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 =10;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 13 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('q_L in component environment (fmol)');
LEGEND_STATES(:,2) = strpad('q_K1 in component environment (fmol)');
LEGEND_STATES(:,3) = strpad('q_K2 in component environment (fmol)');
LEGEND_STATES(:,4) = strpad('q_LK1 in component environment (fmol)');
LEGEND_STATES(:,5) = strpad('q_K2P in component environment (fmol)');
LEGEND_STATES(:,6) = strpad('q_P in component environment (fmol)');
LEGEND_STATES(:,7) = strpad('q_LK1K2 in component environment (fmol)');
LEGEND_ALGEBRAIC(:,8) = strpad('v_Re1 in component RTK (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,9) = strpad('v_Re2 in component RTK (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,10) = strpad('v_Re3 in component RTK (fmol_per_sec)');
LEGEND_CONSTANTS(:,1) = strpad('kappa_Re1 in component RTK_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,2) = strpad('kappa_Re2 in component RTK_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,3) = strpad('kappa_Re3 in component RTK_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,4) = strpad('K_L in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,5) = strpad('K_K1 in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,6) = strpad('K_K2 in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,7) = strpad('K_LK1 in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,8) = strpad('K_K2P in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,9) = strpad('K_P in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,10) = strpad('K_LK1K2 in component RTK_parameters (per_fmol)');
LEGEND_CONSTANTS(:,11) = strpad('R in component constants (J_per_K_per_mol)');
LEGEND_CONSTANTS(:,12) = strpad('T in component constants (kelvin)');
LEGEND_ALGEBRAIC(:,1) = strpad('mu_L in component RTK (J_per_mol)');
LEGEND_ALGEBRAIC(:,2) = strpad('mu_K1 in component RTK (J_per_mol)');
LEGEND_ALGEBRAIC(:,3) = strpad('mu_K2 in component RTK (J_per_mol)');
LEGEND_ALGEBRAIC(:,4) = strpad('mu_LK1 in component RTK (J_per_mol)');
LEGEND_ALGEBRAIC(:,5) = strpad('mu_K2P in component RTK (J_per_mol)');
LEGEND_ALGEBRAIC(:,6) = strpad('mu_P in component RTK (J_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('mu_LK1K2 in component RTK (J_per_mol)');
LEGEND_CONSTANTS(:,13) = strpad('F in component constants (C_per_mol)');
LEGEND_RATES(:,1) = strpad('d/dt q_L in component environment (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_K1 in component environment (fmol)');
LEGEND_RATES(:,3) = strpad('d/dt q_K2 in component environment (fmol)');
LEGEND_RATES(:,4) = strpad('d/dt q_LK1 in component environment (fmol)');
LEGEND_RATES(:,5) = strpad('d/dt q_K2P in component environment (fmol)');
LEGEND_RATES(:,6) = strpad('d/dt q_P in component environment (fmol)');
LEGEND_RATES(:,7) = strpad('d/dt q_LK1K2 in component environment (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 = [];
STATES(:,1) = 1;
STATES(:,2) = 1e-3;
STATES(:,3) = 1e-3;
STATES(:,4) = 1e-6;
STATES(:,5) = 1e-9;
STATES(:,6) = 1;
STATES(:,7) = 1e-9;
CONSTANTS(:,1) = 0.000186898;
CONSTANTS(:,2) = 0.0125535;
CONSTANTS(:,3) = 132.879;
CONSTANTS(:,4) = 197.162;
CONSTANTS(:,5) = 197.162;
CONSTANTS(:,6) = 4.01297e+09;
CONSTANTS(:,7) = 0.00144219;
CONSTANTS(:,8) = 3.79118e-07;
CONSTANTS(:,9) = 2.54645e+07;
CONSTANTS(:,10) = 2.14714e-05;
CONSTANTS(:,11) = 8.31;
CONSTANTS(:,12) = 310;
CONSTANTS(:,13) = 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) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,4).*STATES(:,1));
ALGEBRAIC(:,2) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,5).*STATES(:,2));
ALGEBRAIC(:,4) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,7).*STATES(:,4));
ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,11).*CONSTANTS(:,12))) - exp(ALGEBRAIC(:,4)./( CONSTANTS(:,11).*CONSTANTS(:,12))));
RATES(:,1) = - ALGEBRAIC(:,8);
RATES(:,2) = - ALGEBRAIC(:,8);
ALGEBRAIC(:,3) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,6).*STATES(:,3));
ALGEBRAIC(:,7) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,10).*STATES(:,7));
ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp((ALGEBRAIC(:,4)+ALGEBRAIC(:,3))./( CONSTANTS(:,11).*CONSTANTS(:,12))) - exp(ALGEBRAIC(:,7)./( CONSTANTS(:,11).*CONSTANTS(:,12))));
RATES(:,3) = - ALGEBRAIC(:,9);
ALGEBRAIC(:,5) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,8).*STATES(:,5));
ALGEBRAIC(:,6) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,9).*STATES(:,6));
ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,7))./( CONSTANTS(:,11).*CONSTANTS(:,12))) - exp((ALGEBRAIC(:,4)+ALGEBRAIC(:,5))./( CONSTANTS(:,11).*CONSTANTS(:,12))));
RATES(:,4) = (ALGEBRAIC(:,8) - ALGEBRAIC(:,9))+ALGEBRAIC(:,10);
RATES(:,5) = ALGEBRAIC(:,10);
RATES(:,6) = - ALGEBRAIC(:,10);
RATES(:,7) = ALGEBRAIC(:,9) - 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(:,1) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,4).*STATES(:,1));
ALGEBRAIC(:,2) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,5).*STATES(:,2));
ALGEBRAIC(:,4) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,7).*STATES(:,4));
ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,11).*CONSTANTS(:,12))) - exp(ALGEBRAIC(:,4)./( CONSTANTS(:,11).*CONSTANTS(:,12))));
ALGEBRAIC(:,3) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,6).*STATES(:,3));
ALGEBRAIC(:,7) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,10).*STATES(:,7));
ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp((ALGEBRAIC(:,4)+ALGEBRAIC(:,3))./( CONSTANTS(:,11).*CONSTANTS(:,12))) - exp(ALGEBRAIC(:,7)./( CONSTANTS(:,11).*CONSTANTS(:,12))));
ALGEBRAIC(:,5) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,8).*STATES(:,5));
ALGEBRAIC(:,6) = CONSTANTS(:,11).*CONSTANTS(:,12).*log( CONSTANTS(:,9).*STATES(:,6));
ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,7))./( CONSTANTS(:,11).*CONSTANTS(:,12))) - exp((ALGEBRAIC(:,4)+ALGEBRAIC(:,5))./( CONSTANTS(:,11).*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