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 =4;
end
% There are a total of 6 entries in each of the rate and state variable arrays.
% There are a total of 28 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 (minute)');
LEGEND_CONSTANTS(:,1) = strpad('H_1 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('H_2 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('H_3 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('H_4 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('K_1 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('K_2 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('K_3 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('K_4 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('V_M1 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('V_M3 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('U_M1 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('U_M3 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('V_2 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('V_4 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('U_2 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('U_4 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('K_c1 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,18) = strpad('K_c2 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,19) = strpad('K_d1 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,20) = strpad('K_d2 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,21) = strpad('v_d1 in component parameters (flux)');
LEGEND_CONSTANTS(:,22) = strpad('v_d2 in component parameters (flux)');
LEGEND_CONSTANTS(:,23) = strpad('v_i1 in component parameters (flux)');
LEGEND_CONSTANTS(:,24) = strpad('v_i2 in component parameters (flux)');
LEGEND_CONSTANTS(:,25) = strpad('k_d1 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,26) = strpad('k_d2 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,27) = strpad('K_im1 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('K_im2 in component parameters (dimensionless)');
LEGEND_STATES(:,1) = strpad('C_1 in component C_1 (micromolar)');
LEGEND_STATES(:,2) = strpad('M_2 in component M_2 (dimensionless)');
LEGEND_STATES(:,3) = strpad('X_1 in component X_1 (dimensionless)');
LEGEND_STATES(:,4) = strpad('M_1 in component M_1 (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('V_1 in component V_1 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,2) = strpad('V_3 in component V_3 (first_order_rate_constant)');
LEGEND_STATES(:,5) = strpad('C_2 in component C_2 (micromolar)');
LEGEND_STATES(:,6) = strpad('X_2 in component X_2 (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('U_1 in component U_1 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('U_3 in component U_3 (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt C_1 in component C_1 (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt M_1 in component M_1 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt X_1 in component X_1 (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt C_2 in component C_2 (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt M_2 in component M_2 (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt X_2 in component X_2 (dimensionless)');
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) = 0.01;
CONSTANTS(:,2) = 0.01;
CONSTANTS(:,3) = 0.01;
CONSTANTS(:,4) = 0.01;
CONSTANTS(:,5) = 0.01;
CONSTANTS(:,6) = 0.01;
CONSTANTS(:,7) = 0.01;
CONSTANTS(:,8) = 0.01;
CONSTANTS(:,9) = 0.3;
CONSTANTS(:,10) = 0.1;
CONSTANTS(:,11) = 0.3;
CONSTANTS(:,12) = 0.1;
CONSTANTS(:,13) = 0.15;
CONSTANTS(:,14) = 0.05;
CONSTANTS(:,15) = 0.15;
CONSTANTS(:,16) = 0.05;
CONSTANTS(:,17) = 0.5;
CONSTANTS(:,18) = 0.5;
CONSTANTS(:,19) = 0.02;
CONSTANTS(:,20) = 0.02;
CONSTANTS(:,21) = 0.025;
CONSTANTS(:,22) = 0.025;
CONSTANTS(:,23) = 0.05;
CONSTANTS(:,24) = 0.05;
CONSTANTS(:,25) = 0.001;
CONSTANTS(:,26) = 0.001;
CONSTANTS(:,27) = 0.03;
CONSTANTS(:,28) = 0.03;
STATES(:,1) = 2;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 1;
STATES(:,5) = 0;
STATES(:,6) = 0;
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(:,23).*CONSTANTS(:,27))./(CONSTANTS(:,27)+STATES(:,2)) - ( CONSTANTS(:,21).*STATES(:,3).*STATES(:,1))./(CONSTANTS(:,19)+STATES(:,1))) - CONSTANTS(:,25).*STATES(:,1);
RATES(:,5) = (( CONSTANTS(:,24).*CONSTANTS(:,28))./(CONSTANTS(:,28)+STATES(:,4)) - ( CONSTANTS(:,22).*STATES(:,6).*STATES(:,5))./(CONSTANTS(:,20)+STATES(:,5))) - CONSTANTS(:,26).*STATES(:,5);
ALGEBRAIC(:,1) = (STATES(:,1)./(CONSTANTS(:,17)+STATES(:,1))).*CONSTANTS(:,9);
RATES(:,4) = ( ALGEBRAIC(:,1).*(1.00000 - STATES(:,4)))./(CONSTANTS(:,5)+(1.00000 - STATES(:,4))) - ( CONSTANTS(:,13).*STATES(:,4))./(CONSTANTS(:,6)+STATES(:,4));
ALGEBRAIC(:,2) = STATES(:,4).*CONSTANTS(:,10);
RATES(:,3) = ( ALGEBRAIC(:,2).*(1.00000 - STATES(:,3)))./(CONSTANTS(:,7)+(1.00000 - STATES(:,3))) - ( CONSTANTS(:,14).*STATES(:,3))./(CONSTANTS(:,8)+STATES(:,3));
ALGEBRAIC(:,3) = (STATES(:,5)./(CONSTANTS(:,18)+STATES(:,5))).*CONSTANTS(:,11);
RATES(:,2) = ( ALGEBRAIC(:,3).*(1.00000 - STATES(:,2)))./(CONSTANTS(:,1)+(1.00000 - STATES(:,2))) - ( CONSTANTS(:,15).*STATES(:,2))./(CONSTANTS(:,2)+STATES(:,2));
ALGEBRAIC(:,4) = STATES(:,2).*CONSTANTS(:,12);
RATES(:,6) = ( ALGEBRAIC(:,4).*(1.00000 - STATES(:,6)))./(CONSTANTS(:,3)+(1.00000 - STATES(:,6))) - ( CONSTANTS(:,16).*STATES(:,6))./(CONSTANTS(:,4)+STATES(:,6));
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(:,17)+STATES(:,1))).*CONSTANTS(:,9);
ALGEBRAIC(:,2) = STATES(:,4).*CONSTANTS(:,10);
ALGEBRAIC(:,3) = (STATES(:,5)./(CONSTANTS(:,18)+STATES(:,5))).*CONSTANTS(:,11);
ALGEBRAIC(:,4) = STATES(:,2).*CONSTANTS(:,12);
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