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 =19;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 29 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(:,2) = strpad('v_1 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,26) = strpad('v_2 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,27) = strpad('v_3 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,3) = strpad('v_4 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,28) = strpad('v_5 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,4) = strpad('v_6 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,29) = strpad('v_7 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,5) = strpad('v_8 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,6) = strpad('v_9 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,7) = strpad('v_10 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,8) = strpad('v_11 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,9) = strpad('v_12 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,10) = strpad('v_13 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,11) = strpad('v_14 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,12) = strpad('v_15 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,13) = strpad('v_16 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,14) = strpad('v_17 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,15) = strpad('v_18 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,16) = strpad('v_19 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,18) = strpad('v_20 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,17) = strpad('v_21 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_ALGEBRAIC(:,19) = strpad('v_22 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,1) = strpad('k_1 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,2) = strpad('k_2 in component main (pmol_per_ug_DNA_per_hour)');
LEGEND_CONSTANTS(:,3) = strpad('k_3 in component main (per_hour)');
LEGEND_CONSTANTS(:,4) = strpad('k_4 in component main (per_hour)');
LEGEND_CONSTANTS(:,5) = strpad('k_5 in component main (ug_DNA_per_pmol_per_hour)');
LEGEND_CONSTANTS(:,6) = strpad('k_6 in component main (per_hour)');
LEGEND_CONSTANTS(:,7) = strpad('k_7 in component main (per_hour)');
LEGEND_CONSTANTS(:,8) = strpad('k_8 in component main (per_hour)');
LEGEND_CONSTANTS(:,9) = strpad('k_9 in component main (per_hour)');
LEGEND_CONSTANTS(:,10) = strpad('k_10 in component main (ug_DNA_per_pmol_per_hour)');
LEGEND_CONSTANTS(:,11) = strpad('k_11 in component main (per_hour)');
LEGEND_CONSTANTS(:,12) = strpad('k_12 in component main (per_hour)');
LEGEND_CONSTANTS(:,13) = strpad('k_13 in component main (per_hour)');
LEGEND_CONSTANTS(:,14) = strpad('k_14 in component main (per_hour)');
LEGEND_CONSTANTS(:,15) = strpad('k_15 in component main (per_hour)');
LEGEND_CONSTANTS(:,16) = strpad('k_16 in component main (per_hour)');
LEGEND_CONSTANTS(:,17) = strpad('k_17 in component main (per_hour)');
LEGEND_CONSTANTS(:,18) = strpad('k_18 in component main (per_hour)');
LEGEND_CONSTANTS(:,19) = strpad('k_19 in component main (per_hour)');
LEGEND_CONSTANTS(:,20) = strpad('k_20 in component main (per_hour)');
LEGEND_CONSTANTS(:,21) = strpad('k_21 in component main (per_hour)');
LEGEND_CONSTANTS(:,22) = strpad('k_22 in component main (per_hour)');
LEGEND_ALGEBRAIC(:,1) = strpad('LPS in component main (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('PIP_2 in component main (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('DG in component main (pmol_per_ug_DNA)');
LEGEND_CONSTANTS(:,25) = strpad('GPCho in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,1) = strpad('AA in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,2) = strpad('HETE in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,3) = strpad('PGH_2 in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,4) = strpad('PGE_2 in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,5) = strpad('PGF_2a in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,6) = strpad('PGD_2 in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,7) = strpad('PGJ_2 in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,8) = strpad('dPGD_2 in component main (pmol_per_ug_DNA)');
LEGEND_STATES(:,9) = strpad('dPGJ_2 in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,1) = strpad('d/dt AA in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,2) = strpad('d/dt HETE in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,3) = strpad('d/dt PGH_2 in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,4) = strpad('d/dt PGE_2 in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,5) = strpad('d/dt PGF_2a in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,6) = strpad('d/dt PGD_2 in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,7) = strpad('d/dt PGJ_2 in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,8) = strpad('d/dt dPGD_2 in component main (pmol_per_ug_DNA)');
LEGEND_RATES(:,9) = strpad('d/dt dPGJ_2 in component main (pmol_per_ug_DNA)');
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) = 355.637;
CONSTANTS(:,2) = 1e-15;
CONSTANTS(:,3) = 1e-15;
CONSTANTS(:,4) = 1e-15;
CONSTANTS(:,5) = 1e-15;
CONSTANTS(:,6) = 0.33;
CONSTANTS(:,7) = 1e-15;
CONSTANTS(:,8) = 0.007;
CONSTANTS(:,9) = 0.187;
CONSTANTS(:,10) = 0.024;
CONSTANTS(:,11) = 0.111;
CONSTANTS(:,12) = 0.098;
CONSTANTS(:,13) = 0.204;
CONSTANTS(:,14) = 1e-15;
CONSTANTS(:,15) = 0.061;
CONSTANTS(:,16) = 1e-15;
CONSTANTS(:,17) = 3.116;
CONSTANTS(:,18) = 0.054;
CONSTANTS(:,19) = 0.029;
CONSTANTS(:,20) = 0.014;
CONSTANTS(:,21) = 0.034;
CONSTANTS(:,22) = 0.116;
CONSTANTS(:,23) = 1;
CONSTANTS(:,24) = 0;
CONSTANTS(:,25) = 1;
STATES(:,1) = 25;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
CONSTANTS(:,26) = CONSTANTS(:,23).*CONSTANTS(:,2);
CONSTANTS(:,27) = CONSTANTS(:,24).*CONSTANTS(:,3);
CONSTANTS(:,28) = CONSTANTS(:,24).*CONSTANTS(:,25).*CONSTANTS(:,5);
CONSTANTS(:,29) = CONSTANTS(:,25).*CONSTANTS(:,7);
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) = STATES(:,1).*CONSTANTS(:,8);
ALGEBRAIC(:,6) = STATES(:,2).*CONSTANTS(:,9);
RATES(:,2) = ALGEBRAIC(:,5) - ALGEBRAIC(:,6);
ALGEBRAIC(:,1) = piecewise({VOI<=0.500000, VOI.*2.00000 , VOI>0.500000&VOI<2.00000, 1.00000 - (VOI - 0.500000)./1.50000 }, 0.00000);
ALGEBRAIC(:,2) = ALGEBRAIC(:,1).*CONSTANTS(:,23).*CONSTANTS(:,1);
ALGEBRAIC(:,3) = STATES(:,1).*CONSTANTS(:,4);
ALGEBRAIC(:,4) = ALGEBRAIC(:,1).*CONSTANTS(:,25).*CONSTANTS(:,6);
ALGEBRAIC(:,7) = CONSTANTS(:,24).*STATES(:,1).*CONSTANTS(:,10);
ALGEBRAIC(:,8) = ALGEBRAIC(:,1).*STATES(:,1).*CONSTANTS(:,11);
ALGEBRAIC(:,9) = STATES(:,1).*CONSTANTS(:,12);
RATES(:,1) = ((((((ALGEBRAIC(:,2)+CONSTANTS(:,26)+CONSTANTS(:,27)) - ALGEBRAIC(:,3))+CONSTANTS(:,28)+ALGEBRAIC(:,4)+CONSTANTS(:,29)) - ALGEBRAIC(:,5)) - ALGEBRAIC(:,7)) - ALGEBRAIC(:,8)) - ALGEBRAIC(:,9);
ALGEBRAIC(:,10) = STATES(:,3).*CONSTANTS(:,13);
ALGEBRAIC(:,11) = STATES(:,4).*CONSTANTS(:,14);
RATES(:,4) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
ALGEBRAIC(:,12) = STATES(:,3).*CONSTANTS(:,15);
ALGEBRAIC(:,14) = STATES(:,3).*CONSTANTS(:,17);
RATES(:,3) = (((ALGEBRAIC(:,7)+ALGEBRAIC(:,8)+ALGEBRAIC(:,9)) - ALGEBRAIC(:,10)) - ALGEBRAIC(:,12)) - ALGEBRAIC(:,14);
ALGEBRAIC(:,13) = STATES(:,5).*CONSTANTS(:,16);
RATES(:,5) = ALGEBRAIC(:,12) - ALGEBRAIC(:,13);
ALGEBRAIC(:,15) = STATES(:,6).*CONSTANTS(:,18);
ALGEBRAIC(:,16) = STATES(:,6).*CONSTANTS(:,19);
RATES(:,6) = (ALGEBRAIC(:,14) - ALGEBRAIC(:,15)) - ALGEBRAIC(:,16);
ALGEBRAIC(:,17) = STATES(:,7).*CONSTANTS(:,21);
RATES(:,7) = ALGEBRAIC(:,15) - ALGEBRAIC(:,17);
ALGEBRAIC(:,18) = STATES(:,8).*CONSTANTS(:,20);
RATES(:,8) = ALGEBRAIC(:,16) - ALGEBRAIC(:,18);
ALGEBRAIC(:,19) = STATES(:,9).*CONSTANTS(:,22);
RATES(:,9) = ALGEBRAIC(:,17) - ALGEBRAIC(:,19);
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) = STATES(:,1).*CONSTANTS(:,8);
ALGEBRAIC(:,6) = STATES(:,2).*CONSTANTS(:,9);
ALGEBRAIC(:,1) = piecewise({VOI<=0.500000, VOI.*2.00000 , VOI>0.500000&VOI<2.00000, 1.00000 - (VOI - 0.500000)./1.50000 }, 0.00000);
ALGEBRAIC(:,2) = ALGEBRAIC(:,1).*CONSTANTS(:,23).*CONSTANTS(:,1);
ALGEBRAIC(:,3) = STATES(:,1).*CONSTANTS(:,4);
ALGEBRAIC(:,4) = ALGEBRAIC(:,1).*CONSTANTS(:,25).*CONSTANTS(:,6);
ALGEBRAIC(:,7) = CONSTANTS(:,24).*STATES(:,1).*CONSTANTS(:,10);
ALGEBRAIC(:,8) = ALGEBRAIC(:,1).*STATES(:,1).*CONSTANTS(:,11);
ALGEBRAIC(:,9) = STATES(:,1).*CONSTANTS(:,12);
ALGEBRAIC(:,10) = STATES(:,3).*CONSTANTS(:,13);
ALGEBRAIC(:,11) = STATES(:,4).*CONSTANTS(:,14);
ALGEBRAIC(:,12) = STATES(:,3).*CONSTANTS(:,15);
ALGEBRAIC(:,14) = STATES(:,3).*CONSTANTS(:,17);
ALGEBRAIC(:,13) = STATES(:,5).*CONSTANTS(:,16);
ALGEBRAIC(:,15) = STATES(:,6).*CONSTANTS(:,18);
ALGEBRAIC(:,16) = STATES(:,6).*CONSTANTS(:,19);
ALGEBRAIC(:,17) = STATES(:,7).*CONSTANTS(:,21);
ALGEBRAIC(:,18) = STATES(:,8).*CONSTANTS(:,20);
ALGEBRAIC(:,19) = STATES(:,9).*CONSTANTS(:,22);
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