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 11 entries in each of the rate and state variable arrays.
% There are a total of 18 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('k11 in component kinetic_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k11_ in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k71 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k72 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k12 in component kinetic_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k12_ in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k51 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k52 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k41 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k31 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('k32 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('k42 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('k22 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('k22_ in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('k21 in component kinetic_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('k21_ in component kinetic_constants (first_order_rate_constant)');
LEGEND_STATES(:,1) = strpad('PB in component PB (micromolar)');
LEGEND_CONSTANTS(:,17) = strpad('kreset1 in component kreset1 (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('A1 in component A1 (micromolar)');
LEGEND_STATES(:,3) = strpad('A2 in component A2 (micromolar)');
LEGEND_STATES(:,4) = strpad('PC1 in component PC1 (micromolar)');
LEGEND_STATES(:,5) = strpad('PF1 in component PF1 (micromolar)');
LEGEND_STATES(:,6) = strpad('PG1 in component PG1 (micromolar)');
LEGEND_STATES(:,7) = strpad('PC2 in component PC2 (micromolar)');
LEGEND_STATES(:,8) = strpad('PF2 in component PF2 (micromolar)');
LEGEND_STATES(:,9) = strpad('PD1 in component PD1 (micromolar)');
LEGEND_STATES(:,10) = strpad('PE1 in component PE1 (micromolar)');
LEGEND_STATES(:,11) = strpad('PD2 in component PD2 (micromolar)');
LEGEND_CONSTANTS(:,18) = strpad('PE2 in component PE2 (micromolar)');
LEGEND_RATES(:,1) = strpad('d/dt PB in component PB (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt A1 in component A1 (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt A2 in component A2 (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt PC1 in component PC1 (micromolar)');
LEGEND_RATES(:,9) = strpad('d/dt PD1 in component PD1 (micromolar)');
LEGEND_RATES(:,10) = strpad('d/dt PE1 in component PE1 (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt PF1 in component PF1 (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt PG1 in component PG1 (micromolar)');
LEGEND_RATES(:,7) = strpad('d/dt PC2 in component PC2 (micromolar)');
LEGEND_RATES(:,11) = strpad('d/dt PD2 in component PD2 (micromolar)');
LEGEND_RATES(:,8) = strpad('d/dt PF2 in component PF2 (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 = [];
CONSTANTS(:,1) = 110.0;
CONSTANTS(:,2) = 25.0;
CONSTANTS(:,3) = 0.1;
CONSTANTS(:,4) = 60.0;
CONSTANTS(:,5) = 110.0;
CONSTANTS(:,6) = 0.2;
CONSTANTS(:,7) = 7.0;
CONSTANTS(:,8) = 0.0;
CONSTANTS(:,9) = 60.0;
CONSTANTS(:,10) = 500.0;
CONSTANTS(:,11) = 50.0;
CONSTANTS(:,12) = 70.0;
CONSTANTS(:,13) = 100.0;
CONSTANTS(:,14) = 17.0;
CONSTANTS(:,15) = 100.0;
CONSTANTS(:,16) = 0.2;
STATES(:,1) = 0.1;
CONSTANTS(:,17) = 35.0;
STATES(:,2) = 0.1;
STATES(:,3) = 0.1;
STATES(:,4) = 0.1;
STATES(:,5) = 0.1;
STATES(:,6) = 0.1;
STATES(:,7) = 0.1;
STATES(:,8) = 0.1;
STATES(:,9) = 0.1;
STATES(:,10) = 0.1;
STATES(:,11) = 0.1;
CONSTANTS(:,18) = 0.1;
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(:,2).*STATES(:,4)+ CONSTANTS(:,3).*STATES(:,5)+ CONSTANTS(:,17).*STATES(:,6)+ CONSTANTS(:,6).*STATES(:,7)+ CONSTANTS(:,4).*STATES(:,8)) - ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,5).*STATES(:,3).*STATES(:,1));
RATES(:,2) = CONSTANTS(:,2).*STATES(:,4) - CONSTANTS(:,1).*STATES(:,2).*STATES(:,1);
RATES(:,3) = CONSTANTS(:,6).*STATES(:,7) - CONSTANTS(:,5).*STATES(:,3).*STATES(:,1);
RATES(:,4) = ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1) - (CONSTANTS(:,2)+CONSTANTS(:,15)).*STATES(:,4))+ CONSTANTS(:,16).*STATES(:,9);
RATES(:,9) = CONSTANTS(:,15).*STATES(:,4) - (CONSTANTS(:,16)+CONSTANTS(:,10)).*STATES(:,9);
RATES(:,10) = CONSTANTS(:,10).*STATES(:,9) - CONSTANTS(:,9).*STATES(:,10);
RATES(:,5) = CONSTANTS(:,9).*STATES(:,10) - (CONSTANTS(:,7)+CONSTANTS(:,3)).*STATES(:,5);
RATES(:,6) = CONSTANTS(:,7).*STATES(:,5) - CONSTANTS(:,17).*STATES(:,6);
RATES(:,7) = ( CONSTANTS(:,5).*STATES(:,3).*STATES(:,1) - (CONSTANTS(:,6)+CONSTANTS(:,13)).*STATES(:,7))+ CONSTANTS(:,14).*STATES(:,11);
RATES(:,11) = CONSTANTS(:,13).*STATES(:,7) - (CONSTANTS(:,14)+CONSTANTS(:,11)).*STATES(:,11);
RATES(:,8) = CONSTANTS(:,12).*CONSTANTS(:,18) - (CONSTANTS(:,8)+CONSTANTS(:,4)).*STATES(:,8);
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