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 10 entries in each of the rate and state variable arrays.
% There are a total of 28 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 (day)');
LEGEND_STATES(:,1) = strpad('T in component uninfected_CD4 (cells_per_mm3)');
LEGEND_CONSTANTS(:,1) = strpad('s in component uninfected_CD4 (cells_per_mm3_day)');
LEGEND_CONSTANTS(:,2) = strpad('lambda in component uninfected_CD4 (per_day)');
LEGEND_STATES(:,2) = strpad('T1_star in component productively_infected_CD4 (cells_per_mm3)');
LEGEND_STATES(:,3) = strpad('T2_star in component productively_infected_CD4 (cells_per_mm3)');
LEGEND_CONSTANTS(:,3) = strpad('Tmax in component uninfected_CD4 (cells_per_mm3)');
LEGEND_CONSTANTS(:,4) = strpad('mu in component uninfected_CD4 (per_day)');
LEGEND_CONSTANTS(:,5) = strpad('k1 in component productively_infected_CD4 (ml_per_virons_day)');
LEGEND_CONSTANTS(:,6) = strpad('r1 in component drug_parameters (dimensionless)');
LEGEND_STATES(:,4) = strpad('V1_I in component virus_strain1 (virons_per_ml)');
LEGEND_CONSTANTS(:,7) = strpad('k2 in component productively_infected_CD4 (ml_per_virons_day)');
LEGEND_CONSTANTS(:,8) = strpad('r2 in component drug_parameters (dimensionless)');
LEGEND_STATES(:,5) = strpad('V2_I in component virus_strain2 (virons_per_ml)');
LEGEND_STATES(:,6) = strpad('M in component uninfected_long_lived_cells (cells_per_mm3)');
LEGEND_CONSTANTS(:,9) = strpad('lambda_M in component uninfected_long_lived_cells (cells_per_mm3_day)');
LEGEND_CONSTANTS(:,10) = strpad('mu_M in component uninfected_long_lived_cells (per_day)');
LEGEND_CONSTANTS(:,11) = strpad('k1_M in component productively_infected_long_lived_cells (ml_per_virons_day)');
LEGEND_CONSTANTS(:,12) = strpad('k2_M in component productively_infected_long_lived_cells (ml_per_virons_day)');
LEGEND_CONSTANTS(:,13) = strpad('m11 in component productively_infected_CD4 (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('m21 in component productively_infected_CD4 (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('delta1 in component productively_infected_CD4 (per_day)');
LEGEND_CONSTANTS(:,16) = strpad('m22 in component productively_infected_CD4 (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('m12 in component productively_infected_CD4 (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('delta2 in component productively_infected_CD4 (per_day)');
LEGEND_STATES(:,7) = strpad('M1_star in component productively_infected_long_lived_cells (cells_per_mm3)');
LEGEND_CONSTANTS(:,19) = strpad('delta1_M in component productively_infected_long_lived_cells (per_day)');
LEGEND_STATES(:,8) = strpad('M2_star in component productively_infected_long_lived_cells (cells_per_mm3)');
LEGEND_CONSTANTS(:,20) = strpad('delta2_M in component productively_infected_long_lived_cells (per_day)');
LEGEND_CONSTANTS(:,21) = strpad('p1 in component drug_parameters (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('N1 in component virus_strain1 (virons_per_cell)');
LEGEND_CONSTANTS(:,23) = strpad('N1_M in component virus_strain1 (virons_per_cell)');
LEGEND_STATES(:,9) = strpad('V1 in component virus_strain1 (virons_per_ml)');
LEGEND_CONSTANTS(:,24) = strpad('c1 in component virus_strain1 (per_day)');
LEGEND_CONSTANTS(:,25) = strpad('p2 in component drug_parameters (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('N2 in component virus_strain2 (virons_per_cell)');
LEGEND_CONSTANTS(:,27) = strpad('N2_M in component virus_strain2 (virons_per_cell)');
LEGEND_CONSTANTS(:,28) = strpad('c2 in component virus_strain2 (per_day)');
LEGEND_STATES(:,10) = strpad('V2 in component virus_strain2 (virons_per_ml)');
LEGEND_RATES(:,1) = strpad('d/dt T in component uninfected_CD4 (cells_per_mm3)');
LEGEND_RATES(:,6) = strpad('d/dt M in component uninfected_long_lived_cells (cells_per_mm3)');
LEGEND_RATES(:,2) = strpad('d/dt T1_star in component productively_infected_CD4 (cells_per_mm3)');
LEGEND_RATES(:,3) = strpad('d/dt T2_star in component productively_infected_CD4 (cells_per_mm3)');
LEGEND_RATES(:,7) = strpad('d/dt M1_star in component productively_infected_long_lived_cells (cells_per_mm3)');
LEGEND_RATES(:,8) = strpad('d/dt M2_star in component productively_infected_long_lived_cells (cells_per_mm3)');
LEGEND_RATES(:,4) = strpad('d/dt V1_I in component virus_strain1 (virons_per_ml)');
LEGEND_RATES(:,9) = strpad('d/dt V1 in component virus_strain1 (virons_per_ml)');
LEGEND_RATES(:,5) = strpad('d/dt V2_I in component virus_strain2 (virons_per_ml)');
LEGEND_RATES(:,10) = strpad('d/dt V2 in component virus_strain2 (virons_per_ml)');
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) = 178.81;
CONSTANTS(:,1) = 0;
CONSTANTS(:,2) = 0.01;
STATES(:,2) = 1.19;
STATES(:,3) = 0.004;
CONSTANTS(:,3) = 450;
CONSTANTS(:,4) = 0.0014;
CONSTANTS(:,5) = 3.43E-8;
CONSTANTS(:,6) = 0.9;
STATES(:,4) = 133500;
CONSTANTS(:,7) = 3.43E-8;
CONSTANTS(:,8) = 0.25;
STATES(:,5) = 450;
STATES(:,6) = 49.2;
CONSTANTS(:,9) = 2.0;
CONSTANTS(:,10) = 0.04;
CONSTANTS(:,11) = 4.67E-9;
CONSTANTS(:,12) = 4.67E-9;
CONSTANTS(:,13) = 1;
CONSTANTS(:,14) = 3.4E-5;
CONSTANTS(:,15) = 0.69;
CONSTANTS(:,16) = 1;
CONSTANTS(:,17) = 3.4E-5;
CONSTANTS(:,18) = 0.69;
STATES(:,7) = 0.49;
CONSTANTS(:,19) = 0.062;
STATES(:,8) = 1.7E-3;
CONSTANTS(:,20) = 0.062;
CONSTANTS(:,21) = 0.99;
CONSTANTS(:,22) = 480.1;
CONSTANTS(:,23) = 534.4;
STATES(:,9) = 133500;
CONSTANTS(:,24) = 3.07;
CONSTANTS(:,25) = 0.25;
CONSTANTS(:,26) = 475.3;
CONSTANTS(:,27) = 529.0;
CONSTANTS(:,28) = 3.07;
STATES(:,10) = 450;
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(:,1)+ CONSTANTS(:,2).*STATES(:,1).*(1.00000 - (STATES(:,1)+STATES(:,2)+STATES(:,3))./CONSTANTS(:,3))) - CONSTANTS(:,4).*STATES(:,1)) - CONSTANTS(:,5).*(1.00000 - CONSTANTS(:,6)).*STATES(:,1).*STATES(:,4)) - CONSTANTS(:,7).*(1.00000 - CONSTANTS(:,8)).*STATES(:,1).*STATES(:,5);
RATES(:,6) = ((CONSTANTS(:,9) - CONSTANTS(:,10).*STATES(:,6)) - CONSTANTS(:,11).*(1.00000 - CONSTANTS(:,6)).*STATES(:,6).*STATES(:,4)) - CONSTANTS(:,12).*(1.00000 - CONSTANTS(:,8)).*STATES(:,6).*STATES(:,5);
RATES(:,2) = ( CONSTANTS(:,13).*CONSTANTS(:,5).*(1.00000 - CONSTANTS(:,6)).*STATES(:,1).*STATES(:,4)+ CONSTANTS(:,14).*CONSTANTS(:,7).*(1.00000 - CONSTANTS(:,8)).*STATES(:,1).*STATES(:,5)) - CONSTANTS(:,15).*STATES(:,2);
RATES(:,3) = ( CONSTANTS(:,16).*CONSTANTS(:,7).*(1.00000 - CONSTANTS(:,8)).*STATES(:,1).*STATES(:,5)+ CONSTANTS(:,17).*CONSTANTS(:,5).*(1.00000 - CONSTANTS(:,6)).*STATES(:,1).*STATES(:,4)) - CONSTANTS(:,18).*STATES(:,3);
RATES(:,7) = ( CONSTANTS(:,13).*CONSTANTS(:,11).*(1.00000 - CONSTANTS(:,6)).*STATES(:,6).*STATES(:,4)+ CONSTANTS(:,14).*CONSTANTS(:,12).*(1.00000 - CONSTANTS(:,8)).*STATES(:,6).*STATES(:,5)) - CONSTANTS(:,19).*STATES(:,7);
RATES(:,8) = ( CONSTANTS(:,16).*CONSTANTS(:,12).*(1.00000 - CONSTANTS(:,8)).*STATES(:,6).*STATES(:,5)+ CONSTANTS(:,17).*CONSTANTS(:,11).*(1.00000 - CONSTANTS(:,6)).*STATES(:,6).*STATES(:,4)) - CONSTANTS(:,20).*STATES(:,8);
RATES(:,4) = ( (1.00000 - CONSTANTS(:,21)).*CONSTANTS(:,22).*CONSTANTS(:,15).*STATES(:,2)+ (1.00000 - CONSTANTS(:,21)).*CONSTANTS(:,23).*CONSTANTS(:,19).*STATES(:,7)) - CONSTANTS(:,24).*STATES(:,4);
RATES(:,9) = ( CONSTANTS(:,22).*CONSTANTS(:,15).*STATES(:,2)+ CONSTANTS(:,23).*CONSTANTS(:,19).*STATES(:,7)) - CONSTANTS(:,24).*STATES(:,9);
RATES(:,5) = ( (1.00000 - CONSTANTS(:,25)).*CONSTANTS(:,26).*CONSTANTS(:,18).*STATES(:,3)+ (1.00000 - CONSTANTS(:,25)).*CONSTANTS(:,27).*CONSTANTS(:,20).*STATES(:,8)) - CONSTANTS(:,28).*STATES(:,5);
RATES(:,10) = ( CONSTANTS(:,26).*CONSTANTS(:,18).*STATES(:,3)+ CONSTANTS(:,27).*CONSTANTS(:,20).*STATES(:,8)) - CONSTANTS(:,28).*STATES(:,10);
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