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 =4;
end
% There are a total of 20 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 (hour)');
LEGEND_STATES(:,1) = strpad('S_0 in component S_0 (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('R_0 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('u_s in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('phi in component phi (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('S_1 in component S_1 (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('R_1 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,1) = strpad('epsilon_s in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('alpha in component kinetic_parameters (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('u in component kinetic_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('S_2 in component S_2 (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('R_2 in component R (first_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('S_3 in component S_3 (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('R_3 in component R (first_order_rate_constant)');
LEGEND_STATES(:,5) = strpad('S_4 in component S_4 (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('R_4 in component R (first_order_rate_constant)');
LEGEND_STATES(:,6) = strpad('S_5 in component S_5 (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('R_5 in component R (first_order_rate_constant)');
LEGEND_STATES(:,7) = strpad('S_6 in component S_6 (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('R_6 in component R (first_order_rate_constant)');
LEGEND_STATES(:,8) = strpad('S_7 in component S_7 (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('R_7 in component R (first_order_rate_constant)');
LEGEND_STATES(:,9) = strpad('S_8 in component S_8 (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('R_8 in component R (first_order_rate_constant)');
LEGEND_STATES(:,10) = strpad('M_0 in component M_0 (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('epsilon_m in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,26) = strpad('u_m in component kinetic_parameters (first_order_rate_constant)');
LEGEND_STATES(:,11) = strpad('M_1 in component M_1 (dimensionless)');
LEGEND_STATES(:,12) = strpad('M_1_2 in component M_1 (dimensionless)');
LEGEND_STATES(:,13) = strpad('M_2 in component M_2 (dimensionless)');
LEGEND_STATES(:,14) = strpad('M_3 in component M_3 (dimensionless)');
LEGEND_STATES(:,15) = strpad('M_4 in component M_4 (dimensionless)');
LEGEND_STATES(:,16) = strpad('M_5 in component M_5 (dimensionless)');
LEGEND_STATES(:,17) = strpad('M_6 in component M_6 (dimensionless)');
LEGEND_STATES(:,18) = strpad('M_7 in component M_7 (dimensionless)');
LEGEND_STATES(:,19) = strpad('M_8 in component M_8 (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('r_0 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('r_1 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('r_2 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('r_3 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('r_4 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('r_5 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('r_6 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('r_7 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('r_8 in component R (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('a in component kinetic_parameters (dimensionless)');
LEGEND_STATES(:,20) = strpad('w in component w (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('total_cells in component total_cells (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('stable_total in component total_cells (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('mutant_total in component total_cells (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('beta in component kinetic_parameters (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt S_0 in component S_0 (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt S_1 in component S_1 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt S_2 in component S_2 (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt S_3 in component S_3 (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt S_4 in component S_4 (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt S_5 in component S_5 (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt S_6 in component S_6 (dimensionless)');
LEGEND_RATES(:,8) = strpad('d/dt S_7 in component S_7 (dimensionless)');
LEGEND_RATES(:,9) = strpad('d/dt S_8 in component S_8 (dimensionless)');
LEGEND_RATES(:,10) = strpad('d/dt M_0 in component M_0 (dimensionless)');
LEGEND_RATES(:,11) = strpad('d/dt M_1 in component M_1 (dimensionless)');
LEGEND_RATES(:,12) = strpad('d/dt M_1_2 in component M_1 (dimensionless)');
LEGEND_RATES(:,13) = strpad('d/dt M_2 in component M_2 (dimensionless)');
LEGEND_RATES(:,14) = strpad('d/dt M_3 in component M_3 (dimensionless)');
LEGEND_RATES(:,15) = strpad('d/dt M_4 in component M_4 (dimensionless)');
LEGEND_RATES(:,16) = strpad('d/dt M_5 in component M_5 (dimensionless)');
LEGEND_RATES(:,17) = strpad('d/dt M_6 in component M_6 (dimensionless)');
LEGEND_RATES(:,18) = strpad('d/dt M_7 in component M_7 (dimensionless)');
LEGEND_RATES(:,19) = strpad('d/dt M_8 in component M_8 (dimensionless)');
LEGEND_RATES(:,20) = strpad('d/dt w in component w (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) = 0.5;
STATES(:,2) = 0;
CONSTANTS(:,1) = 0.99;
CONSTANTS(:,2) = 0.6;
CONSTANTS(:,3) = 0.07;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
STATES(:,10) = 0.5;
CONSTANTS(:,4) = 0.1;
STATES(:,11) = 0;
STATES(:,12) = 0;
STATES(:,13) = 0;
STATES(:,14) = 0;
STATES(:,15) = 0;
STATES(:,16) = 0;
STATES(:,17) = 0;
STATES(:,18) = 0;
STATES(:,19) = 0;
CONSTANTS(:,5) = 0.5;
CONSTANTS(:,6) = 0.6;
CONSTANTS(:,7) = 0.7;
CONSTANTS(:,8) = 0.8;
CONSTANTS(:,9) = 0.9;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 1.1;
CONSTANTS(:,12) = 1.2;
CONSTANTS(:,13) = 1.3;
CONSTANTS(:,14) = 0.5;
STATES(:,20) = 0;
CONSTANTS(:,15) = 0.2;
CONSTANTS(:,16) = CONSTANTS(:,5);
CONSTANTS(:,17) = CONSTANTS(:,3).*(1.00000 - ( CONSTANTS(:,15).*CONSTANTS(:,1))./1.00000);
CONSTANTS(:,18) = CONSTANTS(:,6).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,19) = CONSTANTS(:,7).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,20) = CONSTANTS(:,8).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,21) = CONSTANTS(:,9).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,22) = CONSTANTS(:,10).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,23) = CONSTANTS(:,11).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,24) = CONSTANTS(:,12).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,25) = CONSTANTS(:,13).*(1.00000 - CONSTANTS(:,14));
CONSTANTS(:,26) = CONSTANTS(:,3).*(1.00000 - ( CONSTANTS(:,15).*CONSTANTS(:,4))./1.00000);
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(:,11) = STATES(:,10).*1.00000;
ALGEBRAIC(:,1) = ((1.00000 - CONSTANTS(:,17))./1.00000).*( CONSTANTS(:,16).*STATES(:,1)+ CONSTANTS(:,18).*STATES(:,2)+ CONSTANTS(:,19).*STATES(:,3)+ CONSTANTS(:,20).*STATES(:,4)+ CONSTANTS(:,21).*STATES(:,5))+ ((1.00000 - CONSTANTS(:,26))./1.00000).*( CONSTANTS(:,18).*STATES(:,11)+ CONSTANTS(:,19).*STATES(:,13)+ CONSTANTS(:,20).*STATES(:,14)+ CONSTANTS(:,21).*STATES(:,15));
RATES(:,1) = (( CONSTANTS(:,16).*STATES(:,1))./1.00000).*(1.00000 - CONSTANTS(:,17)) - ALGEBRAIC(:,1).*STATES(:,1);
RATES(:,2) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,16).*STATES(:,1))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,18).*STATES(:,2))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,2);
RATES(:,3) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,18).*STATES(:,2))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,19).*STATES(:,3))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,3);
RATES(:,4) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,19).*STATES(:,3))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,20).*STATES(:,4))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,4);
RATES(:,5) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,20).*STATES(:,4))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,21).*STATES(:,5))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,5);
RATES(:,6) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,21).*STATES(:,5))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,22).*STATES(:,6))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,6);
RATES(:,7) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,22).*STATES(:,6))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,23).*STATES(:,7))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,7);
RATES(:,8) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,23).*STATES(:,7))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,24).*STATES(:,8))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,8);
RATES(:,9) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,24).*STATES(:,8))./1.00000).*(1.00000 - CONSTANTS(:,1))+ (( CONSTANTS(:,25).*STATES(:,9))./1.00000).*(1.00000 - CONSTANTS(:,17))) - ALGEBRAIC(:,1).*STATES(:,9);
RATES(:,10) = (( CONSTANTS(:,16).*STATES(:,10))./1.00000).*(1.00000 - CONSTANTS(:,26)) - ALGEBRAIC(:,1).*STATES(:,10);
RATES(:,12) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,16).*STATES(:,10))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,18).*STATES(:,11))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,11);
RATES(:,13) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,18).*STATES(:,11))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,19).*STATES(:,13))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,13);
RATES(:,14) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,19).*STATES(:,13))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,20).*STATES(:,14))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,14);
RATES(:,15) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,20).*STATES(:,15))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,21).*STATES(:,15))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,15);
RATES(:,16) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,21).*STATES(:,15))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,22).*STATES(:,16))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,16);
RATES(:,17) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,22).*STATES(:,16))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,23).*STATES(:,17))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,17);
RATES(:,18) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,23).*STATES(:,17))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,24).*STATES(:,18))./1.00000).*(1.00000 - CONSTANTS(:,26))) - ALGEBRAIC(:,1).*STATES(:,18);
RATES(:,19) = ( (( CONSTANTS(:,2).*CONSTANTS(:,3).*CONSTANTS(:,24).*STATES(:,18))./1.00000).*(1.00000 - CONSTANTS(:,4))+ (( CONSTANTS(:,25).*STATES(:,19))./1.00000).*((1.00000 - CONSTANTS(:,26))+ (( CONSTANTS(:,2).*CONSTANTS(:,3))./1.00000).*(1.00000 - CONSTANTS(:,4)))) - ALGEBRAIC(:,1).*STATES(:,9);
RATES(:,20) = (( (1.00000 - CONSTANTS(:,2)).*CONSTANTS(:,3))./1.00000).*( (1.00000 - CONSTANTS(:,1)).*( CONSTANTS(:,16).*STATES(:,1)+ CONSTANTS(:,18).*STATES(:,2)+ CONSTANTS(:,19).*STATES(:,3)+ CONSTANTS(:,20).*STATES(:,4)+ CONSTANTS(:,21).*STATES(:,5)+ CONSTANTS(:,22).*STATES(:,6)+ CONSTANTS(:,23).*STATES(:,7)+ CONSTANTS(:,24).*STATES(:,8)+ CONSTANTS(:,25).*STATES(:,9))+ (1.00000 - CONSTANTS(:,4)).*( CONSTANTS(:,16).*STATES(:,10)+ CONSTANTS(:,18).*STATES(:,11)+ CONSTANTS(:,19).*STATES(:,13)+ CONSTANTS(:,20).*STATES(:,14)+ CONSTANTS(:,21).*STATES(:,15)+ CONSTANTS(:,22).*STATES(:,16)+ CONSTANTS(:,23).*STATES(:,17)+ CONSTANTS(:,24).*STATES(:,18)+ CONSTANTS(:,25).*STATES(:,19))) - ALGEBRAIC(:,1).*STATES(:,20);
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 - CONSTANTS(:,17))./1.00000).*( CONSTANTS(:,16).*STATES(:,1)+ CONSTANTS(:,18).*STATES(:,2)+ CONSTANTS(:,19).*STATES(:,3)+ CONSTANTS(:,20).*STATES(:,4)+ CONSTANTS(:,21).*STATES(:,5))+ ((1.00000 - CONSTANTS(:,26))./1.00000).*( CONSTANTS(:,18).*STATES(:,11)+ CONSTANTS(:,19).*STATES(:,13)+ CONSTANTS(:,20).*STATES(:,14)+ CONSTANTS(:,21).*STATES(:,15));
ALGEBRAIC(:,2) = STATES(:,1)+STATES(:,2)+STATES(:,3)+STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,8)+STATES(:,9)+STATES(:,10)+STATES(:,13)+STATES(:,14)+STATES(:,15)+STATES(:,16)+STATES(:,17)+STATES(:,18)+STATES(:,19);
ALGEBRAIC(:,3) = STATES(:,1)+STATES(:,2)+STATES(:,3)+STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,8)+STATES(:,9);
ALGEBRAIC(:,4) = STATES(:,10)+STATES(:,13)+STATES(:,14)+STATES(:,15)+STATES(:,16)+STATES(:,17)+STATES(:,18)+STATES(:,19);
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