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 =12;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 26 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 (hour)');
LEGEND_STATES(:,1) = strpad('Cgen_pp in component Cgen_pp (micromolar)');
LEGEND_CONSTANTS(:,23) = strpad('Qpp in component Cgen_pp (litre_hour)');
LEGEND_CONSTANTS(:,1) = strpad('Ppp in component Cgen_pp (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('H_Cgen_pp in component Cgen_pp (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('Vpp in component Cgen_pp (litre)');
LEGEND_ALGEBRAIC(:,9) = strpad('H_Cgen_B in component Cgen_B (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('Qt in component model_parameters (litre_hour)');
LEGEND_ALGEBRAIC(:,7) = strpad('Cgen_B in component Cgen_B (micromolar)');
LEGEND_STATES(:,2) = strpad('Cgen_rp in component Cgen_rp (micromolar)');
LEGEND_CONSTANTS(:,3) = strpad('Prp in component Cgen_rp (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('Qrp in component Cgen_rp (litre_hour)');
LEGEND_ALGEBRAIC(:,2) = strpad('H_Cgen_rp in component Cgen_rp (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('Vrp in component Cgen_rp (litre)');
LEGEND_CONSTANTS(:,5) = strpad('kgen_urine in component Cgen_rp (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('Cgen_l in component Cgen_l (micromolar)');
LEGEND_CONSTANTS(:,25) = strpad('Ql in component Cgen_l (litre_hour)');
LEGEND_ALGEBRAIC(:,3) = strpad('H_Cgen_l in component Cgen_l (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('Vl in component Cgen_l (litre)');
LEGEND_CONSTANTS(:,7) = strpad('Pl in component Cgen_l (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('Vmax in component model_parameters (micromolar_hour)');
LEGEND_CONSTANTS(:,9) = strpad('Km in component model_parameters (micromolar)');
LEGEND_ALGEBRAIC(:,12) = strpad('vinf in component model_parameters (micromole_hour)');
LEGEND_ALGEBRAIC(:,4) = strpad('H_Cgen_GI in component Cgen_GI (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('QGI in component Cgen_GI (litre_hour)');
LEGEND_STATES(:,4) = strpad('Cgen_GI in component Cgen_GI (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('VGI in component Cgen_GI (litre)');
LEGEND_STATES(:,5) = strpad('Ccon_l in component Ccon_l (micromolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('H_Ccon_l in component Ccon_l (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('kbile in component model_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,8) = strpad('H_Ccon_ROB in component Ccon_ROB (dimensionless)');
LEGEND_STATES(:,6) = strpad('Ccon_ROB in component Ccon_ROB (micromolar)');
LEGEND_CONSTANTS(:,12) = strpad('VROB in component Ccon_ROB (litre)');
LEGEND_CONSTANTS(:,13) = strpad('kcon_urine in component Ccon_ROB (first_order_rate_constant)');
LEGEND_STATES(:,7) = strpad('Acon_b in component Acon_b (micromole)');
LEGEND_ALGEBRAIC(:,6) = strpad('d_t_Cgen_l in component Acon_b (hour)');
LEGEND_CONSTANTS(:,14) = strpad('tbasal in component Acon_b (hour)');
LEGEND_CONSTANTS(:,15) = strpad('ct in component Acon_b (hour)');
LEGEND_CONSTANTS(:,16) = strpad('cgen in component Acon_b (litre_hour_micromole)');
LEGEND_CONSTANTS(:,17) = strpad('cv in component model_parameters (micromole_hour)');
LEGEND_ALGEBRAIC(:,10) = strpad('F in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('G in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,11) = strpad('H in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('I in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('epsilon in component model_parameters (hour)');
LEGEND_CONSTANTS(:,19) = strpad('m_rat in component model_parameters (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt Cgen_pp in component Cgen_pp (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt Cgen_rp in component Cgen_rp (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt Cgen_l in component Cgen_l (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt Cgen_GI in component Cgen_GI (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt Ccon_l in component Ccon_l (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt Ccon_ROB in component Ccon_ROB (micromolar)');
LEGEND_RATES(:,7) = strpad('d/dt Acon_b in component Acon_b (micromole)');
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;
CONSTANTS(:,1) = 0.59;
CONSTANTS(:,2) = 0.188;
STATES(:,2) = 0;
CONSTANTS(:,3) = 1.94;
CONSTANTS(:,4) = 0.012;
CONSTANTS(:,5) = 9.5;
STATES(:,3) = 0;
CONSTANTS(:,6) = 0.0092;
CONSTANTS(:,7) = 3.61;
CONSTANTS(:,8) = 25.25;
CONSTANTS(:,9) = 0.6231;
STATES(:,4) = 0;
CONSTANTS(:,10) = 0.011;
STATES(:,5) = 0;
CONSTANTS(:,11) = 111.72;
STATES(:,6) = 0;
CONSTANTS(:,12) = 0.2408;
CONSTANTS(:,13) = 0.0;
STATES(:,7) = 0;
CONSTANTS(:,14) = 0.0865;
CONSTANTS(:,15) = 1.0107;
CONSTANTS(:,16) = 0.06561;
CONSTANTS(:,17) = 1.0;
CONSTANTS(:,18) = 0.1;
CONSTANTS(:,19) = 0.25;
CONSTANTS(:,20) = 14.1000.*power(CONSTANTS(:,19), 0.750000);
CONSTANTS(:,21) = 1.00000;
CONSTANTS(:,22) = 0.00000;
CONSTANTS(:,23) = 0.528000.*CONSTANTS(:,20);
CONSTANTS(:,24) = 0.289000.*CONSTANTS(:,20);
CONSTANTS(:,25) = 0.0300000.*CONSTANTS(:,20);
CONSTANTS(:,26) = 0.153000.*CONSTANTS(:,20);
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(:,5) = piecewise({STATES(:,5)<0.00000, 0.00000 }, 1.00000);
RATES(:,7) = CONSTANTS(:,11).*ALGEBRAIC(:,5).*STATES(:,5).*CONSTANTS(:,6);
ALGEBRAIC(:,3) = piecewise({STATES(:,3)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,8) = piecewise({STATES(:,6)<0.00000, 0.00000 }, 1.00000);
RATES(:,5) = ( CONSTANTS(:,8).*ALGEBRAIC(:,3).*STATES(:,3))./(CONSTANTS(:,9)+ ALGEBRAIC(:,3).*STATES(:,3)) - ( CONSTANTS(:,11).*ALGEBRAIC(:,5).*STATES(:,5)+( (CONSTANTS(:,25)+CONSTANTS(:,26)).*( ALGEBRAIC(:,5).*STATES(:,5) - ALGEBRAIC(:,8).*STATES(:,6)))./CONSTANTS(:,6));
RATES(:,6) = ( (CONSTANTS(:,25)+CONSTANTS(:,26)).*( ALGEBRAIC(:,5).*STATES(:,5) - ALGEBRAIC(:,8).*STATES(:,6)))./CONSTANTS(:,12) - CONSTANTS(:,13).*ALGEBRAIC(:,8).*STATES(:,6);
ALGEBRAIC(:,1) = piecewise({STATES(:,1)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,2) = piecewise({STATES(:,2)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,7) = (( CONSTANTS(:,24).*ALGEBRAIC(:,2).*STATES(:,2))./CONSTANTS(:,3)+( CONSTANTS(:,23).*ALGEBRAIC(:,1).*STATES(:,1))./CONSTANTS(:,1)+( (CONSTANTS(:,25)+CONSTANTS(:,26)).*ALGEBRAIC(:,3).*STATES(:,3))./CONSTANTS(:,7))./CONSTANTS(:,20);
ALGEBRAIC(:,9) = piecewise({ALGEBRAIC(:,7)<0.00000, 0.00000 }, 1.00000);
RATES(:,1) = ( CONSTANTS(:,23).*ALGEBRAIC(:,9).*ALGEBRAIC(:,7) - ( CONSTANTS(:,23).*ALGEBRAIC(:,1).*STATES(:,1))./CONSTANTS(:,1))./CONSTANTS(:,2);
RATES(:,2) = ( CONSTANTS(:,24).*ALGEBRAIC(:,9).*ALGEBRAIC(:,7) - ( CONSTANTS(:,24).*ALGEBRAIC(:,2).*STATES(:,2))./CONSTANTS(:,3))./CONSTANTS(:,4) - CONSTANTS(:,5).*ALGEBRAIC(:,2).*STATES(:,2);
ALGEBRAIC(:,4) = piecewise({STATES(:,4)<0.00000, 0.00000 }, 1.00000);
RATES(:,4) = ( CONSTANTS(:,26).*ALGEBRAIC(:,9).*ALGEBRAIC(:,7) - ( CONSTANTS(:,26).*ALGEBRAIC(:,4).*STATES(:,4))./CONSTANTS(:,3))./CONSTANTS(:,10);
ALGEBRAIC(:,10) = (-2.00000./power(CONSTANTS(:,18), 3.00000)).*power(VOI, 3.00000)+ (3.00000./power(CONSTANTS(:,18), 2.00000)).*power(VOI, 2.00000);
ALGEBRAIC(:,11) = ( 3.00000.*power(1.00000 - VOI, 2.00000))./power(CONSTANTS(:,18), 2.00000) - ( 2.00000.*power(1.00000 - VOI, 3.00000))./power(CONSTANTS(:,18), 3.00000);
ALGEBRAIC(:,12) = piecewise({VOI<CONSTANTS(:,18)&VOI>=0.00000, CONSTANTS(:,17).*ALGEBRAIC(:,10) , VOI<=1.00000 - CONSTANTS(:,18)&VOI>=CONSTANTS(:,18), CONSTANTS(:,17).*CONSTANTS(:,21) , VOI<=1.00000&VOI>1.00000 - CONSTANTS(:,18), CONSTANTS(:,17).*ALGEBRAIC(:,11) , VOI<=1.00000+5.00000./60.0000&VOI>1.00000, CONSTANTS(:,17).*CONSTANTS(:,22) }, NaN);
RATES(:,3) = (( CONSTANTS(:,25).*ALGEBRAIC(:,9).*ALGEBRAIC(:,7) - ( (CONSTANTS(:,25)+CONSTANTS(:,26)).*ALGEBRAIC(:,3).*STATES(:,3))./CONSTANTS(:,7))+ALGEBRAIC(:,12)+( CONSTANTS(:,26).*ALGEBRAIC(:,4).*STATES(:,4))./CONSTANTS(:,3))./CONSTANTS(:,6) - ( CONSTANTS(:,8).*ALGEBRAIC(:,3).*STATES(:,3))./(CONSTANTS(:,9)+ ALGEBRAIC(:,3).*STATES(:,3));
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(:,5) = piecewise({STATES(:,5)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,3) = piecewise({STATES(:,3)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,8) = piecewise({STATES(:,6)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,1) = piecewise({STATES(:,1)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,2) = piecewise({STATES(:,2)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,7) = (( CONSTANTS(:,24).*ALGEBRAIC(:,2).*STATES(:,2))./CONSTANTS(:,3)+( CONSTANTS(:,23).*ALGEBRAIC(:,1).*STATES(:,1))./CONSTANTS(:,1)+( (CONSTANTS(:,25)+CONSTANTS(:,26)).*ALGEBRAIC(:,3).*STATES(:,3))./CONSTANTS(:,7))./CONSTANTS(:,20);
ALGEBRAIC(:,9) = piecewise({ALGEBRAIC(:,7)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,4) = piecewise({STATES(:,4)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,10) = (-2.00000./power(CONSTANTS(:,18), 3.00000)).*power(VOI, 3.00000)+ (3.00000./power(CONSTANTS(:,18), 2.00000)).*power(VOI, 2.00000);
ALGEBRAIC(:,11) = ( 3.00000.*power(1.00000 - VOI, 2.00000))./power(CONSTANTS(:,18), 2.00000) - ( 2.00000.*power(1.00000 - VOI, 3.00000))./power(CONSTANTS(:,18), 3.00000);
ALGEBRAIC(:,12) = piecewise({VOI<CONSTANTS(:,18)&VOI>=0.00000, CONSTANTS(:,17).*ALGEBRAIC(:,10) , VOI<=1.00000 - CONSTANTS(:,18)&VOI>=CONSTANTS(:,18), CONSTANTS(:,17).*CONSTANTS(:,21) , VOI<=1.00000&VOI>1.00000 - CONSTANTS(:,18), CONSTANTS(:,17).*ALGEBRAIC(:,11) , VOI<=1.00000+5.00000./60.0000&VOI>1.00000, CONSTANTS(:,17).*CONSTANTS(:,22) }, NaN);
ALGEBRAIC(:,6) = CONSTANTS(:,14)+ CONSTANTS(:,16).*ALGEBRAIC(:,3).*STATES(:,3).*exp( - (VOI./CONSTANTS(:,15)));
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