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 =2;
end
% There are a total of 13 entries in each of the rate and state variable arrays.
% There are a total of 30 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('cAMP in component cAMP (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('Ko in component cAMP (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('Ka in component cAMP (per_micromolar)');
LEGEND_CONSTANTS(:,3) = strpad('Kb in component cAMP (per_micromolar)');
LEGEND_CONSTANTS(:,4) = strpad('Kdsm in component cAMP (micromolar)');
LEGEND_CONSTANTS(:,5) = strpad('Vmsm in component cAMP (flux)');
LEGEND_CONSTANTS(:,6) = strpad('Vdsm in component cAMP (flux)');
LEGEND_ALGEBRAIC(:,1) = strpad('ACTH in component cAMP (micromolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('IS in component IS (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('Crpt in component IS (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('K in component IS (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('Kd in component IS (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('n in component IS (dimensionless)');
LEGEND_STATES(:,2) = strpad('V in component V (flux)');
LEGEND_CONSTANTS(:,11) = strpad('P in component V (micromolar_per_minute2)');
LEGEND_CONSTANTS(:,12) = strpad('Q in component V (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('W in component W (flux)');
LEGEND_CONSTANTS(:,13) = strpad('T in component W (micromolar2_per_minute2)');
LEGEND_CONSTANTS(:,14) = strpad('U in component W (first_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('CHOC in component CHOC (micromolar)');
LEGEND_CONSTANTS(:,15) = strpad('Lmtr in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,5) = strpad('Kmtr in component Kmtr (first_order_rate_constant)');
LEGEND_STATES(:,6) = strpad('CHOM in component CHOM (micromolar)');
LEGEND_CONSTANTS(:,16) = strpad('Kbac in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,7) = strpad('Kfor in component Kfor (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('Kcb in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('Kcf in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,8) = strpad('CHON in component CHON (micromolar)');
LEGEND_STATES(:,9) = strpad('CHOL in component CHOL (micromolar)');
LEGEND_CONSTANTS(:,19) = strpad('C in component Kmtr (per_minute2)');
LEGEND_CONSTANTS(:,20) = strpad('D in component Kmtr (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('R in component Kfor (per_minute2)');
LEGEND_CONSTANTS(:,22) = strpad('S in component Kfor (first_order_rate_constant)');
LEGEND_CONSTANTS(:,23) = strpad('Vm in component model_parameters (flux)');
LEGEND_CONSTANTS(:,24) = strpad('Km in component model_parameters (micromolar)');
LEGEND_STATES(:,10) = strpad('PREG in component PREG (micromolar)');
LEGEND_CONSTANTS(:,25) = strpad('Vmptr in component model_parameters (flux)');
LEGEND_CONSTANTS(:,26) = strpad('Kmptr in component model_parameters (micromolar)');
LEGEND_STATES(:,11) = strpad('PRO in component PRO (micromolar)');
LEGEND_CONSTANTS(:,27) = strpad('HA in component PRO (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('AH in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,12) = strpad('HYPR in component HYPR (micromolar)');
LEGEND_CONSTANTS(:,29) = strpad('HY in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,13) = strpad('CORT in component CORT (micromolar)');
LEGEND_CONSTANTS(:,30) = strpad('LH in component CORT (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt cAMP in component cAMP (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt V in component V (flux)');
LEGEND_RATES(:,3) = strpad('d/dt W in component W (flux)');
LEGEND_RATES(:,4) = strpad('d/dt CHOC in component CHOC (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt CHOM in component CHOM (micromolar)');
LEGEND_RATES(:,9) = strpad('d/dt CHOL in component CHOL (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt Kmtr in component Kmtr (first_order_rate_constant)');
LEGEND_RATES(:,7) = strpad('d/dt Kfor in component Kfor (first_order_rate_constant)');
LEGEND_RATES(:,8) = strpad('d/dt CHON in component CHON (micromolar)');
LEGEND_RATES(:,10) = strpad('d/dt PREG in component PREG (micromolar)');
LEGEND_RATES(:,11) = strpad('d/dt PRO in component PRO (micromolar)');
LEGEND_RATES(:,12) = strpad('d/dt HYPR in component HYPR (micromolar)');
LEGEND_RATES(:,13) = strpad('d/dt CORT in component CORT (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 = [];
STATES(:,1) = 0.95;
CONSTANTS(:,1) = 0.013;
CONSTANTS(:,2) = 10;
CONSTANTS(:,3) = 1000000.0;
CONSTANTS(:,4) = 10.0;
CONSTANTS(:,5) = 6.0;
CONSTANTS(:,6) = 10.0;
CONSTANTS(:,7) = 3.0;
CONSTANTS(:,8) = 80.0;
CONSTANTS(:,9) = 2.11;
CONSTANTS(:,10) = 4.0;
STATES(:,2) = 11.3;
CONSTANTS(:,11) = 0.052;
CONSTANTS(:,12) = 0.042;
STATES(:,3) = 10.0;
CONSTANTS(:,13) = 8.0;
CONSTANTS(:,14) = 0.0015;
STATES(:,4) = 532.0;
CONSTANTS(:,15) = 1.65;
STATES(:,5) = 0.446;
STATES(:,6) = 139.0;
CONSTANTS(:,16) = 10.0;
STATES(:,7) = 0.370;
CONSTANTS(:,17) = 0.01;
CONSTANTS(:,18) = 0.00033;
STATES(:,8) = 3.03;
STATES(:,9) = 3000.0;
CONSTANTS(:,19) = 6.25;
CONSTANTS(:,20) = 125.0;
CONSTANTS(:,21) = 3.0;
CONSTANTS(:,22) = 76.0;
CONSTANTS(:,23) = 1890.0;
CONSTANTS(:,24) = 270.0;
STATES(:,10) = 6.56;
CONSTANTS(:,25) = 500.0;
CONSTANTS(:,26) = 150.0;
STATES(:,11) = 0.64;
CONSTANTS(:,27) = 0.5;
CONSTANTS(:,28) = 16.4;
STATES(:,12) = 0.64;
CONSTANTS(:,29) = 16.4;
STATES(:,13) = 5.2;
CONSTANTS(:,30) = 0.724;
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(:,3) = CONSTANTS(:,13).*power(STATES(:,4), -1.00000) - CONSTANTS(:,14).*STATES(:,3);
RATES(:,4) = (STATES(:,2)+STATES(:,3)+ CONSTANTS(:,15).*STATES(:,6)) - STATES(:,5).*STATES(:,4);
RATES(:,6) = ( STATES(:,5).*STATES(:,4)+ CONSTANTS(:,16).*STATES(:,8)+ CONSTANTS(:,18).*STATES(:,9)) - ( CONSTANTS(:,15).*STATES(:,6)+ CONSTANTS(:,17).*STATES(:,6)+ STATES(:,7).*STATES(:,6));
RATES(:,9) = CONSTANTS(:,17).*STATES(:,6) - CONSTANTS(:,18).*STATES(:,9);
RATES(:,8) = STATES(:,7).*STATES(:,6) - ( CONSTANTS(:,16).*STATES(:,8)+( CONSTANTS(:,23).*STATES(:,8))./(CONSTANTS(:,24)+STATES(:,8)));
RATES(:,10) = ( CONSTANTS(:,23).*STATES(:,8))./(CONSTANTS(:,24)+STATES(:,8)) - ( CONSTANTS(:,25).*STATES(:,10))./(CONSTANTS(:,26)+STATES(:,10));
RATES(:,11) = CONSTANTS(:,27).*(( CONSTANTS(:,25).*STATES(:,10))./(CONSTANTS(:,26)+STATES(:,10))) - CONSTANTS(:,28).*STATES(:,11);
RATES(:,12) = CONSTANTS(:,28).*STATES(:,11) - CONSTANTS(:,29).*STATES(:,12);
RATES(:,13) = CONSTANTS(:,29).*STATES(:,12) - CONSTANTS(:,30).*STATES(:,13);
ALGEBRAIC(:,1) = piecewise({VOI>=0.00000&VOI<10.0000, 1.20000e-05 , VOI>=10.0000&VOI<20.0000, 1.60000e-05 , VOI>=20.0000&VOI<35.0000, 1.20000e-05 , VOI>=35.0000&VOI<45.0000, 1.60000e-05 }, 1.20000e-05);
RATES(:,1) = ( CONSTANTS(:,5).*CONSTANTS(:,1).*(1.00000+ CONSTANTS(:,3).*ALGEBRAIC(:,1)))./((1.00000+ CONSTANTS(:,2).*ALGEBRAIC(:,1))+ CONSTANTS(:,1).*(1.00000+ CONSTANTS(:,3).*ALGEBRAIC(:,1))) - ( CONSTANTS(:,6).*STATES(:,1))./(CONSTANTS(:,4)+STATES(:,1));
ALGEBRAIC(:,2) = ( CONSTANTS(:,8).*CONSTANTS(:,7).*power(STATES(:,1), CONSTANTS(:,10)))./(power(CONSTANTS(:,9), CONSTANTS(:,10))+power(STATES(:,1), CONSTANTS(:,10)));
RATES(:,2) = CONSTANTS(:,11).*ALGEBRAIC(:,2) - CONSTANTS(:,12).*STATES(:,2);
RATES(:,5) = CONSTANTS(:,19).*ALGEBRAIC(:,2) - CONSTANTS(:,20).*STATES(:,5);
RATES(:,7) = CONSTANTS(:,21).*ALGEBRAIC(:,2) - CONSTANTS(:,22).*STATES(:,7);
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) = piecewise({VOI>=0.00000&VOI<10.0000, 1.20000e-05 , VOI>=10.0000&VOI<20.0000, 1.60000e-05 , VOI>=20.0000&VOI<35.0000, 1.20000e-05 , VOI>=35.0000&VOI<45.0000, 1.60000e-05 }, 1.20000e-05);
ALGEBRAIC(:,2) = ( CONSTANTS(:,8).*CONSTANTS(:,7).*power(STATES(:,1), CONSTANTS(:,10)))./(power(CONSTANTS(:,9), CONSTANTS(:,10))+power(STATES(:,1), CONSTANTS(:,10)));
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
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