)');
LEGEND_RATES(:,6) = strpad('d/dt q_I in component Inhib1 (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) = 1.117E-03;
CONSTANTS(:,2) = 9.994E-04;
CONSTANTS(:,3) = 1e-13;
CONSTANTS(:,4) = 8.512E-03;
CONSTANTS(:,5) = 1e-13;
CONSTANTS(:,6) = 1.140E-02;
STATES(:,1) = 1e-16;
STATES(:,2) = 1e-16;
STATES(:,3) = 1e-16;
STATES(:,4) = 1e-16;
STATES(:,5) = 1e-16;
STATES(:,6) = 1e-16;
CONSTANTS(:,7) = 20.9606;
CONSTANTS(:,8) = 22.2706;
CONSTANTS(:,9) = 5.39341;
CONSTANTS(:,10) = 5.30013;
CONSTANTS(:,11) = 0.284433;
CONSTANTS(:,12) = 0.133405;
CONSTANTS(:,13) = 1.38688;
CONSTANTS(:,14) = 0.0704691;
CONSTANTS(:,15) = 0.342795;
CONSTANTS(:,16) = 0.150247;
CONSTANTS(:,17) = 8.31;
CONSTANTS(:,18) = 310;
CONSTANTS(:,19) = 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) = STATES(:,1)+CONSTANTS(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,11).*ALGEBRAIC(:,1));
ALGEBRAIC(:,3) = STATES(:,3)+CONSTANTS(:,3);
ALGEBRAIC(:,9) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,13).*ALGEBRAIC(:,3));
ALGEBRAIC(:,6) = STATES(:,6)+CONSTANTS(:,6);
ALGEBRAIC(:,12) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,16).*ALGEBRAIC(:,6));
ALGEBRAIC(:,13) = CONSTANTS(:,7).*(exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,12))./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,17).*CONSTANTS(:,18))));
ALGEBRAIC(:,2) = STATES(:,2)+CONSTANTS(:,2);
ALGEBRAIC(:,8) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,12).*ALGEBRAIC(:,2));
ALGEBRAIC(:,14) = CONSTANTS(:,8).*(exp(ALGEBRAIC(:,9)./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,8))./( CONSTANTS(:,17).*CONSTANTS(:,18))));
RATES(:,1) = ALGEBRAIC(:,14) - ALGEBRAIC(:,13);
RATES(:,3) = ALGEBRAIC(:,13) - ALGEBRAIC(:,14);
ALGEBRAIC(:,4) = STATES(:,4)+CONSTANTS(:,4);
ALGEBRAIC(:,10) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,14).*ALGEBRAIC(:,4));
ALGEBRAIC(:,5) = STATES(:,5)+CONSTANTS(:,5);
ALGEBRAIC(:,11) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,15).*ALGEBRAIC(:,5));
ALGEBRAIC(:,15) = CONSTANTS(:,9).*(exp((ALGEBRAIC(:,10)+ALGEBRAIC(:,8))./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp(ALGEBRAIC(:,11)./( CONSTANTS(:,17).*CONSTANTS(:,18))));
RATES(:,2) = ALGEBRAIC(:,14) - ALGEBRAIC(:,15);
ALGEBRAIC(:,16) = CONSTANTS(:,10).*(exp(ALGEBRAIC(:,11)./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp((ALGEBRAIC(:,10)+ALGEBRAIC(:,12))./( CONSTANTS(:,17).*CONSTANTS(:,18))));
RATES(:,4) = ALGEBRAIC(:,16) - ALGEBRAIC(:,15);
RATES(:,5) = ALGEBRAIC(:,15) - ALGEBRAIC(:,16);
RATES(:,6) = ALGEBRAIC(:,16) - ALGEBRAIC(:,13);
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) = STATES(:,1)+CONSTANTS(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,11).*ALGEBRAIC(:,1));
ALGEBRAIC(:,3) = STATES(:,3)+CONSTANTS(:,3);
ALGEBRAIC(:,9) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,13).*ALGEBRAIC(:,3));
ALGEBRAIC(:,6) = STATES(:,6)+CONSTANTS(:,6);
ALGEBRAIC(:,12) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,16).*ALGEBRAIC(:,6));
ALGEBRAIC(:,13) = CONSTANTS(:,7).*(exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,12))./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,17).*CONSTANTS(:,18))));
ALGEBRAIC(:,2) = STATES(:,2)+CONSTANTS(:,2);
ALGEBRAIC(:,8) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,12).*ALGEBRAIC(:,2));
ALGEBRAIC(:,14) = CONSTANTS(:,8).*(exp(ALGEBRAIC(:,9)./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,8))./( CONSTANTS(:,17).*CONSTANTS(:,18))));
ALGEBRAIC(:,4) = STATES(:,4)+CONSTANTS(:,4);
ALGEBRAIC(:,10) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,14).*ALGEBRAIC(:,4));
ALGEBRAIC(:,5) = STATES(:,5)+CONSTANTS(:,5);
ALGEBRAIC(:,11) = CONSTANTS(:,17).*CONSTANTS(:,18).*log( CONSTANTS(:,15).*ALGEBRAIC(:,5));
ALGEBRAIC(:,15) = CONSTANTS(:,9).*(exp((ALGEBRAIC(:,10)+ALGEBRAIC(:,8))./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp(ALGEBRAIC(:,11)./( CONSTANTS(:,17).*CONSTANTS(:,18))));
ALGEBRAIC(:,16) = CONSTANTS(:,10).*(exp(ALGEBRAIC(:,11)./( CONSTANTS(:,17).*CONSTANTS(:,18))) - exp((ALGEBRAIC(:,10)+ALGEBRAIC(:,12))./( CONSTANTS(:,17).*CONSTANTS(:,18))));
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