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 (minute)');
LEGEND_STATES(:,1) = strpad('S1 in component S1 (millimolar)');
LEGEND_CONSTANTS(:,1) = strpad('Jo in component glucose_influx_rate (flux)');
LEGEND_ALGEBRAIC(:,4) = strpad('v1 in component v1 (flux)');
LEGEND_STATES(:,2) = strpad('S2 in component S2 (millimolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('v2 in component v2 (flux)');
LEGEND_ALGEBRAIC(:,9) = strpad('v6 in component v6 (flux)');
LEGEND_STATES(:,3) = strpad('S3 in component S3 (millimolar)');
LEGEND_ALGEBRAIC(:,6) = strpad('v3 in component v3 (flux)');
LEGEND_STATES(:,4) = strpad('S4 in component S4 (millimolar)');
LEGEND_ALGEBRAIC(:,7) = strpad('v4 in component v4 (flux)');
LEGEND_ALGEBRAIC(:,11) = strpad('J in component S4_flux_rate_across_the_plasma_membrane (flux)');
LEGEND_STATES(:,5) = strpad('S4_ex in component S4_ex (millimolar)');
LEGEND_CONSTANTS(:,2) = strpad('phi in component S4_ex (dimensionless)');
LEGEND_ALGEBRAIC(:,10) = strpad('v7 in component v7 (flux)');
LEGEND_STATES(:,6) = strpad('A3 in component A3 (millimolar)');
LEGEND_ALGEBRAIC(:,8) = strpad('v5 in component v5 (flux)');
LEGEND_CONSTANTS(:,3) = strpad('A in component A2 (millimolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('A2 in component A2 (millimolar)');
LEGEND_STATES(:,7) = strpad('N2 in component N2 (millimolar)');
LEGEND_CONSTANTS(:,4) = strpad('N in component N1 (millimolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('N1 in component N1 (millimolar)');
LEGEND_CONSTANTS(:,5) = strpad('K_I in component v1 (millimolar)');
LEGEND_CONSTANTS(:,6) = strpad('k_1 in component v1 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('q in component v1 (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('f_A3 in component v1 (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('k_2 in component v2 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k_3 in component v3 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k_4 in component v4 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('k_5 in component v5 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('k_6 in component v6 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('k in component v7 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('kappa in component S4_flux_rate_across_the_plasma_membrane (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt S1 in component S1 (millimolar)');
LEGEND_RATES(:,2) = strpad('d/dt S2 in component S2 (millimolar)');
LEGEND_RATES(:,3) = strpad('d/dt S3 in component S3 (millimolar)');
LEGEND_RATES(:,4) = strpad('d/dt S4 in component S4 (millimolar)');
LEGEND_RATES(:,5) = strpad('d/dt S4_ex in component S4_ex (millimolar)');
LEGEND_RATES(:,6) = strpad('d/dt A3 in component A3 (millimolar)');
LEGEND_RATES(:,7) = strpad('d/dt N2 in component N2 (millimolar)');
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) = 5.8;
CONSTANTS(:,1) = 3.0;
STATES(:,2) = 0.9;
STATES(:,3) = 0.2;
STATES(:,4) = 0.2;
STATES(:,5) = 0.1;
CONSTANTS(:,2) = 0.1;
STATES(:,6) = 2.4;
CONSTANTS(:,3) = 4.0;
STATES(:,7) = 0.1;
CONSTANTS(:,4) = 1.0;
CONSTANTS(:,5) = 0.52;
CONSTANTS(:,6) = 100.0;
CONSTANTS(:,7) = 4.0;
CONSTANTS(:,8) = 6.0;
CONSTANTS(:,9) = 16.0;
CONSTANTS(:,10) = 100.0;
CONSTANTS(:,11) = 1.28;
CONSTANTS(:,12) = 12.0;
CONSTANTS(:,13) = 1.3;
CONSTANTS(:,14) = 13.0;
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
ALGEBRAIC(:,3) = power(1.00000+power(STATES(:,6)./CONSTANTS(:,5), CONSTANTS(:,7)), -1.00000);
ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,1).*STATES(:,6).*ALGEBRAIC(:,3);
RATES(:,1) = CONSTANTS(:,1) - ALGEBRAIC(:,4);
ALGEBRAIC(:,2) = CONSTANTS(:,4) - STATES(:,7);
ALGEBRAIC(:,5) = CONSTANTS(:,8).*STATES(:,2).*ALGEBRAIC(:,2);
ALGEBRAIC(:,1) = CONSTANTS(:,3) - STATES(:,6);
ALGEBRAIC(:,6) = CONSTANTS(:,9).*STATES(:,3).*ALGEBRAIC(:,1);
RATES(:,3) = ALGEBRAIC(:,5) - ALGEBRAIC(:,6);
ALGEBRAIC(:,8) = CONSTANTS(:,11).*STATES(:,6);
RATES(:,6) = 2.00000.*ALGEBRAIC(:,6) - ( 2.00000.*ALGEBRAIC(:,4)+ALGEBRAIC(:,8));
ALGEBRAIC(:,9) = CONSTANTS(:,12).*STATES(:,2).*STATES(:,7);
RATES(:,2) = 2.00000.*ALGEBRAIC(:,4) - (ALGEBRAIC(:,5)+ALGEBRAIC(:,9));
ALGEBRAIC(:,7) = CONSTANTS(:,10).*STATES(:,4).*STATES(:,7);
RATES(:,7) = ALGEBRAIC(:,5) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,9));
ALGEBRAIC(:,11) = CONSTANTS(:,14).*(STATES(:,4) - STATES(:,5));
RATES(:,4) = ALGEBRAIC(:,6) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,11));
ALGEBRAIC(:,10) = CONSTANTS(:,13).*STATES(:,5);
RATES(:,5) = CONSTANTS(:,2).*ALGEBRAIC(:,11) - ALGEBRAIC(:,10);
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(:,3) = power(1.00000+power(STATES(:,6)./CONSTANTS(:,5), CONSTANTS(:,7)), -1.00000);
ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,1).*STATES(:,6).*ALGEBRAIC(:,3);
ALGEBRAIC(:,2) = CONSTANTS(:,4) - STATES(:,7);
ALGEBRAIC(:,5) = CONSTANTS(:,8).*STATES(:,2).*ALGEBRAIC(:,2);
ALGEBRAIC(:,1) = CONSTANTS(:,3) - STATES(:,6);
ALGEBRAIC(:,6) = CONSTANTS(:,9).*STATES(:,3).*ALGEBRAIC(:,1);
ALGEBRAIC(:,8) = CONSTANTS(:,11).*STATES(:,6);
ALGEBRAIC(:,9) = CONSTANTS(:,12).*STATES(:,2).*STATES(:,7);
ALGEBRAIC(:,7) = CONSTANTS(:,10).*STATES(:,4).*STATES(:,7);
ALGEBRAIC(:,11) = CONSTANTS(:,14).*(STATES(:,4) - STATES(:,5));
ALGEBRAIC(:,10) = CONSTANTS(:,13).*STATES(:,5);
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