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 =0;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 27 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('G_a in component G_a (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('k1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('k2 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('k3 in component model_parameters (dimensionless)');
LEGEND_STATES(:,2) = strpad('PLC in component PLC (micromolar)');
LEGEND_STATES(:,3) = strpad('Ca_cyt in component Ca_cyt (micromolar)');
LEGEND_CONSTANTS(:,4) = strpad('K4 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('k5 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('K6 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('k7 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('k8 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('K9 in component model_parameters (dimensionless)');
LEGEND_STATES(:,4) = strpad('Ca_ER in component Ca_ER (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('k10 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('K11 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('k16 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('K17 in component model_parameters (dimensionless)');
LEGEND_STATES(:,5) = strpad('Ca_mit in component Ca_mit (micromolar)');
LEGEND_CONSTANTS(:,14) = strpad('k18 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('K19 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('k20 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('K21 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('k12 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('k13 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('k14 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('K15 in component model_parameters (dimensionless)');
LEGEND_STATES(:,6) = strpad('Enz in component Enz (micromolar)');
LEGEND_CONSTANTS(:,22) = strpad('k_act in component Enz (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('K_M in component Enz (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('k_inact in component Enz (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('p in component Enz (dimensionless)');
LEGEND_STATES(:,7) = strpad('Pro in component Pro (micromolar)');
LEGEND_CONSTANTS(:,26) = strpad('k_enz in component Pro (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('k_rem in component Pro (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt G_a in component G_a (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt PLC in component PLC (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt Ca_ER in component Ca_ER (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt Ca_mit in component Ca_mit (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt Ca_cyt in component Ca_cyt (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt Enz in component Enz (micromolar)');
LEGEND_RATES(:,7) = strpad('d/dt Pro in component Pro (micromolar)');
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) = 0.01;
CONSTANTS(:,1) = 0.55;
CONSTANTS(:,2) = 0;
CONSTANTS(:,3) = 0.0001;
STATES(:,2) = 0.01;
STATES(:,3) = 0.01;
CONSTANTS(:,4) = 0.783;
CONSTANTS(:,5) = 1.24;
CONSTANTS(:,6) = 0.7;
CONSTANTS(:,7) = 5.82;
CONSTANTS(:,8) = 32.24;
CONSTANTS(:,9) = 29.09;
STATES(:,4) = 10;
CONSTANTS(:,10) = 0.93;
CONSTANTS(:,11) = 2.667;
CONSTANTS(:,12) = 20.9;
CONSTANTS(:,13) = 0.05;
STATES(:,5) = 0.001;
CONSTANTS(:,14) = 79;
CONSTANTS(:,15) = 2;
CONSTANTS(:,16) = 1.5;
CONSTANTS(:,17) = 1.5;
CONSTANTS(:,18) = 0.76;
CONSTANTS(:,19) = 0;
CONSTANTS(:,20) = 149;
CONSTANTS(:,21) = 0.16;
STATES(:,6) = 0;
CONSTANTS(:,22) = 0.1;
CONSTANTS(:,23) = 0.02;
CONSTANTS(:,24) = 0.043;
CONSTANTS(:,25) = 4;
STATES(:,7) = 0;
CONSTANTS(:,26) = 3;
CONSTANTS(:,27) = 3;
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
RATES(:,1) = ((CONSTANTS(:,1)+ CONSTANTS(:,2).*STATES(:,1)) - ( CONSTANTS(:,3).*STATES(:,1).*STATES(:,2))./(STATES(:,1)+CONSTANTS(:,4))) - ( CONSTANTS(:,5).*STATES(:,3).*STATES(:,1))./(STATES(:,1)+CONSTANTS(:,6));
RATES(:,2) = CONSTANTS(:,7).*STATES(:,1) - ( CONSTANTS(:,8).*STATES(:,2))./(STATES(:,2)+CONSTANTS(:,9));
RATES(:,4) = - (STATES(:,4) - STATES(:,3)).*(( CONSTANTS(:,10).*STATES(:,3).*power(STATES(:,2), 4.00000))./(power(STATES(:,2), 4.00000)+power(CONSTANTS(:,11), 4.00000)))+( CONSTANTS(:,12).*STATES(:,3))./(STATES(:,3)+CONSTANTS(:,13));
RATES(:,5) = ( CONSTANTS(:,14).*power(STATES(:,3), 8.00000))./(power(CONSTANTS(:,15), 8.00000)+power(STATES(:,3), 8.00000)) - (STATES(:,5) - STATES(:,3)).*(( CONSTANTS(:,16).*STATES(:,3))./(STATES(:,3)+CONSTANTS(:,17)));
RATES(:,3) = (((( (STATES(:,4) - STATES(:,3)).*(( CONSTANTS(:,10).*STATES(:,3).*power(STATES(:,2), 4.00000))./(power(STATES(:,2), 4.00000)+power(CONSTANTS(:,11), 4.00000)))+ CONSTANTS(:,18).*STATES(:,2)+ CONSTANTS(:,19).*STATES(:,1)) - ( CONSTANTS(:,20).*STATES(:,3))./(CONSTANTS(:,21)+STATES(:,3))) - ( CONSTANTS(:,12).*STATES(:,3))./(CONSTANTS(:,13)+STATES(:,3))) - ( CONSTANTS(:,14).*power(STATES(:,3), 8.00000))./(power(CONSTANTS(:,15), 8.00000)+power(STATES(:,3), 8.00000)))+ (STATES(:,5) - STATES(:,3)).*(( CONSTANTS(:,16).*STATES(:,3))./(STATES(:,3)+CONSTANTS(:,17)));
RATES(:,6) = ( CONSTANTS(:,22).*power(STATES(:,3), CONSTANTS(:,25)))./(power(CONSTANTS(:,23), CONSTANTS(:,25))+power(STATES(:,3), CONSTANTS(:,25))) - CONSTANTS(:,24).*STATES(:,6);
RATES(:,7) = CONSTANTS(:,26).*STATES(:,6) - CONSTANTS(:,27).*STATES(:,7);
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
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