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 =6;
end
% There are a total of 12 entries in each of the rate and state variable arrays.
% There are a total of 43 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('Asp in component Asp (millimolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('vAKI in component vAKI (flux)');
LEGEND_ALGEBRAIC(:,5) = strpad('vAKIII in component vAKIII (flux)');
LEGEND_STATES(:,2) = strpad('aspp in component aspp (millimolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('vASD in component vASD (flux)');
LEGEND_STATES(:,3) = strpad('ASA in component ASA (millimolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('vHDH in component vHDH (flux)');
LEGEND_STATES(:,4) = strpad('hs in component hs (millimolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('vHK in component vHK (flux)');
LEGEND_STATES(:,5) = strpad('hsp in component hsp (millimolar)');
LEGEND_ALGEBRAIC(:,6) = strpad('vTS in component vTS (flux)');
LEGEND_STATES(:,6) = strpad('Thr in component Thr (millimolar)');
LEGEND_STATES(:,7) = strpad('ATP in component ATP (millimolar)');
LEGEND_STATES(:,8) = strpad('ADP in component ADP (millimolar)');
LEGEND_STATES(:,9) = strpad('NADPH in component NADPH (millimolar)');
LEGEND_STATES(:,10) = strpad('NADP in component NADP (millimolar)');
LEGEND_STATES(:,11) = strpad('Pi in component Pi (millimolar)');
LEGEND_STATES(:,12) = strpad('Lys in component Lys (millimolar)');
LEGEND_CONSTANTS(:,1) = strpad('K_asp in component vAKI (millimolar)');
LEGEND_CONSTANTS(:,2) = strpad('K_ATP in component vAKI (millimolar)');
LEGEND_CONSTANTS(:,3) = strpad('K_aspp in component vAKI (millimolar)');
LEGEND_CONSTANTS(:,4) = strpad('K_ADP in component vAKI (millimolar)');
LEGEND_CONSTANTS(:,5) = strpad('K_iThr in component vAKI (millimolar)');
LEGEND_CONSTANTS(:,6) = strpad('alpha in component vAKI (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('h_Thr in component vAKI (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('K_eq in component vAKI (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('V_max_AK_I in component vAKI (flux)');
LEGEND_CONSTANTS(:,10) = strpad('K_aspp in component vASD (millimolar)');
LEGEND_CONSTANTS(:,11) = strpad('K_NADPH in component vASD (millimolar)');
LEGEND_CONSTANTS(:,12) = strpad('K_ASA in component vASD (millimolar)');
LEGEND_CONSTANTS(:,13) = strpad('K_NADP in component vASD (millimolar)');
LEGEND_CONSTANTS(:,14) = strpad('K_Pi in component vASD (millimolar)');
LEGEND_CONSTANTS(:,15) = strpad('K_eq in component vASD (millimolar)');
LEGEND_CONSTANTS(:,16) = strpad('V_max_ASD in component vASD (flux)');
LEGEND_CONSTANTS(:,17) = strpad('K_ASA in component vHDH (millimolar)');
LEGEND_CONSTANTS(:,18) = strpad('K_NADPH in component vHDH (millimolar)');
LEGEND_CONSTANTS(:,19) = strpad('K_hs in component vHDH (millimolar)');
LEGEND_CONSTANTS(:,20) = strpad('K_NADP in component vHDH (millimolar)');
LEGEND_CONSTANTS(:,21) = strpad('K_iThr in component vHDH (millimolar)');
LEGEND_CONSTANTS(:,22) = strpad('alpha in component vHDH (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('h in component vHDH (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('K_eq in component vHDH (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('V_max_HDH in component vHDH (flux)');
LEGEND_CONSTANTS(:,26) = strpad('K_hs in component vHK (millimolar)');
LEGEND_CONSTANTS(:,27) = strpad('K_ATP in component vHK (millimolar)');
LEGEND_CONSTANTS(:,28) = strpad('K_iThr in component vHK (millimolar)');
LEGEND_CONSTANTS(:,29) = strpad('K_iLys in component vHK (millimolar)');
LEGEND_CONSTANTS(:,30) = strpad('K_ihs in component vHK (millimolar)');
LEGEND_CONSTANTS(:,31) = strpad('K_iATP in component vHK (millimolar)');
LEGEND_CONSTANTS(:,32) = strpad('V_max_HK in component vHK (flux)');
LEGEND_CONSTANTS(:,33) = strpad('K_hsp in component vTS (millimolar)');
LEGEND_CONSTANTS(:,34) = strpad('V_max_TS in component vTS (flux)');
LEGEND_CONSTANTS(:,35) = strpad('K_asp in component vAKIII (millimolar)');
LEGEND_CONSTANTS(:,36) = strpad('K_ATP in component vAKIII (millimolar)');
LEGEND_CONSTANTS(:,37) = strpad('K_aspp in component vAKIII (millimolar)');
LEGEND_CONSTANTS(:,38) = strpad('K_ADP in component vAKIII (millimolar)');
LEGEND_CONSTANTS(:,39) = strpad('K_iLys in component vAKIII (millimolar)');
LEGEND_CONSTANTS(:,40) = strpad('h_Lys in component vAKIII (dimensionless)');
LEGEND_CONSTANTS(:,41) = strpad('K_eq in component vAKIII (dimensionless)');
LEGEND_CONSTANTS(:,42) = strpad('V_max_AK_III in component vAKIII (flux)');
LEGEND_RATES(:,1) = strpad('d/dt Asp in component Asp (millimolar)');
LEGEND_RATES(:,2) = strpad('d/dt aspp in component aspp (millimolar)');
LEGEND_RATES(:,3) = strpad('d/dt ASA in component ASA (millimolar)');
LEGEND_RATES(:,4) = strpad('d/dt hs in component hs (millimolar)');
LEGEND_RATES(:,5) = strpad('d/dt hsp in component hsp (millimolar)');
LEGEND_RATES(:,6) = strpad('d/dt Thr in component Thr (millimolar)');
LEGEND_RATES(:,7) = strpad('d/dt ATP in component ATP (millimolar)');
LEGEND_RATES(:,8) = strpad('d/dt ADP in component ADP (millimolar)');
LEGEND_RATES(:,9) = strpad('d/dt NADPH in component NADPH (millimolar)');
LEGEND_RATES(:,10) = strpad('d/dt NADP in component NADP (millimolar)');
LEGEND_RATES(:,11) = strpad('d/dt Pi in component Pi (millimolar)');
LEGEND_RATES(:,12) = strpad('d/dt Lys in component Lys (millimolar)');
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) = 10;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 30;
STATES(:,8) = 0;
STATES(:,9) = 0;
STATES(:,10) = 0;
STATES(:,11) = 0;
STATES(:,12) = 0;
CONSTANTS(:,1) = 0.97;
CONSTANTS(:,2) = 0.98;
CONSTANTS(:,3) = 0.017;
CONSTANTS(:,4) = 0.25;
CONSTANTS(:,5) = 0.167;
CONSTANTS(:,6) = 2.47;
CONSTANTS(:,7) = 4.09;
CONSTANTS(:,8) = 0.00064;
CONSTANTS(:,9) = 463;
CONSTANTS(:,10) = 0.022;
CONSTANTS(:,11) = 0.029;
CONSTANTS(:,12) = 0.11;
CONSTANTS(:,13) = 0.144;
CONSTANTS(:,14) = 10.2;
CONSTANTS(:,15) = 284000;
CONSTANTS(:,16) = 598;
CONSTANTS(:,17) = 0.24;
CONSTANTS(:,18) = 0.037;
CONSTANTS(:,19) = 3.39;
CONSTANTS(:,20) = 0.067;
CONSTANTS(:,21) = 0.097;
CONSTANTS(:,22) = 3.93;
CONSTANTS(:,23) = 1.41;
CONSTANTS(:,24) = 100000000000;
CONSTANTS(:,25) = 2585;
CONSTANTS(:,26) = 0.11;
CONSTANTS(:,27) = 0.072;
CONSTANTS(:,28) = 1.09;
CONSTANTS(:,29) = 9.45;
CONSTANTS(:,30) = 4.7;
CONSTANTS(:,31) = 4.35;
CONSTANTS(:,32) = 483;
CONSTANTS(:,33) = 0.31;
CONSTANTS(:,34) = 208;
CONSTANTS(:,35) = 0.32;
CONSTANTS(:,36) = 0.22;
CONSTANTS(:,37) = 0.017;
CONSTANTS(:,38) = 0.25;
CONSTANTS(:,39) = 0.391;
CONSTANTS(:,40) = 2.8;
CONSTANTS(:,41) = 0.00064;
CONSTANTS(:,42) = 299;
CONSTANTS(:,42) = 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(:,12) = CONSTANTS(:,42);
ALGEBRAIC(:,2) = ( CONSTANTS(:,16).*( STATES(:,2).*STATES(:,9) - ( STATES(:,3).*STATES(:,10).*STATES(:,11))./CONSTANTS(:,15)))./( ( CONSTANTS(:,10).*(1.00000+STATES(:,3)./CONSTANTS(:,12)).*(1.00000+STATES(:,11)./CONSTANTS(:,14))+STATES(:,2)).*( CONSTANTS(:,11).*(1.00000+STATES(:,10)./CONSTANTS(:,13))+STATES(:,9)));
ALGEBRAIC(:,3) = ( CONSTANTS(:,25).*( STATES(:,3).*STATES(:,9) - ( STATES(:,4).*STATES(:,10))./CONSTANTS(:,24)))./( ((1.00000+power(STATES(:,6)./CONSTANTS(:,21), CONSTANTS(:,23)))./(1.00000+power(STATES(:,6)./( CONSTANTS(:,22).*CONSTANTS(:,21)), CONSTANTS(:,23)))).*(CONSTANTS(:,17)+( STATES(:,4).*CONSTANTS(:,17))./CONSTANTS(:,19)+STATES(:,3)).*( CONSTANTS(:,18).*(1.00000+STATES(:,10)./CONSTANTS(:,20))+STATES(:,9)));
RATES(:,3) = ALGEBRAIC(:,2) - ALGEBRAIC(:,3);
RATES(:,9) = - ALGEBRAIC(:,2) - ALGEBRAIC(:,3);
RATES(:,10) = ALGEBRAIC(:,2)+ALGEBRAIC(:,3);
ALGEBRAIC(:,4) = ( CONSTANTS(:,32).*STATES(:,4).*STATES(:,7))./( (( CONSTANTS(:,26).*(1.00000+STATES(:,7)./CONSTANTS(:,31)))./(1.00000+STATES(:,6)./CONSTANTS(:,28))+STATES(:,4)).*( CONSTANTS(:,27).*(1.00000+STATES(:,4)./CONSTANTS(:,30))+STATES(:,7)).*(1.00000+STATES(:,12)./CONSTANTS(:,29)));
RATES(:,4) = ALGEBRAIC(:,3) - ALGEBRAIC(:,4);
ALGEBRAIC(:,1) = ( CONSTANTS(:,9).*( STATES(:,1).*STATES(:,7) - ( STATES(:,2).*STATES(:,8))./CONSTANTS(:,8)))./( (( CONSTANTS(:,1).*(1.00000+power(STATES(:,6)./CONSTANTS(:,5), CONSTANTS(:,7))))./(1.00000+power(STATES(:,6)./( CONSTANTS(:,5).*CONSTANTS(:,6)), CONSTANTS(:,7)))+( STATES(:,2).*CONSTANTS(:,1))./CONSTANTS(:,3)+STATES(:,1)).*( CONSTANTS(:,2).*(1.00000+STATES(:,8)./CONSTANTS(:,4))+STATES(:,7)));
ALGEBRAIC(:,5) = ( CONSTANTS(:,42).*( STATES(:,1).*STATES(:,7) - ( STATES(:,2).*STATES(:,8))./CONSTANTS(:,41)))./( (1.00000+power(STATES(:,12)./CONSTANTS(:,39), CONSTANTS(:,40))).*( CONSTANTS(:,35).*(1.00000+STATES(:,2)./CONSTANTS(:,37))+STATES(:,1)).*( CONSTANTS(:,36).*(1.00000+STATES(:,8)./CONSTANTS(:,38))+STATES(:,7)));
RATES(:,1) = - ALGEBRAIC(:,1) - ALGEBRAIC(:,5);
RATES(:,2) = (ALGEBRAIC(:,1)+ALGEBRAIC(:,5)) - ALGEBRAIC(:,2);
ALGEBRAIC(:,6) = ( CONSTANTS(:,34).*STATES(:,5))./(CONSTANTS(:,33)+STATES(:,5));
RATES(:,5) = ALGEBRAIC(:,4)+ALGEBRAIC(:,6);
RATES(:,6) = ALGEBRAIC(:,6);
RATES(:,7) = ( - ALGEBRAIC(:,1) - ALGEBRAIC(:,5)) - ALGEBRAIC(:,4);
RATES(:,8) = ALGEBRAIC(:,1)+ALGEBRAIC(:,5)+ALGEBRAIC(:,4);
RATES(:,11) = ALGEBRAIC(:,2)+ALGEBRAIC(:,6);
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(:,16).*( STATES(:,2).*STATES(:,9) - ( STATES(:,3).*STATES(:,10).*STATES(:,11))./CONSTANTS(:,15)))./( ( CONSTANTS(:,10).*(1.00000+STATES(:,3)./CONSTANTS(:,12)).*(1.00000+STATES(:,11)./CONSTANTS(:,14))+STATES(:,2)).*( CONSTANTS(:,11).*(1.00000+STATES(:,10)./CONSTANTS(:,13))+STATES(:,9)));
ALGEBRAIC(:,3) = ( CONSTANTS(:,25).*( STATES(:,3).*STATES(:,9) - ( STATES(:,4).*STATES(:,10))./CONSTANTS(:,24)))./( ((1.00000+power(STATES(:,6)./CONSTANTS(:,21), CONSTANTS(:,23)))./(1.00000+power(STATES(:,6)./( CONSTANTS(:,22).*CONSTANTS(:,21)), CONSTANTS(:,23)))).*(CONSTANTS(:,17)+( STATES(:,4).*CONSTANTS(:,17))./CONSTANTS(:,19)+STATES(:,3)).*( CONSTANTS(:,18).*(1.00000+STATES(:,10)./CONSTANTS(:,20))+STATES(:,9)));
ALGEBRAIC(:,4) = ( CONSTANTS(:,32).*STATES(:,4).*STATES(:,7))./( (( CONSTANTS(:,26).*(1.00000+STATES(:,7)./CONSTANTS(:,31)))./(1.00000+STATES(:,6)./CONSTANTS(:,28))+STATES(:,4)).*( CONSTANTS(:,27).*(1.00000+STATES(:,4)./CONSTANTS(:,30))+STATES(:,7)).*(1.00000+STATES(:,12)./CONSTANTS(:,29)));
ALGEBRAIC(:,1) = ( CONSTANTS(:,9).*( STATES(:,1).*STATES(:,7) - ( STATES(:,2).*STATES(:,8))./CONSTANTS(:,8)))./( (( CONSTANTS(:,1).*(1.00000+power(STATES(:,6)./CONSTANTS(:,5), CONSTANTS(:,7))))./(1.00000+power(STATES(:,6)./( CONSTANTS(:,5).*CONSTANTS(:,6)), CONSTANTS(:,7)))+( STATES(:,2).*CONSTANTS(:,1))./CONSTANTS(:,3)+STATES(:,1)).*( CONSTANTS(:,2).*(1.00000+STATES(:,8)./CONSTANTS(:,4))+STATES(:,7)));
ALGEBRAIC(:,5) = ( CONSTANTS(:,42).*( STATES(:,1).*STATES(:,7) - ( STATES(:,2).*STATES(:,8))./CONSTANTS(:,41)))./( (1.00000+power(STATES(:,12)./CONSTANTS(:,39), CONSTANTS(:,40))).*( CONSTANTS(:,35).*(1.00000+STATES(:,2)./CONSTANTS(:,37))+STATES(:,1)).*( CONSTANTS(:,36).*(1.00000+STATES(:,8)./CONSTANTS(:,38))+STATES(:,7)));
ALGEBRAIC(:,6) = ( CONSTANTS(:,34).*STATES(:,5))./(CONSTANTS(:,33)+STATES(:,5));
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