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 =17;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 19 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_STATES(:,1) = strpad('C_6PG in component C_6PG (millimolar)');
LEGEND_CONSTANTS(:,1) = strpad('mu in component model_constants (per_hour)');
LEGEND_ALGEBRAIC(:,4) = strpad('rG6PDH in component rG6PDH (flux)');
LEGEND_ALGEBRAIC(:,10) = strpad('r6PGDH in component r6PGDH (flux)');
LEGEND_STATES(:,2) = strpad('C_Ru5P in component C_Ru5P (millimolar)');
LEGEND_ALGEBRAIC(:,12) = strpad('rRu5PE in component rRu5PE (flux)');
LEGEND_ALGEBRAIC(:,11) = strpad('rR5PI in component rR5PI (flux)');
LEGEND_STATES(:,3) = strpad('C_R5P in component C_R5P (millimolar)');
LEGEND_ALGEBRAIC(:,13) = strpad('rTKL1 in component rTKL1 (flux)');
LEGEND_ALGEBRAIC(:,14) = strpad('rRPPK in component rRPPK (flux)');
LEGEND_STATES(:,4) = strpad('C_X5P in component C_X5P (millimolar)');
LEGEND_ALGEBRAIC(:,16) = strpad('rTKL2 in component rTKL2 (flux)');
LEGEND_STATES(:,5) = strpad('C_S7P in component C_S7P (millimolar)');
LEGEND_ALGEBRAIC(:,15) = strpad('rTAL in component rTAL (flux)');
LEGEND_STATES(:,6) = strpad('C_E4P in component C_E4P (millimolar)');
LEGEND_ALGEBRAIC(:,17) = strpad('rPKDA in component rPKDA (flux)');
LEGEND_STATES(:,7) = strpad('C_G6P in component C_G6P (millimolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('dC_G6P_dt in component C_G6P (flux)');
LEGEND_STATES(:,8) = strpad('C_NADP in component C_NADP (millimolar)');
LEGEND_STATES(:,9) = strpad('C_NADPH in component C_NADPH (millimolar)');
LEGEND_STATES(:,10) = strpad('C_MgATP in component C_MgATP (millimolar)');
LEGEND_CONSTANTS(:,2) = strpad('K_NADP_1 in component rG6PDH (millimolar)');
LEGEND_CONSTANTS(:,3) = strpad('Ki_NADPH_1 in component rG6PDH (millimolar)');
LEGEND_CONSTANTS(:,4) = strpad('Ki_MgATP_1 in component rG6PDH (millimolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('I_NADPH_1 in component rG6PDH (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('I_MgATP_1 in component rG6PDH (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('rmax_G6PDH in component rG6PDH (flux)');
LEGEND_CONSTANTS(:,6) = strpad('K_NADP_2 in component r6PGDH (millimolar)');
LEGEND_CONSTANTS(:,7) = strpad('Ki_NADPH_2 in component r6PGDH (millimolar)');
LEGEND_CONSTANTS(:,8) = strpad('Ki_MgATP_2 in component r6PGDH (millimolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('I_NADPH_2 in component r6PGDH (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('I_MgATP_2 in component r6PGDH (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('rmax_6PGDH in component r6PGDH (flux)');
LEGEND_CONSTANTS(:,10) = strpad('rmax_R5PI in component rR5PI (millimole_per_second)');
LEGEND_CONSTANTS(:,11) = strpad('rmax_Ru5PE in component rRu5PE (millimole_per_second)');
LEGEND_CONSTANTS(:,12) = strpad('rmax_TKL1 in component rTKL1 (millimole_per_second)');
LEGEND_CONSTANTS(:,13) = strpad('C_GAP in component model_constants (millimolar)');
LEGEND_CONSTANTS(:,14) = strpad('rmax_TAL in component rTAL (millimole_per_second)');
LEGEND_CONSTANTS(:,15) = strpad('rmax_TKL2 in component rTKL2 (millimole_per_second)');
LEGEND_CONSTANTS(:,16) = strpad('K_PKDA in component rPKDA (millimolar)');
LEGEND_CONSTANTS(:,17) = strpad('rmax_PKDA in component rPKDA (millimole_per_second)');
LEGEND_CONSTANTS(:,18) = strpad('K_RPPK in component rRPPK (millimolar)');
LEGEND_CONSTANTS(:,19) = strpad('rmax_RPPK in component rRPPK (millimole_per_second)');
LEGEND_ALGEBRAIC(:,8) = strpad('rHK in component rHK (flux)');
LEGEND_ALGEBRAIC(:,6) = strpad('qs in component model_constants (flux)');
LEGEND_ALGEBRAIC(:,9) = strpad('rPGI in component rPGI (flux)');
LEGEND_RATES(:,1) = strpad('d/dt C_6PG in component C_6PG (millimolar)');
LEGEND_RATES(:,2) = strpad('d/dt C_Ru5P in component C_Ru5P (millimolar)');
LEGEND_RATES(:,3) = strpad('d/dt C_R5P in component C_R5P (millimolar)');
LEGEND_RATES(:,4) = strpad('d/dt C_X5P in component C_X5P (millimolar)');
LEGEND_RATES(:,5) = strpad('d/dt C_S7P in component C_S7P (millimolar)');
LEGEND_RATES(:,6) = strpad('d/dt C_E4P in component C_E4P (millimolar)');
LEGEND_RATES(:,7) = strpad('d/dt C_G6P in component C_G6P (millimolar)');
LEGEND_RATES(:,8) = strpad('d/dt C_NADP in component C_NADP (millimolar)');
LEGEND_RATES(:,9) = strpad('d/dt C_NADPH in component C_NADPH (millimolar)');
LEGEND_RATES(:,10) = strpad('d/dt C_MgATP in component C_MgATP (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) = 0.25;
CONSTANTS(:,1) = 1.0;
STATES(:,2) = 0.033;
STATES(:,3) = 0.118;
STATES(:,4) = 0.041;
STATES(:,5) = 0.082;
STATES(:,6) = 0.029;
STATES(:,7) = 0.9;
STATES(:,8) = 0.168;
STATES(:,9) = 0.168;
STATES(:,10) = 2.3;
CONSTANTS(:,2) = 0.116;
CONSTANTS(:,3) = 1.702;
CONSTANTS(:,4) = 0.33;
CONSTANTS(:,5) = 44.19;
CONSTANTS(:,6) = 1.848;
CONSTANTS(:,7) = 0.055;
CONSTANTS(:,8) = 0.109;
CONSTANTS(:,9) = 0.654;
CONSTANTS(:,10) = 0.57;
CONSTANTS(:,11) = 0.85;
CONSTANTS(:,12) = 3.24;
CONSTANTS(:,13) = 0.064;
CONSTANTS(:,14) = 3.0;
CONSTANTS(:,15) = 10.5;
CONSTANTS(:,16) = 0.0032;
CONSTANTS(:,17) = 0.004;
CONSTANTS(:,18) = 0.0034;
CONSTANTS(:,19) = 0.003;
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(:,8) = -1.48000./(9.17000+ 16.1000.*VOI+ 0.480000.*power(VOI, 2.00000))+ (( 1.48000.*VOI)./( (9.17000+ 16.1000.*VOI+ 0.480000.*power(VOI, 2.00000)).*(9.17000+ 16.1000.*VOI+ 0.480000.*power(VOI, 2.00000)))).*(16.1000+ 0.960000.*VOI);
RATES(:,9) = 0.516000./(25.3900+ 0.370000.*VOI+ 0.500000.*power(VOI, 2.00000)) - (( 0.516000.*VOI)./( (25.3900+ 0.370000.*VOI+ 0.500000.*power(VOI, 2.00000)).*(25.3900+ 0.370000.*VOI+ 0.500000.*power(VOI, 2.00000)))).*(0.370000+ 1.00000.*VOI);
RATES(:,10) = 29.8300./(29.7700+ 13.4200.*VOI+ 0.0500000.*power(VOI, 2.00000)) - (( 29.8300.*VOI)./( (29.7700+ 13.4200.*VOI+ 0.0500000.*power(VOI, 2.00000)).*(29.7700+ 13.4200.*VOI+ 0.0500000.*power(VOI, 2.00000)))).*(13.4200+ 0.100000.*VOI);
ALGEBRAIC(:,1) = 44.1000./(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000))+ (( 44.1000.*VOI)./( (48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)).*(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)))).*(1.00000+ 0.900000.*VOI);
RATES(:,7) = ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = 1.00000+STATES(:,9)./CONSTANTS(:,3);
ALGEBRAIC(:,3) = 1.00000+STATES(:,10)./CONSTANTS(:,4);
ALGEBRAIC(:,4) = CONSTANTS(:,5).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,2).*ALGEBRAIC(:,2)).*ALGEBRAIC(:,3)));
ALGEBRAIC(:,5) = 1.00000+STATES(:,9)./CONSTANTS(:,7);
ALGEBRAIC(:,7) = 1.00000+STATES(:,10)./CONSTANTS(:,8);
ALGEBRAIC(:,10) = CONSTANTS(:,9).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,6).*ALGEBRAIC(:,5)).*ALGEBRAIC(:,7)));
RATES(:,1) = ALGEBRAIC(:,4) - (ALGEBRAIC(:,10)+ CONSTANTS(:,1).*STATES(:,1));
ALGEBRAIC(:,12) = 1.00000.*CONSTANTS(:,11).*STATES(:,2);
ALGEBRAIC(:,11) = 1.00000.*CONSTANTS(:,10).*STATES(:,2);
RATES(:,2) = ALGEBRAIC(:,10) - (ALGEBRAIC(:,11)+ALGEBRAIC(:,12)+ CONSTANTS(:,1).*STATES(:,2));
ALGEBRAIC(:,13) = 1.00000.*CONSTANTS(:,12).*STATES(:,4).*STATES(:,3);
ALGEBRAIC(:,14) = 1.00000.*CONSTANTS(:,19).*(STATES(:,3)./(STATES(:,3)+CONSTANTS(:,18)));
RATES(:,3) = ALGEBRAIC(:,11) - (ALGEBRAIC(:,13)+ALGEBRAIC(:,14)+ CONSTANTS(:,1).*STATES(:,3));
ALGEBRAIC(:,15) = 1.00000.*CONSTANTS(:,14).*CONSTANTS(:,13).*STATES(:,5);
RATES(:,5) = ALGEBRAIC(:,13) - (ALGEBRAIC(:,15)+ CONSTANTS(:,1).*STATES(:,5));
ALGEBRAIC(:,16) = 1.00000.*CONSTANTS(:,15).*STATES(:,6).*STATES(:,4);
RATES(:,4) = ALGEBRAIC(:,12) - (ALGEBRAIC(:,13)+ALGEBRAIC(:,16)+ CONSTANTS(:,1).*STATES(:,4));
ALGEBRAIC(:,17) = 1.00000.*CONSTANTS(:,17).*(STATES(:,6)./(STATES(:,6)+CONSTANTS(:,16)));
RATES(:,6) = ALGEBRAIC(:,15) - (ALGEBRAIC(:,16)+ALGEBRAIC(:,17)+ CONSTANTS(:,1).*STATES(:,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(:,1) = 44.1000./(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000))+ (( 44.1000.*VOI)./( (48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)).*(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)))).*(1.00000+ 0.900000.*VOI);
ALGEBRAIC(:,2) = 1.00000+STATES(:,9)./CONSTANTS(:,3);
ALGEBRAIC(:,3) = 1.00000+STATES(:,10)./CONSTANTS(:,4);
ALGEBRAIC(:,4) = CONSTANTS(:,5).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,2).*ALGEBRAIC(:,2)).*ALGEBRAIC(:,3)));
ALGEBRAIC(:,5) = 1.00000+STATES(:,9)./CONSTANTS(:,7);
ALGEBRAIC(:,7) = 1.00000+STATES(:,10)./CONSTANTS(:,8);
ALGEBRAIC(:,10) = CONSTANTS(:,9).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,6).*ALGEBRAIC(:,5)).*ALGEBRAIC(:,7)));
ALGEBRAIC(:,12) = 1.00000.*CONSTANTS(:,11).*STATES(:,2);
ALGEBRAIC(:,11) = 1.00000.*CONSTANTS(:,10).*STATES(:,2);
ALGEBRAIC(:,13) = 1.00000.*CONSTANTS(:,12).*STATES(:,4).*STATES(:,3);
ALGEBRAIC(:,14) = 1.00000.*CONSTANTS(:,19).*(STATES(:,3)./(STATES(:,3)+CONSTANTS(:,18)));
ALGEBRAIC(:,15) = 1.00000.*CONSTANTS(:,14).*CONSTANTS(:,13).*STATES(:,5);
ALGEBRAIC(:,16) = 1.00000.*CONSTANTS(:,15).*STATES(:,6).*STATES(:,4);
ALGEBRAIC(:,17) = 1.00000.*CONSTANTS(:,17).*(STATES(:,6)./(STATES(:,6)+CONSTANTS(:,16)));
ALGEBRAIC(:,6) = piecewise({VOI<0.00000, 0.131000 }, 0.546000);
ALGEBRAIC(:,8) = ALGEBRAIC(:,6);
ALGEBRAIC(:,9) = ALGEBRAIC(:,6) - (ALGEBRAIC(:,4)+ CONSTANTS(:,1).*STATES(:,7)+ALGEBRAIC(:,1));
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