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 =6;
end
% There are a total of 13 entries in each of the rate and state variable arrays.
% There are a total of 23 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('Cdk2_CycE in component Cdk2_CycE (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('kwee in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('kon in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k25A in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('koff in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('kassoc in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('kdissoc in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,5) = strpad('phi in component kinetic_parameters (dimensionless)');
LEGEND_STATES(:,2) = strpad('Wee1_a in component Wee1_a (dimensionless)');
LEGEND_STATES(:,3) = strpad('PCdk2_CycE in component PCdk2_CycE (dimensionless)');
LEGEND_STATES(:,4) = strpad('Xic in component Xic (dimensionless)');
LEGEND_STATES(:,5) = strpad('Cdk2_CycErem in component Cdk2_CycErem (dimensionless)');
LEGEND_STATES(:,6) = strpad('Xic_Cdk2_CycE in component Xic_Cdk2_CycE (dimensionless)');
LEGEND_STATES(:,7) = strpad('PCdk2_CycErem in component PCdk2_CycErem (dimensionless)');
LEGEND_STATES(:,8) = strpad('Xic_PCdk2_CycE in component Xic_PCdk2_CycE (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('Jwact in component Wee1_a (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('Jwinact in component Wee1_a (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('Wee1_total in component Wee1_a (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('kwact in component Wee1_a (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('kwinact in component Wee1_a (first_order_rate_constant)');
LEGEND_STATES(:,9) = strpad('Kin_a in component Kin_a (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('Jiact in component Kin_a (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('Jiinact in component Kin_a (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('kiact in component Kin_a (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('kiinact in component Kin_a (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('kedeg in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('kxdeg in component kinetic_parameters (first_order_rate_constant)');
LEGEND_STATES(:,10) = strpad('Deg_a in component Deg_a (dimensionless)');
LEGEND_STATES(:,11) = strpad('Xic_Cdk2_CycErem in component Xic_Cdk2_CycErem (dimensionless)');
LEGEND_STATES(:,12) = strpad('Xic_PCdk2_CycErem in component Xic_PCdk2_CycErem (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('Heav in component Deg_a (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('kdact in component Deg_a (first_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('theta in component Deg_a (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('x in component Deg_a (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('Deg in component kinetic_parameters (dimensionless)');
LEGEND_STATES(:,13) = strpad('Xicrem in component Xicrem (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('Cyc_total in component Cyc_total (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('Xic_total in component Xic_total (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('epsilon in component kinetic_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('pool in component kinetic_parameters (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('n in component kinetic_parameters (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('L in component kinetic_parameters (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt Cdk2_CycE in component Cdk2_CycE (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt PCdk2_CycE in component PCdk2_CycE (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt Wee1_a in component Wee1_a (dimensionless)');
LEGEND_RATES(:,9) = strpad('d/dt Kin_a in component Kin_a (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt Cdk2_CycErem in component Cdk2_CycErem (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt PCdk2_CycErem in component PCdk2_CycErem (dimensionless)');
LEGEND_RATES(:,10) = strpad('d/dt Deg_a in component Deg_a (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt Xic in component Xic (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt Xic_Cdk2_CycE in component Xic_Cdk2_CycE (dimensionless)');
LEGEND_RATES(:,8) = strpad('d/dt Xic_PCdk2_CycE in component Xic_PCdk2_CycE (dimensionless)');
LEGEND_RATES(:,11) = strpad('d/dt Xic_Cdk2_CycErem in component Xic_Cdk2_CycErem (dimensionless)');
LEGEND_RATES(:,12) = strpad('d/dt Xic_PCdk2_CycErem in component Xic_PCdk2_CycErem (dimensionless)');
LEGEND_RATES(:,13) = strpad('d/dt Xicrem in component Xicrem (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) = 0.06;
CONSTANTS(:,1) = 1.5;
CONSTANTS(:,2) = 0.02;
CONSTANTS(:,3) = 0.1;
CONSTANTS(:,4) = 0.0001;
CONSTANTS(:,5) = 0.1;
CONSTANTS(:,6) = 0.001;
STATES(:,2) = 1.02;
STATES(:,3) = 0.94;
STATES(:,4) = 3;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
CONSTANTS(:,7) = 0.01;
CONSTANTS(:,8) = 0.01;
CONSTANTS(:,9) = 8;
CONSTANTS(:,10) = 0.75;
CONSTANTS(:,11) = 1.5;
STATES(:,9) = 0.6;
CONSTANTS(:,12) = 0.01;
CONSTANTS(:,13) = 0.01;
CONSTANTS(:,14) = 0.15;
CONSTANTS(:,15) = 0.6;
CONSTANTS(:,16) = 0.017;
CONSTANTS(:,17) = 0.01;
STATES(:,10) = 0;
STATES(:,11) = 0;
STATES(:,12) = 0;
CONSTANTS(:,18) = 0.023;
CONSTANTS(:,19) = 0.3;
CONSTANTS(:,20) = 0;
STATES(:,13) = 0;
CONSTANTS(:,21) = 0.001;
CONSTANTS(:,22) = 4;
CONSTANTS(:,23) = 0.4;
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(:,2) = ( CONSTANTS(:,10).*(CONSTANTS(:,9) - STATES(:,2)))./((CONSTANTS(:,7)+CONSTANTS(:,9)) - STATES(:,2)) - ( CONSTANTS(:,11).*STATES(:,9).*STATES(:,2))./(CONSTANTS(:,8)+STATES(:,2));
RATES(:,9) = ( CONSTANTS(:,14).*(1.00000 - STATES(:,9)))./((CONSTANTS(:,12)+1.00000) - STATES(:,9)) - ( CONSTANTS(:,15).*STATES(:,1).*STATES(:,9))./(CONSTANTS(:,13)+STATES(:,9));
RATES(:,4) = CONSTANTS(:,6).*(STATES(:,6)+STATES(:,8)+STATES(:,11)+STATES(:,12)) - CONSTANTS(:,5).*STATES(:,4).*(STATES(:,1)+STATES(:,3)+STATES(:,5)+STATES(:,7));
RATES(:,13) = ( CONSTANTS(:,16).*STATES(:,10).*STATES(:,11)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,12)) - CONSTANTS(:,17).*STATES(:,13);
ALGEBRAIC(:,1) = STATES(:,5)+STATES(:,7)+STATES(:,11)+STATES(:,12);
ALGEBRAIC(:,5) = (CONSTANTS(:,21)+power(ALGEBRAIC(:,1), CONSTANTS(:,22)))./(power(CONSTANTS(:,23), CONSTANTS(:,22))+power(ALGEBRAIC(:,1), CONSTANTS(:,22)));
RATES(:,1) = ( CONSTANTS(:,3).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,5)+ CONSTANTS(:,6).*STATES(:,6)) - ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,1)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,1));
RATES(:,3) = ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,7)+ CONSTANTS(:,6).*STATES(:,8)) - ( CONSTANTS(:,3).*STATES(:,3)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,3));
RATES(:,5) = ( CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,1)+ CONSTANTS(:,17).*STATES(:,11)+ CONSTANTS(:,6).*STATES(:,11)) - ( CONSTANTS(:,4).*STATES(:,5)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,5)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,5));
RATES(:,7) = ( CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,3)+ CONSTANTS(:,17).*STATES(:,12)+ CONSTANTS(:,6).*STATES(:,12)) - ( CONSTANTS(:,4).*STATES(:,7)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,7)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,7));
ALGEBRAIC(:,2) = STATES(:,5) - CONSTANTS(:,19);
ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,2)<0.00000, 0.00000 }, 1.00000);
RATES(:,10) = CONSTANTS(:,18).*ALGEBRAIC(:,6);
RATES(:,6) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,11)+ CONSTANTS(:,3).*STATES(:,8)) - ( CONSTANTS(:,6).*STATES(:,6)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,6)+ CONSTANTS(:,1).*STATES(:,2).*STATES(:,6));
RATES(:,8) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,12)+ CONSTANTS(:,1).*STATES(:,2).*STATES(:,6)) - ( CONSTANTS(:,6).*STATES(:,8)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,8)+ CONSTANTS(:,3).*STATES(:,8));
RATES(:,11) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,5)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,6)) - ( CONSTANTS(:,6).*STATES(:,11)+ CONSTANTS(:,4).*STATES(:,11)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,11)+ CONSTANTS(:,17).*STATES(:,11));
RATES(:,12) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,7)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,8)) - ( CONSTANTS(:,6).*STATES(:,12)+ CONSTANTS(:,4).*STATES(:,12)+ CONSTANTS(:,16).*CONSTANTS(:,20).*STATES(:,12)+ CONSTANTS(:,17).*STATES(:,12));
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) = STATES(:,5)+STATES(:,7)+STATES(:,11)+STATES(:,12);
ALGEBRAIC(:,5) = (CONSTANTS(:,21)+power(ALGEBRAIC(:,1), CONSTANTS(:,22)))./(power(CONSTANTS(:,23), CONSTANTS(:,22))+power(ALGEBRAIC(:,1), CONSTANTS(:,22)));
ALGEBRAIC(:,2) = STATES(:,5) - CONSTANTS(:,19);
ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,2)<0.00000, 0.00000 }, 1.00000);
ALGEBRAIC(:,3) = STATES(:,8)+STATES(:,6)+STATES(:,12)+STATES(:,11)+STATES(:,7)+STATES(:,5)+STATES(:,1)+STATES(:,3);
ALGEBRAIC(:,4) = (STATES(:,4)+STATES(:,8)+STATES(:,6)+STATES(:,12)+STATES(:,11)+STATES(:,13))./3.00000;
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