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 =2;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 26 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('R in component R (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('phi_1 in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('phi_2 in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,22) = strpad('phi_2b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,1) = strpad('k_1b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('l_2b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('I_1 in component I_1 (dimensionless)');
LEGEND_STATES(:,3) = strpad('O in component O (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('p in component reaction_rate_constants (micromolar)');
LEGEND_CONSTANTS(:,23) = strpad('phi_3 in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,24) = strpad('phi_4 in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,25) = strpad('phi_4b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k_3b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('A in component A (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('S in component S (dimensionless)');
LEGEND_STATES(:,5) = strpad('I_2 in component I_2 (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('phi_5 in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,2) = strpad('open_probability in component open_probability (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('k_1a in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k_2a in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k_2b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k_3a in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k_4a in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k_4b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('l_2a in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('l_4a in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('l_4b in component reaction_rate_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('l_6a in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('l_6b in component reaction_rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('L_1 in component reaction_rate_constants (micromolar)');
LEGEND_CONSTANTS(:,17) = strpad('L_3 in component reaction_rate_constants (micromolar)');
LEGEND_CONSTANTS(:,18) = strpad('L_5 in component reaction_rate_constants (micromolar)');
LEGEND_CONSTANTS(:,19) = strpad('c in component reaction_rate_constants (micromolar)');
LEGEND_RATES(:,1) = strpad('d/dt R in component R (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt O in component O (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt I_1 in component I_1 (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt I_2 in component I_2 (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt A in component A (dimensionless)');
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) = 1;
CONSTANTS(:,1) = 0.04;
CONSTANTS(:,2) = 0.8;
STATES(:,2) = 0;
STATES(:,3) = 0;
CONSTANTS(:,3) = 10;
CONSTANTS(:,4) = 29.8;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,5) = 0.64;
CONSTANTS(:,6) = 37.4;
CONSTANTS(:,7) = 1.4;
CONSTANTS(:,8) = 0.11;
CONSTANTS(:,9) = 4;
CONSTANTS(:,10) = 0.54;
CONSTANTS(:,11) = 1.7;
CONSTANTS(:,12) = 1.7;
CONSTANTS(:,13) = 2.5;
CONSTANTS(:,14) = 4707;
CONSTANTS(:,15) = 11.4;
CONSTANTS(:,16) = 0.12;
CONSTANTS(:,17) = 0.025;
CONSTANTS(:,18) = 54.7;
CONSTANTS(:,19) = 1;
CONSTANTS(:,20) = ( ( CONSTANTS(:,5).*CONSTANTS(:,16)+CONSTANTS(:,11)).*CONSTANTS(:,19))./(CONSTANTS(:,16)+ CONSTANTS(:,19).*(1.00000+CONSTANTS(:,16)./CONSTANTS(:,17)));
CONSTANTS(:,21) = ( CONSTANTS(:,6).*CONSTANTS(:,17)+ CONSTANTS(:,12).*CONSTANTS(:,19))./(CONSTANTS(:,17)+ CONSTANTS(:,19).*(1.00000+CONSTANTS(:,17)./CONSTANTS(:,16)));
CONSTANTS(:,22) = (CONSTANTS(:,7)+ CONSTANTS(:,13).*CONSTANTS(:,19))./(1.00000+CONSTANTS(:,19)./CONSTANTS(:,18));
CONSTANTS(:,23) = ( CONSTANTS(:,8).*CONSTANTS(:,18))./(CONSTANTS(:,19)+CONSTANTS(:,18));
CONSTANTS(:,24) = ( ( CONSTANTS(:,9).*CONSTANTS(:,18)+CONSTANTS(:,14)).*CONSTANTS(:,19))./(CONSTANTS(:,19)+CONSTANTS(:,18));
CONSTANTS(:,25) = ( CONSTANTS(:,16).*(CONSTANTS(:,10)+CONSTANTS(:,15)))./(CONSTANTS(:,19)+CONSTANTS(:,16));
CONSTANTS(:,26) = ( ( CONSTANTS(:,5).*CONSTANTS(:,16)+CONSTANTS(:,11)).*CONSTANTS(:,19))./(CONSTANTS(:,19)+CONSTANTS(:,16));
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(:,1) = ( CONSTANTS(:,22).*STATES(:,3)+ (CONSTANTS(:,1)+CONSTANTS(:,2)).*STATES(:,2)) - ( CONSTANTS(:,21).*CONSTANTS(:,3).*STATES(:,1)+ CONSTANTS(:,20).*STATES(:,1));
RATES(:,2) = CONSTANTS(:,20).*STATES(:,1) - (CONSTANTS(:,1)+CONSTANTS(:,2)).*STATES(:,2);
RATES(:,5) = CONSTANTS(:,26).*STATES(:,4) - (CONSTANTS(:,1)+CONSTANTS(:,2)).*STATES(:,5);
RATES(:,4) = ( CONSTANTS(:,24).*STATES(:,3)+ (CONSTANTS(:,1)+CONSTANTS(:,2)).*STATES(:,5)) - ( CONSTANTS(:,25).*STATES(:,4)+ CONSTANTS(:,26).*STATES(:,4));
ALGEBRAIC(:,1) = 1.00000 - (STATES(:,1)+STATES(:,3)+STATES(:,4)+STATES(:,2)+STATES(:,5));
RATES(:,3) = ( CONSTANTS(:,21).*CONSTANTS(:,3).*STATES(:,1)+ CONSTANTS(:,25).*STATES(:,4)+ CONSTANTS(:,4).*ALGEBRAIC(:,1)) - (CONSTANTS(:,22)+CONSTANTS(:,24)+ 1.00000.*CONSTANTS(:,23)).*STATES(:,3);
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) = 1.00000 - (STATES(:,1)+STATES(:,3)+STATES(:,4)+STATES(:,2)+STATES(:,5));
ALGEBRAIC(:,2) = power( 0.100000.*STATES(:,3)+ 0.900000.*STATES(:,4), 4.00000);
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