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 3 entries in each of the rate and state variable arrays.
% There are a total of 28 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_CONSTANTS(:,28) = strpad('v_GK in component v_GK (flux)');
LEGEND_CONSTANTS(:,1) = strpad('V_GK_min in component v_GK (enzyme_activity)');
LEGEND_CONSTANTS(:,25) = strpad('V_GK in component v_GK (enzyme_activity)');
LEGEND_CONSTANTS(:,2) = strpad('Sgk in component v_GK (millimolar)');
LEGEND_CONSTANTS(:,3) = strpad('h_GK in component v_GK (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('Glc in component Glc (millimolar)');
LEGEND_CONSTANTS(:,4) = strpad('min_to_sec in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('dw_per_ml in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('v_PFK in component v_PFK (flux)');
LEGEND_CONSTANTS(:,6) = strpad('V_PFK_min in component v_PFK (enzyme_activity)');
LEGEND_CONSTANTS(:,23) = strpad('V_PFK in component v_PFK (enzyme_activity)');
LEGEND_CONSTANTS(:,7) = strpad('Spfk in component v_PFK (millimolar)');
LEGEND_CONSTANTS(:,8) = strpad('Sfba in component v_PFK (millimolar)');
LEGEND_CONSTANTS(:,9) = strpad('Xpfk in component v_PFK (millimolar)');
LEGEND_CONSTANTS(:,10) = strpad('hx in component v_PFK (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('alpha in component v_PFK (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('h_PFK in component v_PFK (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('h_act in component v_PFK (dimensionless)');
LEGEND_STATES(:,1) = strpad('FBP in component FBP (millimolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('F6P in component F6P (millimolar)');
LEGEND_ALGEBRAIC(:,6) = strpad('v_FBA in component v_FBA (flux)');
LEGEND_CONSTANTS(:,14) = strpad('V_FBA_min in component v_FBA (enzyme_activity)');
LEGEND_CONSTANTS(:,24) = strpad('V_FBA in component v_FBA (enzyme_activity)');
LEGEND_CONSTANTS(:,15) = strpad('Qfba in component v_FBA (millimolar)');
LEGEND_CONSTANTS(:,16) = strpad('Sfba in component v_FBA (millimolar)');
LEGEND_CONSTANTS(:,17) = strpad('Pfba in component v_FBA (millimolar)');
LEGEND_CONSTANTS(:,18) = strpad('Keq_FBA in component v_FBA (millimolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('G3P in component G3P (millimolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('DHAP in component DHAP (millimolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('v_GAPDH in component v_GAPDH (flux)');
LEGEND_CONSTANTS(:,19) = strpad('V_GAPDH_min in component v_GAPDH (enzyme_activity)');
LEGEND_CONSTANTS(:,26) = strpad('V_GAPDH in component v_GAPDH (enzyme_activity)');
LEGEND_CONSTANTS(:,20) = strpad('Sgapdh in component v_GAPDH (millimolar)');
LEGEND_STATES(:,2) = strpad('G6P_F6P in component G6P_F6P (millimolar)');
LEGEND_CONSTANTS(:,21) = strpad('Keq_GPI in component F6P (dimensionless)');
LEGEND_STATES(:,3) = strpad('DHAP_G3P in component DHAP_G3P (millimolar)');
LEGEND_CONSTANTS(:,22) = strpad('Keq_TPI in component G3P (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt G6P_F6P in component G6P_F6P (millimolar)');
LEGEND_RATES(:,1) = strpad('d/dt FBP in component FBP (millimolar)');
LEGEND_RATES(:,3) = strpad('d/dt DHAP_G3P in component DHAP_G3P (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 = [];
CONSTANTS(:,1) = 10.0;
CONSTANTS(:,2) = 8.0;
CONSTANTS(:,3) = 1.7;
CONSTANTS(:,4) = 60.0;
CONSTANTS(:,5) = 0.3333;
CONSTANTS(:,6) = 100.0;
CONSTANTS(:,7) = 4.0;
CONSTANTS(:,8) = 0.005;
CONSTANTS(:,9) = 0.01;
CONSTANTS(:,10) = 2.5;
CONSTANTS(:,11) = 5.0;
CONSTANTS(:,12) = 2.5;
CONSTANTS(:,13) = 1.0;
STATES(:,1) = 0.00063612;
CONSTANTS(:,14) = 25.0;
CONSTANTS(:,15) = 0.275;
CONSTANTS(:,16) = 0.005;
CONSTANTS(:,17) = 0.5;
CONSTANTS(:,18) = 0.1;
CONSTANTS(:,19) = 250.0;
CONSTANTS(:,20) = 0.005;
STATES(:,2) = 3.71728;
CONSTANTS(:,21) = 0.3;
STATES(:,3) = 0.00262966;
CONSTANTS(:,22) = 0.045455;
CONSTANTS(:,23) = ( CONSTANTS(:,6).*CONSTANTS(:,5))./CONSTANTS(:,4);
CONSTANTS(:,24) = ( CONSTANTS(:,14).*CONSTANTS(:,5))./CONSTANTS(:,4);
CONSTANTS(:,25) = ( CONSTANTS(:,1).*CONSTANTS(:,5))./CONSTANTS(:,4);
CONSTANTS(:,26) = ( CONSTANTS(:,19).*CONSTANTS(:,5))./CONSTANTS(:,4);
CONSTANTS(:,27) = 10.0000;
CONSTANTS(:,28) = ( CONSTANTS(:,25).*power(CONSTANTS(:,27)./CONSTANTS(:,2), CONSTANTS(:,3)))./(1.00000+power(CONSTANTS(:,27)./CONSTANTS(:,2), CONSTANTS(:,3)));
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(:,1) = ( STATES(:,2).*CONSTANTS(:,21))./(1.00000+CONSTANTS(:,21));
ALGEBRAIC(:,2) = ( CONSTANTS(:,23).*power(ALGEBRAIC(:,1)./CONSTANTS(:,7), CONSTANTS(:,12) - (CONSTANTS(:,12) - CONSTANTS(:,13)).*((STATES(:,1)./CONSTANTS(:,8))./(1.00000+STATES(:,1)./CONSTANTS(:,8)))))./(power(ALGEBRAIC(:,1)./CONSTANTS(:,7), CONSTANTS(:,12) - (CONSTANTS(:,12) - CONSTANTS(:,13)).*((STATES(:,1)./CONSTANTS(:,8))./(1.00000+STATES(:,1)./CONSTANTS(:,8))))+(1.00000+power(STATES(:,1)./CONSTANTS(:,9), CONSTANTS(:,10)))./(1.00000+ power(CONSTANTS(:,11), CONSTANTS(:,12) - (CONSTANTS(:,12) - CONSTANTS(:,13)).*((STATES(:,1)./CONSTANTS(:,8))./(1.00000+STATES(:,1)./CONSTANTS(:,8)))).*power(STATES(:,1)./CONSTANTS(:,9), CONSTANTS(:,10))));
RATES(:,2) = CONSTANTS(:,28) - ALGEBRAIC(:,2);
ALGEBRAIC(:,3) = ( STATES(:,3).*CONSTANTS(:,22))./(1.00000+CONSTANTS(:,22));
ALGEBRAIC(:,5) = STATES(:,3) - ALGEBRAIC(:,3);
ALGEBRAIC(:,6) = ( CONSTANTS(:,24).*(STATES(:,1)./CONSTANTS(:,16) - ( ALGEBRAIC(:,3).*ALGEBRAIC(:,5))./( CONSTANTS(:,17).*CONSTANTS(:,15).*CONSTANTS(:,18))))./(1.00000+STATES(:,1)./CONSTANTS(:,16)+ALGEBRAIC(:,5)./CONSTANTS(:,15)+( ALGEBRAIC(:,3).*ALGEBRAIC(:,5))./( CONSTANTS(:,17).*CONSTANTS(:,15)));
RATES(:,1) = ALGEBRAIC(:,2) - ALGEBRAIC(:,6);
ALGEBRAIC(:,4) = ( CONSTANTS(:,26).*ALGEBRAIC(:,3))./(CONSTANTS(:,20)+ALGEBRAIC(:,3));
RATES(:,3) = 2.00000.*ALGEBRAIC(:,6) - ALGEBRAIC(:,4);
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) = ( STATES(:,2).*CONSTANTS(:,21))./(1.00000+CONSTANTS(:,21));
ALGEBRAIC(:,2) = ( CONSTANTS(:,23).*power(ALGEBRAIC(:,1)./CONSTANTS(:,7), CONSTANTS(:,12) - (CONSTANTS(:,12) - CONSTANTS(:,13)).*((STATES(:,1)./CONSTANTS(:,8))./(1.00000+STATES(:,1)./CONSTANTS(:,8)))))./(power(ALGEBRAIC(:,1)./CONSTANTS(:,7), CONSTANTS(:,12) - (CONSTANTS(:,12) - CONSTANTS(:,13)).*((STATES(:,1)./CONSTANTS(:,8))./(1.00000+STATES(:,1)./CONSTANTS(:,8))))+(1.00000+power(STATES(:,1)./CONSTANTS(:,9), CONSTANTS(:,10)))./(1.00000+ power(CONSTANTS(:,11), CONSTANTS(:,12) - (CONSTANTS(:,12) - CONSTANTS(:,13)).*((STATES(:,1)./CONSTANTS(:,8))./(1.00000+STATES(:,1)./CONSTANTS(:,8)))).*power(STATES(:,1)./CONSTANTS(:,9), CONSTANTS(:,10))));
ALGEBRAIC(:,3) = ( STATES(:,3).*CONSTANTS(:,22))./(1.00000+CONSTANTS(:,22));
ALGEBRAIC(:,5) = STATES(:,3) - ALGEBRAIC(:,3);
ALGEBRAIC(:,6) = ( CONSTANTS(:,24).*(STATES(:,1)./CONSTANTS(:,16) - ( ALGEBRAIC(:,3).*ALGEBRAIC(:,5))./( CONSTANTS(:,17).*CONSTANTS(:,15).*CONSTANTS(:,18))))./(1.00000+STATES(:,1)./CONSTANTS(:,16)+ALGEBRAIC(:,5)./CONSTANTS(:,15)+( ALGEBRAIC(:,3).*ALGEBRAIC(:,5))./( CONSTANTS(:,17).*CONSTANTS(:,15)));
ALGEBRAIC(:,4) = ( CONSTANTS(:,26).*ALGEBRAIC(:,3))./(CONSTANTS(:,20)+ALGEBRAIC(:,3));
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