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 =18;
end
% There are a total of 4 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 (second)');
LEGEND_STATES(:,1) = strpad('HCO3_int in component concentrations (mM)');
LEGEND_STATES(:,2) = strpad('HCO3_ext in component concentrations (mM)');
LEGEND_STATES(:,3) = strpad('Cl_int in component concentrations (mM)');
LEGEND_STATES(:,4) = strpad('Cl_ext in component concentrations (mM)');
LEGEND_ALGEBRAIC(:,13) = strpad('J_AE1_HCO3 in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,18) = strpad('J_AE1_Cl in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,14) = strpad('J_HCO3_influx in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,15) = strpad('J_Cl_influx in component AE1 (mM_per_s)');
LEGEND_CONSTANTS(:,1) = strpad('K_HCO3_ext in component AE1 (mM)');
LEGEND_CONSTANTS(:,2) = strpad('K_HCO3_int in component AE1 (mM)');
LEGEND_CONSTANTS(:,3) = strpad('K_Cl_ext in component AE1 (mM)');
LEGEND_CONSTANTS(:,4) = strpad('K_Cl_int in component AE1 (mM)');
LEGEND_CONSTANTS(:,5) = strpad('P_HCO3_ext in component AE1 (per_s)');
LEGEND_CONSTANTS(:,6) = strpad('P_HCO3_int in component AE1 (per_s)');
LEGEND_CONSTANTS(:,7) = strpad('P_Cl_ext in component AE1 (per_s)');
LEGEND_CONSTANTS(:,8) = strpad('P_Cl_int in component AE1 (per_s)');
LEGEND_ALGEBRAIC(:,2) = strpad('beta_ext in component AE1 (dimensionless)');
LEGEND_ALGEBRAIC(:,9) = strpad('beta_int in component AE1 (dimensionless)');
LEGEND_ALGEBRAIC(:,10) = strpad('gamma_ext in component AE1 (dimensionless)');
LEGEND_ALGEBRAIC(:,11) = strpad('gamma_int in component AE1 (dimensionless)');
LEGEND_ALGEBRAIC(:,12) = strpad('sigma in component AE1 (per_s)');
LEGEND_CONSTANTS(:,9) = strpad('x_Tmax in component AE1 (mM)');
LEGEND_CONSTANTS(:,10) = strpad('K_I in component AE1 (mM)');
LEGEND_ALGEBRAIC(:,1) = strpad('x_T in component AE1 (mM)');
LEGEND_ALGEBRAIC(:,16) = strpad('x_ext in component AE1 (mM)');
LEGEND_ALGEBRAIC(:,17) = strpad('x_int in component AE1 (mM)');
LEGEND_ALGEBRAIC(:,3) = strpad('Jo_bm in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,4) = strpad('Ji_bm in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,5) = strpad('Js_bm in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,6) = strpad('Jo_cm in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,7) = strpad('Ji_cm in component AE1 (mM_per_s)');
LEGEND_ALGEBRAIC(:,8) = strpad('Js_cm in component AE1 (mM_per_s)');
LEGEND_RATES(:,1) = strpad('d/dt HCO3_int in component concentrations (mM)');
LEGEND_RATES(:,2) = strpad('d/dt HCO3_ext in component concentrations (mM)');
LEGEND_RATES(:,3) = strpad('d/dt Cl_int in component concentrations (mM)');
LEGEND_RATES(:,4) = strpad('d/dt Cl_ext in component concentrations (mM)');
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) = 26.0;
STATES(:,2) = 26.0;
STATES(:,3) = 1.0;
STATES(:,4) = 114.0;
CONSTANTS(:,1) = 198;
CONSTANTS(:,2) = 198;
CONSTANTS(:,3) = 50;
CONSTANTS(:,4) = 50;
CONSTANTS(:,5) = 1247;
CONSTANTS(:,6) = 135;
CONSTANTS(:,7) = 562;
CONSTANTS(:,8) = 61;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 172;
CONSTANTS(:,10) = 0.00000;
CONSTANTS(:,11) = 0.00000;
CONSTANTS(:,12) = 1.00000;
CONSTANTS(:,13) = 0.00000;
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(:,10);
RATES(:,2) = CONSTANTS(:,11);
RATES(:,3) = CONSTANTS(:,12);
RATES(:,4) = CONSTANTS(:,13);
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(:,9)./(1.00000+STATES(:,1)./CONSTANTS(:,10));
ALGEBRAIC(:,2) = STATES(:,2)./CONSTANTS(:,1);
ALGEBRAIC(:,3) = power( (1.00000./ALGEBRAIC(:,1)).*(1.00000./CONSTANTS(:,5)+1.00000./CONSTANTS(:,6)+CONSTANTS(:,2)./( CONSTANTS(:,6).*STATES(:,1))), - 1.00000);
ALGEBRAIC(:,4) = power( (1.00000./ALGEBRAIC(:,1)).*(1.00000./CONSTANTS(:,5)+1.00000./CONSTANTS(:,6)+CONSTANTS(:,1)./( CONSTANTS(:,5).*STATES(:,2))), - 1.00000);
ALGEBRAIC(:,5) = power( (1.00000./ALGEBRAIC(:,1)).*(1.00000./CONSTANTS(:,5)+1.00000./CONSTANTS(:,6)), - 1.00000);
ALGEBRAIC(:,6) = power( (1.00000./ALGEBRAIC(:,1)).*(1.00000./CONSTANTS(:,7)+1.00000./CONSTANTS(:,8)+CONSTANTS(:,4)./( CONSTANTS(:,8).*STATES(:,3))), - 1.00000);
ALGEBRAIC(:,7) = power( (1.00000./ALGEBRAIC(:,1)).*(1.00000./CONSTANTS(:,7)+1.00000./CONSTANTS(:,8)+CONSTANTS(:,3)./( CONSTANTS(:,7).*STATES(:,4))), - 1.00000);
ALGEBRAIC(:,8) = power( (1.00000./ALGEBRAIC(:,1)).*(1.00000./CONSTANTS(:,7)+1.00000./CONSTANTS(:,8)), - 1.00000);
ALGEBRAIC(:,9) = STATES(:,1)./CONSTANTS(:,2);
ALGEBRAIC(:,10) = STATES(:,4)./CONSTANTS(:,3);
ALGEBRAIC(:,11) = STATES(:,3)./CONSTANTS(:,4);
ALGEBRAIC(:,12) = (1.00000+ALGEBRAIC(:,2)+ALGEBRAIC(:,10)).*( CONSTANTS(:,6).*ALGEBRAIC(:,9)+ CONSTANTS(:,8).*ALGEBRAIC(:,11))+ (1.00000+ALGEBRAIC(:,9)+ALGEBRAIC(:,11)).*( CONSTANTS(:,5).*ALGEBRAIC(:,2)+ CONSTANTS(:,7).*ALGEBRAIC(:,10));
ALGEBRAIC(:,13) = (ALGEBRAIC(:,1)./ALGEBRAIC(:,12)).*( CONSTANTS(:,6).*ALGEBRAIC(:,9).*CONSTANTS(:,7).*ALGEBRAIC(:,10) - CONSTANTS(:,5).*ALGEBRAIC(:,2).*CONSTANTS(:,8).*ALGEBRAIC(:,11));
ALGEBRAIC(:,14) = (ALGEBRAIC(:,1)./ALGEBRAIC(:,12)).*CONSTANTS(:,5).*ALGEBRAIC(:,2).*( CONSTANTS(:,6).*ALGEBRAIC(:,9)+ CONSTANTS(:,8).*ALGEBRAIC(:,11));
ALGEBRAIC(:,15) = (ALGEBRAIC(:,1)./ALGEBRAIC(:,12)).*CONSTANTS(:,7).*ALGEBRAIC(:,10).*( CONSTANTS(:,6).*ALGEBRAIC(:,9)+ CONSTANTS(:,8).*ALGEBRAIC(:,11));
ALGEBRAIC(:,16) = ( ALGEBRAIC(:,1).*( CONSTANTS(:,6).*ALGEBRAIC(:,9)+ CONSTANTS(:,8).*ALGEBRAIC(:,11)))./ALGEBRAIC(:,12);
ALGEBRAIC(:,17) = ( ALGEBRAIC(:,1).*( CONSTANTS(:,5).*ALGEBRAIC(:,2)+ CONSTANTS(:,7).*ALGEBRAIC(:,10)))./ALGEBRAIC(:,12);
ALGEBRAIC(:,18) = - ALGEBRAIC(:,13);
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