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 =8;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 35 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 (minute)');
LEGEND_STATES(:,1) = strpad('Y in component Y (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('k1 in component Y (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,7) = strpad('k2 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k3 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('C in component C (dimensionless)');
LEGEND_STATES(:,2) = strpad('M in component M (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('kwee in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,6) = strpad('kcdc25 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('preMPF in component preMPF (dimensionless)');
LEGEND_STATES(:,4) = strpad('Cdc25P in component Cdc25P (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('k25 in component Cdc25P (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('Km25 in component Cdc25P (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('k25r in component Cdc25P (first_order_rate_constant)');
LEGEND_CONSTANTS(:,34) = strpad('k25ro in component Cdc25P (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('Km25r in component Cdc25P (dimensionless)');
LEGEND_CONSTANTS(:,33) = strpad('p in component p (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('Cdc25 in component Cdc25 (dimensionless)');
LEGEND_STATES(:,5) = strpad('Wee1 in component Wee1 (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('kw in component Wee1 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('Kmw in component Wee1 (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('kwr in component Wee1 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,35) = strpad('kwro in component Wee1 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('Kmwr in component Wee1 (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('Wee1P in component Wee1P (dimensionless)');
LEGEND_STATES(:,6) = strpad('IEP in component IEP (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('kie in component IEP (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('Kmie in component IEP (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('kier in component IEP (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('Kmier in component IEP (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('IE in component IE (dimensionless)');
LEGEND_STATES(:,7) = strpad('APC_ in component APC_ (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('kap in component APC_ (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('Kmap in component APC_ (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('kapr in component APC_ (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('Kmapr in component APC_ (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('APC in component APC (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('Cdc2tot in component C (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('Cdc25tot in component Cdc25 (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('Wee1tot in component Wee1P (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('IEtot in component IE (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('APCtot in component APC (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('R in component p (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('s in component p (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('q in component p (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('V2 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,28) = strpad('V2_ in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,29) = strpad('V25 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,30) = strpad('V25_ in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,31) = strpad('Vwee in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,32) = strpad('Vwee_ in component kinetic_parameters (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt Y in component Y (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt M in component M (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt preMPF in component preMPF (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt Cdc25P in component Cdc25P (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt Wee1 in component Wee1 (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt IEP in component IEP (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt APC_ in component APC_ (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) = 0.01577552;
CONSTANTS(:,1) = 0.024;
CONSTANTS(:,2) = 1.15;
STATES(:,2) = 0.0142077;
STATES(:,3) = 0.02541723;
STATES(:,4) = 0.4844362;
CONSTANTS(:,3) = 18;
CONSTANTS(:,4) = 0.1;
CONSTANTS(:,5) = 0.8;
CONSTANTS(:,6) = 1;
STATES(:,5) = 0.5155638;
CONSTANTS(:,7) = 18;
CONSTANTS(:,8) = 0.1;
CONSTANTS(:,9) = 0.8;
CONSTANTS(:,10) = 1;
STATES(:,6) = 0.002287817;
CONSTANTS(:,11) = 4.5;
CONSTANTS(:,12) = 0.01;
CONSTANTS(:,13) = 0.34;
CONSTANTS(:,14) = 0.01;
STATES(:,7) = 0.5051103;
CONSTANTS(:,15) = 0.3;
CONSTANTS(:,16) = 0.01;
CONSTANTS(:,17) = 0.3;
CONSTANTS(:,18) = 1;
CONSTANTS(:,19) = 1;
CONSTANTS(:,20) = 1;
CONSTANTS(:,21) = 1;
CONSTANTS(:,22) = 1;
CONSTANTS(:,23) = 1;
CONSTANTS(:,24) = 1;
CONSTANTS(:,25) = 0.021;
CONSTANTS(:,26) = 1;
CONSTANTS(:,27) = 0.01;
CONSTANTS(:,28) = 0.6;
CONSTANTS(:,29) = 0.04;
CONSTANTS(:,30) = 0.4;
CONSTANTS(:,31) = 0.025;
CONSTANTS(:,32) = 2.5;
CONSTANTS(:,33) = CONSTANTS(:,25).*CONSTANTS(:,24)+CONSTANTS(:,26);
CONSTANTS(:,34) = CONSTANTS(:,5)./CONSTANTS(:,33);
CONSTANTS(:,35) = CONSTANTS(:,9)./CONSTANTS(:,33);
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(:,22) - STATES(:,6);
RATES(:,6) = ( CONSTANTS(:,11).*STATES(:,2).*ALGEBRAIC(:,2))./(CONSTANTS(:,12)+ALGEBRAIC(:,2)) - ( CONSTANTS(:,13).*STATES(:,6))./(CONSTANTS(:,14)+STATES(:,6));
ALGEBRAIC(:,3) = CONSTANTS(:,20) - STATES(:,4);
RATES(:,4) = ( CONSTANTS(:,3).*STATES(:,2).*ALGEBRAIC(:,3))./(CONSTANTS(:,4)+ALGEBRAIC(:,3)) - ( CONSTANTS(:,5).*STATES(:,4))./(CONSTANTS(:,6)+STATES(:,4));
ALGEBRAIC(:,4) = CONSTANTS(:,21) - STATES(:,5);
RATES(:,5) = ( - CONSTANTS(:,7).*STATES(:,2).*STATES(:,5))./(CONSTANTS(:,8)+STATES(:,5))+( CONSTANTS(:,9).*ALGEBRAIC(:,4))./(CONSTANTS(:,10)+ALGEBRAIC(:,4));
ALGEBRAIC(:,5) = CONSTANTS(:,23) - STATES(:,7);
RATES(:,7) = ( CONSTANTS(:,15).*STATES(:,6).*ALGEBRAIC(:,5))./(CONSTANTS(:,16)+ALGEBRAIC(:,5)) - ( CONSTANTS(:,17).*STATES(:,7))./(CONSTANTS(:,18)+STATES(:,7));
ALGEBRAIC(:,7) = CONSTANTS(:,27).*ALGEBRAIC(:,5)+ CONSTANTS(:,28).*STATES(:,7);
ALGEBRAIC(:,1) = CONSTANTS(:,19) - (STATES(:,2)+STATES(:,3));
RATES(:,1) = CONSTANTS(:,1) - ( ALGEBRAIC(:,7).*STATES(:,1)+ CONSTANTS(:,2).*STATES(:,1).*ALGEBRAIC(:,1));
ALGEBRAIC(:,8) = CONSTANTS(:,31).*ALGEBRAIC(:,4)+ CONSTANTS(:,32).*STATES(:,5);
ALGEBRAIC(:,6) = CONSTANTS(:,29).*ALGEBRAIC(:,3)+ CONSTANTS(:,30).*STATES(:,4);
RATES(:,2) = ( ALGEBRAIC(:,6).*STATES(:,3)+ CONSTANTS(:,2).*STATES(:,1).*ALGEBRAIC(:,1)) - ( ALGEBRAIC(:,7).*STATES(:,2)+ ALGEBRAIC(:,8).*STATES(:,2));
RATES(:,3) = ALGEBRAIC(:,8).*STATES(:,2) - ( ALGEBRAIC(:,7).*STATES(:,3)+ ALGEBRAIC(:,6).*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(:,2) = CONSTANTS(:,22) - STATES(:,6);
ALGEBRAIC(:,3) = CONSTANTS(:,20) - STATES(:,4);
ALGEBRAIC(:,4) = CONSTANTS(:,21) - STATES(:,5);
ALGEBRAIC(:,5) = CONSTANTS(:,23) - STATES(:,7);
ALGEBRAIC(:,7) = CONSTANTS(:,27).*ALGEBRAIC(:,5)+ CONSTANTS(:,28).*STATES(:,7);
ALGEBRAIC(:,1) = CONSTANTS(:,19) - (STATES(:,2)+STATES(:,3));
ALGEBRAIC(:,8) = CONSTANTS(:,31).*ALGEBRAIC(:,4)+ CONSTANTS(:,32).*STATES(:,5);
ALGEBRAIC(:,6) = CONSTANTS(:,29).*ALGEBRAIC(:,3)+ CONSTANTS(:,30).*STATES(:,4);
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