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 =8;
end
% There are a total of 6 entries in each of the rate and state variable arrays.
% There are a total of 21 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 (min)');
LEGEND_CONSTANTS(:,1) = strpad('Vp in component environment (l)');
LEGEND_CONSTANTS(:,2) = strpad('Vi in component environment (l)');
LEGEND_CONSTANTS(:,3) = strpad('Vg in component environment (l)');
LEGEND_CONSTANTS(:,4) = strpad('E in component environment (l_per_min)');
LEGEND_STATES(:,1) = strpad('Ip in component plasma_insulin (mU)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ip_conc in component plasma_insulin (mU_per_l)');
LEGEND_CONSTANTS(:,5) = strpad('tp in component plasma_insulin (min)');
LEGEND_ALGEBRAIC(:,2) = strpad('f1_G in component plasma_insulin (mU_per_min)');
LEGEND_CONSTANTS(:,6) = strpad('Rm in component plasma_insulin (mU_per_min)');
LEGEND_CONSTANTS(:,7) = strpad('C1 in component plasma_insulin (mg_per_l)');
LEGEND_CONSTANTS(:,8) = strpad('a1 in component plasma_insulin (mg_per_l)');
LEGEND_STATES(:,2) = strpad('Ii in component intercellular_insulin (mU)');
LEGEND_STATES(:,3) = strpad('G in component glucose (mg)');
LEGEND_ALGEBRAIC(:,3) = strpad('Ii_conc in component intercellular_insulin (mU_per_l)');
LEGEND_CONSTANTS(:,9) = strpad('ti in component intercellular_insulin (min)');
LEGEND_ALGEBRAIC(:,4) = strpad('G_conc in component glucose (mg_per_dl)');
LEGEND_CONSTANTS(:,10) = strpad('Gin in component glucose (mg_per_min)');
LEGEND_ALGEBRAIC(:,5) = strpad('f2_G in component glucose (mg_per_min)');
LEGEND_ALGEBRAIC(:,6) = strpad('f3_G in component glucose (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('f4_Ii in component glucose (mg_per_min)');
LEGEND_ALGEBRAIC(:,8) = strpad('f5_x3 in component glucose (mg_per_min)');
LEGEND_CONSTANTS(:,11) = strpad('C2 in component glucose (mg_per_l)');
LEGEND_CONSTANTS(:,12) = strpad('C3 in component glucose (mg_per_l)');
LEGEND_CONSTANTS(:,13) = strpad('C4 in component glucose (mU_per_l)');
LEGEND_CONSTANTS(:,14) = strpad('C5 in component glucose (mU_per_l)');
LEGEND_CONSTANTS(:,15) = strpad('U0 in component glucose (mg_per_min)');
LEGEND_CONSTANTS(:,16) = strpad('Um in component glucose (mg_per_min)');
LEGEND_CONSTANTS(:,17) = strpad('Ub in component glucose (mg_per_min)');
LEGEND_CONSTANTS(:,18) = strpad('beta in component glucose (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('Rg in component glucose (mg_per_min)');
LEGEND_CONSTANTS(:,20) = strpad('alpha in component glucose (l_per_mU)');
LEGEND_STATES(:,4) = strpad('x3 in component delay (min)');
LEGEND_CONSTANTS(:,21) = strpad('td in component delay (min)');
LEGEND_STATES(:,5) = strpad('x1 in component delay (min)');
LEGEND_STATES(:,6) = strpad('x2 in component delay (min)');
LEGEND_RATES(:,1) = strpad('d/dt Ip in component plasma_insulin (mU)');
LEGEND_RATES(:,2) = strpad('d/dt Ii in component intercellular_insulin (mU)');
LEGEND_RATES(:,3) = strpad('d/dt G in component glucose (mg)');
LEGEND_RATES(:,5) = strpad('d/dt x1 in component delay (min)');
LEGEND_RATES(:,6) = strpad('d/dt x2 in component delay (min)');
LEGEND_RATES(:,4) = strpad('d/dt x3 in component delay (min)');
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) = 3;
CONSTANTS(:,2) = 11;
CONSTANTS(:,3) = 10;
CONSTANTS(:,4) = 0.2;
STATES(:,1) = 93.36441699;
CONSTANTS(:,5) = 6;
CONSTANTS(:,6) = 210;
CONSTANTS(:,7) = 2000;
CONSTANTS(:,8) = 300;
STATES(:,2) = 243.2865183;
STATES(:,3) = 12342.61665;
CONSTANTS(:,9) = 100;
CONSTANTS(:,10) = 216;
CONSTANTS(:,11) = 144;
CONSTANTS(:,12) = 1000;
CONSTANTS(:,13) = 80;
CONSTANTS(:,14) = 26;
CONSTANTS(:,15) = 40;
CONSTANTS(:,16) = 940;
CONSTANTS(:,17) = 72;
CONSTANTS(:,18) = 1.77;
CONSTANTS(:,19) = 180;
CONSTANTS(:,20) = 0.29;
STATES(:,4) = 104.5878705;
CONSTANTS(:,21) = 36;
STATES(:,5) = 110.420253;
STATES(:,6) = 112.7601171;
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(:,2) = CONSTANTS(:,4).*(STATES(:,1)./CONSTANTS(:,1) - STATES(:,2)./CONSTANTS(:,2)) - STATES(:,2)./CONSTANTS(:,9);
RATES(:,5) = (3.00000./CONSTANTS(:,21)).*(STATES(:,1)./1.00000 - STATES(:,5));
RATES(:,6) = (3.00000./CONSTANTS(:,21)).*(STATES(:,5) - STATES(:,6));
RATES(:,4) = (3.00000./CONSTANTS(:,21)).*(STATES(:,6) - STATES(:,4));
ALGEBRAIC(:,2) = CONSTANTS(:,6)./(1.00000+exp((CONSTANTS(:,7) - STATES(:,3)./CONSTANTS(:,3))./CONSTANTS(:,8)));
RATES(:,1) = ALGEBRAIC(:,2) - ( CONSTANTS(:,4).*(STATES(:,1)./CONSTANTS(:,1) - STATES(:,2)./CONSTANTS(:,2))+STATES(:,1)./CONSTANTS(:,5));
ALGEBRAIC(:,5) = CONSTANTS(:,17).*(1.00000 - exp( - STATES(:,3)./( CONSTANTS(:,11).*CONSTANTS(:,3))));
ALGEBRAIC(:,6) = STATES(:,3)./( CONSTANTS(:,12).*CONSTANTS(:,3));
ALGEBRAIC(:,7) = CONSTANTS(:,15)+(CONSTANTS(:,16) - CONSTANTS(:,15))./(1.00000+exp( - CONSTANTS(:,18).*log( (STATES(:,2)./CONSTANTS(:,13)).*(1.00000./CONSTANTS(:,2)+1.00000./( CONSTANTS(:,4).*CONSTANTS(:,9))))));
ALGEBRAIC(:,8) = CONSTANTS(:,19)./(1.00000+exp( CONSTANTS(:,20).*(( STATES(:,4).*1.00000)./CONSTANTS(:,1) - CONSTANTS(:,14))));
RATES(:,3) = CONSTANTS(:,10)+ALGEBRAIC(:,8)+ - (ALGEBRAIC(:,5)+ ALGEBRAIC(:,6).*ALGEBRAIC(:,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(:,2) = CONSTANTS(:,6)./(1.00000+exp((CONSTANTS(:,7) - STATES(:,3)./CONSTANTS(:,3))./CONSTANTS(:,8)));
ALGEBRAIC(:,5) = CONSTANTS(:,17).*(1.00000 - exp( - STATES(:,3)./( CONSTANTS(:,11).*CONSTANTS(:,3))));
ALGEBRAIC(:,6) = STATES(:,3)./( CONSTANTS(:,12).*CONSTANTS(:,3));
ALGEBRAIC(:,7) = CONSTANTS(:,15)+(CONSTANTS(:,16) - CONSTANTS(:,15))./(1.00000+exp( - CONSTANTS(:,18).*log( (STATES(:,2)./CONSTANTS(:,13)).*(1.00000./CONSTANTS(:,2)+1.00000./( CONSTANTS(:,4).*CONSTANTS(:,9))))));
ALGEBRAIC(:,8) = CONSTANTS(:,19)./(1.00000+exp( CONSTANTS(:,20).*(( STATES(:,4).*1.00000)./CONSTANTS(:,1) - CONSTANTS(:,14))));
ALGEBRAIC(:,1) = STATES(:,1)./CONSTANTS(:,1);
ALGEBRAIC(:,3) = STATES(:,2)./CONSTANTS(:,2);
ALGEBRAIC(:,4) = STATES(:,3)./( CONSTANTS(:,3).*10.0000);
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