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 =0;
end
% There are a total of 11 entries in each of the rate and state variable arrays.
% There are a total of 30 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('t in component environment (s)');
LEGEND_CONSTANTS(:,1) = strpad('kf5 in component RAF (per_um_s)');
LEGEND_CONSTANTS(:,2) = strpad('kb5 in component RAF (per_s)');
LEGEND_CONSTANTS(:,3) = strpad('km1 in component RAF (um)');
LEGEND_CONSTANTS(:,4) = strpad('km2 in component RAF (um)');
LEGEND_CONSTANTS(:,5) = strpad('km3 in component RAF (um)');
LEGEND_CONSTANTS(:,6) = strpad('km4 in component RAF (um)');
LEGEND_CONSTANTS(:,7) = strpad('Vmax1 in component RAF (per_s)');
LEGEND_CONSTANTS(:,8) = strpad('Vmax2 in component RAF (per_s)');
LEGEND_CONSTANTS(:,9) = strpad('Vmax3 in component RAF (per_s)');
LEGEND_CONSTANTS(:,10) = strpad('Vmax4 in component RAF (per_s)');
LEGEND_CONSTANTS(:,11) = strpad('PKC in component undefinedvariables (um)');
LEGEND_CONSTANTS(:,12) = strpad('PP2A in component RAF (um)');
LEGEND_STATES(:,1) = strpad('MAPK_star in component MAPK (um)');
LEGEND_STATES(:,2) = strpad('Raf in component RAF (um)');
LEGEND_STATES(:,3) = strpad('Raf_star in component RAF (um)');
LEGEND_STATES(:,4) = strpad('Raf_star_star in component RAF (um)');
LEGEND_STATES(:,5) = strpad('GTPRas in component RAF (um)');
LEGEND_STATES(:,6) = strpad('GTPRasRaf_star in component RAF (um)');
LEGEND_CONSTANTS(:,13) = strpad('km6 in component MAPKK (um)');
LEGEND_CONSTANTS(:,14) = strpad('km7 in component MAPKK (um)');
LEGEND_CONSTANTS(:,15) = strpad('km8 in component MAPKK (um)');
LEGEND_CONSTANTS(:,16) = strpad('km9 in component MAPKK (um)');
LEGEND_CONSTANTS(:,17) = strpad('Vmax6 in component MAPKK (per_s)');
LEGEND_CONSTANTS(:,18) = strpad('Vmax7 in component MAPKK (per_s)');
LEGEND_CONSTANTS(:,19) = strpad('Vmax8 in component MAPKK (per_s)');
LEGEND_CONSTANTS(:,20) = strpad('Vmax9 in component MAPKK (per_s)');
LEGEND_CONSTANTS(:,21) = strpad('PP2A in component MAPKK (um)');
LEGEND_STATES(:,7) = strpad('MAPKK in component MAPKK (um)');
LEGEND_STATES(:,8) = strpad('MAPKK_star in component MAPKK (um)');
LEGEND_STATES(:,9) = strpad('MAPKK_star_star in component MAPKK (um)');
LEGEND_CONSTANTS(:,22) = strpad('km10 in component MAPK (um)');
LEGEND_CONSTANTS(:,23) = strpad('km11 in component MAPK (um)');
LEGEND_CONSTANTS(:,24) = strpad('km12 in component MAPK (um)');
LEGEND_CONSTANTS(:,25) = strpad('km13 in component MAPK (um)');
LEGEND_CONSTANTS(:,26) = strpad('Vmax10 in component MAPK (per_s)');
LEGEND_CONSTANTS(:,27) = strpad('Vmax11 in component MAPK (per_s)');
LEGEND_CONSTANTS(:,28) = strpad('Vmax12 in component MAPK (per_s)');
LEGEND_CONSTANTS(:,29) = strpad('Vmax13 in component MAPK (per_s)');
LEGEND_STATES(:,10) = strpad('MAPK in component MAPK (um)');
LEGEND_STATES(:,11) = strpad('MAPK_tyr in component MAPK (um)');
LEGEND_CONSTANTS(:,30) = strpad('MKP1 in component MAPK (um)');
LEGEND_RATES(:,6) = strpad('d/dt GTPRasRaf_star in component RAF (um)');
LEGEND_RATES(:,5) = strpad('d/dt GTPRas in component RAF (um)');
LEGEND_RATES(:,2) = strpad('d/dt Raf in component RAF (um)');
LEGEND_RATES(:,3) = strpad('d/dt Raf_star in component RAF (um)');
LEGEND_RATES(:,4) = strpad('d/dt Raf_star_star in component RAF (um)');
LEGEND_RATES(:,7) = strpad('d/dt MAPKK in component MAPKK (um)');
LEGEND_RATES(:,8) = strpad('d/dt MAPKK_star in component MAPKK (um)');
LEGEND_RATES(:,9) = strpad('d/dt MAPKK_star_star in component MAPKK (um)');
LEGEND_RATES(:,10) = strpad('d/dt MAPK in component MAPK (um)');
LEGEND_RATES(:,11) = strpad('d/dt MAPK_tyr in component MAPK (um)');
LEGEND_RATES(:,1) = strpad('d/dt MAPK_star in component MAPK (um)');
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) = 0.00004;
CONSTANTS(:,2) = 0.5;
CONSTANTS(:,3) = 66.666666667;
CONSTANTS(:,4) = 25.64166667;
CONSTANTS(:,5) = 15.6565;
CONSTANTS(:,6) = 15.6565;
CONSTANTS(:,7) = 4;
CONSTANTS(:,8) = 10;
CONSTANTS(:,9) = 6;
CONSTANTS(:,10) = 6;
CONSTANTS(:,11) = 0.1;
CONSTANTS(:,12) = 0.224;
STATES(:,1) = 0;
STATES(:,2) = 0.1;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0.1;
STATES(:,6) = 0;
CONSTANTS(:,13) = 0.159091667;
CONSTANTS(:,14) = 0.159091667;
CONSTANTS(:,15) = 15.6565;
CONSTANTS(:,16) = 15.6565;
CONSTANTS(:,17) = 0.105;
CONSTANTS(:,18) = 0.105;
CONSTANTS(:,19) = 6;
CONSTANTS(:,20) = 6;
CONSTANTS(:,21) = 0.224;
STATES(:,7) = 0.18;
STATES(:,8) = 0;
STATES(:,9) = 0;
CONSTANTS(:,22) = 0.046296667;
CONSTANTS(:,23) = 0.046296667;
CONSTANTS(:,24) = 0.066666667;
CONSTANTS(:,25) = 0.066666667;
CONSTANTS(:,26) = 0.15;
CONSTANTS(:,27) = 0.15;
CONSTANTS(:,28) = 1;
CONSTANTS(:,29) = 1;
STATES(:,10) = 0.36;
STATES(:,11) = 0;
CONSTANTS(:,30) = 0.032;
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(:,6) = STATES(:,5).*STATES(:,3).*CONSTANTS(:,1) - STATES(:,6).*CONSTANTS(:,2);
RATES(:,5) = - STATES(:,5).*STATES(:,3).*CONSTANTS(:,1)+ STATES(:,6).*CONSTANTS(:,2);
RATES(:,2) = ( - CONSTANTS(:,11).*STATES(:,2).*CONSTANTS(:,7))./(CONSTANTS(:,3)+STATES(:,2))+( STATES(:,3).*CONSTANTS(:,12).*CONSTANTS(:,9))./(CONSTANTS(:,5)+STATES(:,3));
RATES(:,3) = ((( CONSTANTS(:,11).*STATES(:,2).*CONSTANTS(:,7))./(CONSTANTS(:,3)+STATES(:,2)) - ( STATES(:,3).*CONSTANTS(:,12).*CONSTANTS(:,9))./(CONSTANTS(:,5)+STATES(:,3))) - ( STATES(:,3).*STATES(:,1).*CONSTANTS(:,8))./(CONSTANTS(:,4)+STATES(:,3)))+( STATES(:,4).*CONSTANTS(:,12).*CONSTANTS(:,10))./(CONSTANTS(:,6)+STATES(:,4));
RATES(:,4) = ( STATES(:,3).*STATES(:,1).*CONSTANTS(:,8))./(CONSTANTS(:,4)+STATES(:,3)) - ( STATES(:,4).*CONSTANTS(:,12).*CONSTANTS(:,10))./(CONSTANTS(:,6)+STATES(:,4));
RATES(:,7) = ( - STATES(:,7).*CONSTANTS(:,17).*STATES(:,6))./(CONSTANTS(:,13)+STATES(:,7))+( STATES(:,8).*CONSTANTS(:,19).*CONSTANTS(:,21))./(CONSTANTS(:,15)+STATES(:,8));
RATES(:,8) = ((( STATES(:,7).*CONSTANTS(:,17).*STATES(:,6))./(CONSTANTS(:,13)+STATES(:,7)) - ( STATES(:,8).*CONSTANTS(:,19).*CONSTANTS(:,21))./(CONSTANTS(:,15)+STATES(:,8))) - ( STATES(:,8).*CONSTANTS(:,18).*STATES(:,6))./(CONSTANTS(:,14)+STATES(:,8)))+( STATES(:,9).*CONSTANTS(:,20).*CONSTANTS(:,21))./(CONSTANTS(:,16)+STATES(:,9));
RATES(:,9) = ( STATES(:,8).*CONSTANTS(:,18).*STATES(:,6))./(CONSTANTS(:,14)+STATES(:,8)) - ( STATES(:,9).*CONSTANTS(:,20).*CONSTANTS(:,21))./(CONSTANTS(:,16)+STATES(:,9));
RATES(:,10) = ( - STATES(:,10).*CONSTANTS(:,26).*STATES(:,9))./(CONSTANTS(:,22)+STATES(:,10))+( STATES(:,11).*CONSTANTS(:,28).*CONSTANTS(:,30))./(CONSTANTS(:,24)+STATES(:,11));
RATES(:,11) = ((( STATES(:,10).*CONSTANTS(:,26).*STATES(:,9))./(CONSTANTS(:,22)+STATES(:,10)) - ( STATES(:,11).*CONSTANTS(:,28).*CONSTANTS(:,30))./(CONSTANTS(:,24)+STATES(:,11))) - ( STATES(:,11).*CONSTANTS(:,27).*STATES(:,9))./(CONSTANTS(:,23)+STATES(:,11)))+( STATES(:,1).*CONSTANTS(:,29).*CONSTANTS(:,30))./(CONSTANTS(:,25)+STATES(:,1));
RATES(:,1) = ( STATES(:,11).*CONSTANTS(:,27).*STATES(:,9))./(CONSTANTS(:,23)+STATES(:,11)) - ( STATES(:,1).*CONSTANTS(:,29).*CONSTANTS(:,30))./(CONSTANTS(:,25)+STATES(:,1));
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
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