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 =11;
end
% There are a total of 4 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 (hour)');
LEGEND_ALGEBRAIC(:,1) = strpad('Metin in component environment (flux)');
LEGEND_STATES(:,1) = strpad('Met in component Met (micromolar)');
LEGEND_ALGEBRAIC(:,8) = strpad('V_MS in component V_MS (flux)');
LEGEND_ALGEBRAIC(:,11) = strpad('V_BHMT in component V_BHMT (flux)');
LEGEND_ALGEBRAIC(:,2) = strpad('V_MATI in component V_MATI (flux)');
LEGEND_ALGEBRAIC(:,4) = strpad('V_MATIII in component V_MATIII (flux)');
LEGEND_STATES(:,2) = strpad('AdoMet in component AdoMet (micromolar)');
LEGEND_ALGEBRAIC(:,7) = strpad('V_METH in component V_METH (flux)');
LEGEND_ALGEBRAIC(:,5) = strpad('V_GNMT in component V_GNMT (flux)');
LEGEND_STATES(:,3) = strpad('AdoHcy in component AdoHcy (micromolar)');
LEGEND_ALGEBRAIC(:,9) = strpad('V_AH in component V_AH (flux)');
LEGEND_STATES(:,4) = strpad('Hcy in component Hcy (micromolar)');
LEGEND_ALGEBRAIC(:,10) = strpad('V_CBS in component V_CBS (flux)');
LEGEND_CONSTANTS(:,1) = strpad('V_MATImax in component V_MATI (flux)');
LEGEND_CONSTANTS(:,2) = strpad('Km_MATI in component V_MATI (micromolar)');
LEGEND_CONSTANTS(:,3) = strpad('Ki_MATI in component V_MATI (micromolar)');
LEGEND_CONSTANTS(:,4) = strpad('V_MATIIImax in component V_MATIII (flux)');
LEGEND_ALGEBRAIC(:,3) = strpad('Km1_MATIII in component V_MATIII (micromolar)');
LEGEND_CONSTANTS(:,5) = strpad('Km2_MATIII in component V_MATIII (micromolar)');
LEGEND_CONSTANTS(:,6) = strpad('V_GNMTmax in component V_GNMT (flux)');
LEGEND_CONSTANTS(:,7) = strpad('Km_GNMT in component V_GNMT (micromolar)');
LEGEND_CONSTANTS(:,8) = strpad('Ki_GNMT in component V_GNMT (micromolar)');
LEGEND_CONSTANTS(:,9) = strpad('V_METHmax in component V_METH (flux)');
LEGEND_ALGEBRAIC(:,6) = strpad('Km1_METH in component V_METH (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('Km2_METH_A in component V_METH (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('five_mTHF in component V_MS (micromolar)');
LEGEND_CONSTANTS(:,12) = strpad('V_MSmax in component V_MS (flux)');
LEGEND_CONSTANTS(:,13) = strpad('Kd_MS in component V_MS (micromolar)');
LEGEND_CONSTANTS(:,14) = strpad('Km_Hcy_MS in component V_MS (micromolar)');
LEGEND_CONSTANTS(:,15) = strpad('Km_five_mTHF_MS in component V_MS (micromolar)');
LEGEND_CONSTANTS(:,16) = strpad('alpha1 in component V_AH (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('alpha2 in component V_AH (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('beta1 in component V_CBS (second_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('beta2 in component V_CBS (first_order_rate_constant)');
LEGEND_CONSTANTS(:,20) = strpad('V_BHMTmax in component V_BHMT (flux)');
LEGEND_CONSTANTS(:,21) = strpad('Km_BHMT in component V_BHMT (micromolar)');
LEGEND_RATES(:,1) = strpad('d/dt Met in component Met (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt AdoMet in component AdoMet (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt AdoHcy in component AdoHcy (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt Hcy in component Hcy (micromolar)');
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) = 53.5;
STATES(:,2) = 137.6;
STATES(:,3) = 13.2;
STATES(:,4) = 0.88;
CONSTANTS(:,1) = 561;
CONSTANTS(:,2) = 41;
CONSTANTS(:,3) = 50;
CONSTANTS(:,4) = 22870;
CONSTANTS(:,5) = 21.1;
CONSTANTS(:,6) = 10600;
CONSTANTS(:,7) = 4500;
CONSTANTS(:,8) = 20;
CONSTANTS(:,9) = 4521;
CONSTANTS(:,10) = 10;
CONSTANTS(:,11) = 5.2;
CONSTANTS(:,12) = 500;
CONSTANTS(:,13) = 1;
CONSTANTS(:,14) = 0.1;
CONSTANTS(:,15) = 25;
CONSTANTS(:,16) = 100;
CONSTANTS(:,17) = 10;
CONSTANTS(:,18) = 1.7;
CONSTANTS(:,19) = 30;
CONSTANTS(:,20) = 2500;
CONSTANTS(:,21) = 12;
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(:,2) = CONSTANTS(:,1)./(1.00000+ (CONSTANTS(:,2)./STATES(:,1)).*(1.00000+STATES(:,2)./CONSTANTS(:,3)));
ALGEBRAIC(:,3) = 20000.0./(1.00000+ 5.70000.*power(STATES(:,2)./(STATES(:,2)+600.000), 2.00000));
ALGEBRAIC(:,4) = CONSTANTS(:,4)./(1.00000+( ALGEBRAIC(:,3).*CONSTANTS(:,5))./(power(STATES(:,1), 2.00000)+ STATES(:,1).*CONSTANTS(:,5)));
ALGEBRAIC(:,6) = 1.00000.*(1.00000+STATES(:,3)./4.00000);
ALGEBRAIC(:,7) = CONSTANTS(:,9)./(1.00000+ALGEBRAIC(:,6)./STATES(:,2)+CONSTANTS(:,10)+( CONSTANTS(:,10).*ALGEBRAIC(:,6))./STATES(:,2));
ALGEBRAIC(:,5) = ( (CONSTANTS(:,6)./(1.00000+power(CONSTANTS(:,7)./STATES(:,2), 2.30000))).*1.00000)./(1.00000+STATES(:,3)./CONSTANTS(:,8));
RATES(:,2) = (ALGEBRAIC(:,2)+ALGEBRAIC(:,4)) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,5));
ALGEBRAIC(:,9) = CONSTANTS(:,16).*(STATES(:,3) - CONSTANTS(:,17).*STATES(:,4));
RATES(:,3) = (ALGEBRAIC(:,7)+ALGEBRAIC(:,5)) - ALGEBRAIC(:,9);
ALGEBRAIC(:,1) = piecewise({VOI<2.00000||VOI>=8.00000, 200.000 , VOI>=2.00000&VOI<5.00000, 300.000 , VOI>=5.00000&VOI<8.00000, 100.000 }, 200.000);
ALGEBRAIC(:,8) = ( CONSTANTS(:,12).*CONSTANTS(:,11).*STATES(:,4))./( CONSTANTS(:,13).*CONSTANTS(:,14)+ CONSTANTS(:,14).*CONSTANTS(:,11)+ CONSTANTS(:,15).*STATES(:,4)+ CONSTANTS(:,11).*STATES(:,4));
ALGEBRAIC(:,11) = ( (0.700000 - 0.0250000.*((STATES(:,2)+STATES(:,3)) - 150.000)).*CONSTANTS(:,20).*STATES(:,4))./(CONSTANTS(:,21)+STATES(:,4));
RATES(:,1) = (ALGEBRAIC(:,8)+ALGEBRAIC(:,11)+ALGEBRAIC(:,1)) - (ALGEBRAIC(:,2)+ALGEBRAIC(:,4));
ALGEBRAIC(:,10) = ( CONSTANTS(:,18).*(STATES(:,2)+STATES(:,3)) - CONSTANTS(:,19)).*STATES(:,4);
RATES(:,4) = ALGEBRAIC(:,9) - (ALGEBRAIC(:,10)+ALGEBRAIC(:,8)+ALGEBRAIC(:,11));
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(:,1)./(1.00000+ (CONSTANTS(:,2)./STATES(:,1)).*(1.00000+STATES(:,2)./CONSTANTS(:,3)));
ALGEBRAIC(:,3) = 20000.0./(1.00000+ 5.70000.*power(STATES(:,2)./(STATES(:,2)+600.000), 2.00000));
ALGEBRAIC(:,4) = CONSTANTS(:,4)./(1.00000+( ALGEBRAIC(:,3).*CONSTANTS(:,5))./(power(STATES(:,1), 2.00000)+ STATES(:,1).*CONSTANTS(:,5)));
ALGEBRAIC(:,6) = 1.00000.*(1.00000+STATES(:,3)./4.00000);
ALGEBRAIC(:,7) = CONSTANTS(:,9)./(1.00000+ALGEBRAIC(:,6)./STATES(:,2)+CONSTANTS(:,10)+( CONSTANTS(:,10).*ALGEBRAIC(:,6))./STATES(:,2));
ALGEBRAIC(:,5) = ( (CONSTANTS(:,6)./(1.00000+power(CONSTANTS(:,7)./STATES(:,2), 2.30000))).*1.00000)./(1.00000+STATES(:,3)./CONSTANTS(:,8));
ALGEBRAIC(:,9) = CONSTANTS(:,16).*(STATES(:,3) - CONSTANTS(:,17).*STATES(:,4));
ALGEBRAIC(:,1) = piecewise({VOI<2.00000||VOI>=8.00000, 200.000 , VOI>=2.00000&VOI<5.00000, 300.000 , VOI>=5.00000&VOI<8.00000, 100.000 }, 200.000);
ALGEBRAIC(:,8) = ( CONSTANTS(:,12).*CONSTANTS(:,11).*STATES(:,4))./( CONSTANTS(:,13).*CONSTANTS(:,14)+ CONSTANTS(:,14).*CONSTANTS(:,11)+ CONSTANTS(:,15).*STATES(:,4)+ CONSTANTS(:,11).*STATES(:,4));
ALGEBRAIC(:,11) = ( (0.700000 - 0.0250000.*((STATES(:,2)+STATES(:,3)) - 150.000)).*CONSTANTS(:,20).*STATES(:,4))./(CONSTANTS(:,21)+STATES(:,4));
ALGEBRAIC(:,10) = ( CONSTANTS(:,18).*(STATES(:,2)+STATES(:,3)) - CONSTANTS(:,19)).*STATES(:,4);
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