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 =9;
end
% There are a total of 16 entries in each of the rate and state variable arrays.
% There are a total of 14 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('B0 in component B0 (cells_per_GC)');
LEGEND_CONSTANTS(:,1) = strpad('pr in component kinetic_parameters (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('mu in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('rho in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('delta_B in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('CT_star in component CT_star (cells_per_GC)');
LEGEND_STATES(:,2) = strpad('B1 in component B1 (cells_per_GC)');
LEGEND_ALGEBRAIC(:,5) = strpad('alpha_B in component alpha_B (dimensionless)');
LEGEND_STATES(:,3) = strpad('B2 in component B2 (cells_per_GC)');
LEGEND_STATES(:,4) = strpad('B3 in component B3 (cells_per_GC)');
LEGEND_STATES(:,5) = strpad('B4 in component B4 (cells_per_GC)');
LEGEND_STATES(:,6) = strpad('B5 in component B5 (cells_per_GC)');
LEGEND_STATES(:,7) = strpad('B6 in component B6 (cells_per_GC)');
LEGEND_STATES(:,8) = strpad('B7 in component B7 (cells_per_GC)');
LEGEND_STATES(:,9) = strpad('B8 in component B8 (cells_per_GC)');
LEGEND_STATES(:,10) = strpad('B9 in component B9 (cells_per_GC)');
LEGEND_STATES(:,11) = strpad('B10 in component B10 (cells_per_GC)');
LEGEND_ALGEBRAIC(:,2) = strpad('B_sum in component centroblasts_sum (cells_per_GC)');
LEGEND_STATES(:,12) = strpad('C in component C (cells_per_GC)');
LEGEND_CONSTANTS(:,5) = strpad('d in component C (first_order_rate_constant)');
LEGEND_STATES(:,13) = strpad('C_star in component C_star (cells_per_GC)');
LEGEND_ALGEBRAIC(:,3) = strpad('CA in component CA (cells_per_GC)');
LEGEND_ALGEBRAIC(:,6) = strpad('C_starsum in component centrocytes_sum (cells_per_GC)');
LEGEND_STATES(:,14) = strpad('M in component M (cells_per_GC)');
LEGEND_STATES(:,15) = strpad('A in component A (cells_per_GC)');
LEGEND_CONSTANTS(:,6) = strpad('z in component A (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('u in component A (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('log_A in component A (dimensionless)');
LEGEND_STATES(:,16) = strpad('T in component T (cells_per_GC)');
LEGEND_CONSTANTS(:,8) = strpad('p in component T (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('sigma in component T (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('delta_T in component T (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,7) = strpad('alpha_T in component alpha_T (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('SA in component CA (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('ST in component CT_star (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('KB in component alpha_B (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('KT in component alpha_T (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('total in component total (cells_per_GC)');
LEGEND_ALGEBRAIC(:,9) = strpad('log_total in component total (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt B0 in component B0 (cells_per_GC)');
LEGEND_RATES(:,2) = strpad('d/dt B1 in component B1 (cells_per_GC)');
LEGEND_RATES(:,3) = strpad('d/dt B2 in component B2 (cells_per_GC)');
LEGEND_RATES(:,4) = strpad('d/dt B3 in component B3 (cells_per_GC)');
LEGEND_RATES(:,5) = strpad('d/dt B4 in component B4 (cells_per_GC)');
LEGEND_RATES(:,6) = strpad('d/dt B5 in component B5 (cells_per_GC)');
LEGEND_RATES(:,7) = strpad('d/dt B6 in component B6 (cells_per_GC)');
LEGEND_RATES(:,8) = strpad('d/dt B7 in component B7 (cells_per_GC)');
LEGEND_RATES(:,9) = strpad('d/dt B8 in component B8 (cells_per_GC)');
LEGEND_RATES(:,10) = strpad('d/dt B9 in component B9 (cells_per_GC)');
LEGEND_RATES(:,11) = strpad('d/dt B10 in component B10 (cells_per_GC)');
LEGEND_RATES(:,12) = strpad('d/dt C in component C (cells_per_GC)');
LEGEND_RATES(:,13) = strpad('d/dt C_star in component C_star (cells_per_GC)');
LEGEND_RATES(:,14) = strpad('d/dt M in component M (cells_per_GC)');
LEGEND_RATES(:,15) = strpad('d/dt A in component A (cells_per_GC)');
LEGEND_RATES(:,16) = strpad('d/dt T in component T (cells_per_GC)');
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) = 3;
CONSTANTS(:,1) = 0.15;
CONSTANTS(:,2) = 3;
CONSTANTS(:,3) = 4;
CONSTANTS(:,4) = 0.8;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
STATES(:,10) = 0;
STATES(:,11) = 0;
STATES(:,12) = 0;
CONSTANTS(:,5) = 2;
STATES(:,13) = 0;
STATES(:,14) = 0;
STATES(:,15) = 500;
CONSTANTS(:,6) = 0.02;
CONSTANTS(:,7) = 0.15;
STATES(:,16) = 0;
CONSTANTS(:,8) = 2;
CONSTANTS(:,9) = 5;
CONSTANTS(:,10) = 0.8;
CONSTANTS(:,11) = 500;
CONSTANTS(:,12) = 50;
CONSTANTS(:,13) = 1e4;
CONSTANTS(:,14) = 100;
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(:,12) = CONSTANTS(:,5).*CONSTANTS(:,3).*STATES(:,11).*1.00000 - CONSTANTS(:,2).*STATES(:,12);
ALGEBRAIC(:,1) = ( STATES(:,13).*STATES(:,16))./( CONSTANTS(:,12).*1.00000+STATES(:,13));
RATES(:,1) = CONSTANTS(:,1).*CONSTANTS(:,2).*ALGEBRAIC(:,1) - ( CONSTANTS(:,3).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,1));
ALGEBRAIC(:,3) = ( STATES(:,12).*STATES(:,15))./( CONSTANTS(:,11).*1.00000+STATES(:,15));
RATES(:,13) = CONSTANTS(:,2).*ALGEBRAIC(:,3) - CONSTANTS(:,2).*STATES(:,13);
RATES(:,14) = (1.00000 - CONSTANTS(:,1)).*CONSTANTS(:,2).*ALGEBRAIC(:,1);
RATES(:,15) = - CONSTANTS(:,6).*STATES(:,15) - CONSTANTS(:,7).*ALGEBRAIC(:,3).*1.00000;
ALGEBRAIC(:,2) = STATES(:,2)+STATES(:,2)+STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,7)+STATES(:,8)+STATES(:,9)+STATES(:,10)+STATES(:,11);
ALGEBRAIC(:,5) = CONSTANTS(:,13)./(CONSTANTS(:,13)+ALGEBRAIC(:,2)./1.00000);
RATES(:,2) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,1) - ( CONSTANTS(:,3).*STATES(:,2)+ CONSTANTS(:,4).*STATES(:,2));
RATES(:,3) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,2) - ( CONSTANTS(:,3).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,3));
RATES(:,4) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,3) - ( CONSTANTS(:,3).*STATES(:,4)+ CONSTANTS(:,4).*STATES(:,4));
RATES(:,5) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,4) - ( CONSTANTS(:,3).*STATES(:,5)+ CONSTANTS(:,4).*STATES(:,5));
RATES(:,6) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,5) - ( CONSTANTS(:,3).*STATES(:,6)+ CONSTANTS(:,4).*STATES(:,6));
RATES(:,7) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,6) - ( CONSTANTS(:,3).*STATES(:,7)+ CONSTANTS(:,4).*STATES(:,7));
RATES(:,8) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,7) - ( CONSTANTS(:,3).*STATES(:,8)+ CONSTANTS(:,4).*STATES(:,8));
RATES(:,9) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,8) - ( CONSTANTS(:,3).*STATES(:,9)+ CONSTANTS(:,4).*STATES(:,9));
RATES(:,10) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,9) - ( CONSTANTS(:,3).*STATES(:,10)+ CONSTANTS(:,4).*STATES(:,10));
RATES(:,11) = CONSTANTS(:,3).*(1.00000+ALGEBRAIC(:,5)).*STATES(:,10) - ( CONSTANTS(:,3).*STATES(:,11)+ CONSTANTS(:,4).*STATES(:,11));
ALGEBRAIC(:,7) = CONSTANTS(:,14)./(CONSTANTS(:,14)+STATES(:,16)./1.00000);
RATES(:,16) = ( CONSTANTS(:,9).*1.00000+ CONSTANTS(:,8).*ALGEBRAIC(:,7).*ALGEBRAIC(:,1)) - CONSTANTS(:,10).*STATES(:,16);
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(:,13).*STATES(:,16))./( CONSTANTS(:,12).*1.00000+STATES(:,13));
ALGEBRAIC(:,3) = ( STATES(:,12).*STATES(:,15))./( CONSTANTS(:,11).*1.00000+STATES(:,15));
ALGEBRAIC(:,2) = STATES(:,2)+STATES(:,2)+STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,7)+STATES(:,8)+STATES(:,9)+STATES(:,10)+STATES(:,11);
ALGEBRAIC(:,5) = CONSTANTS(:,13)./(CONSTANTS(:,13)+ALGEBRAIC(:,2)./1.00000);
ALGEBRAIC(:,7) = CONSTANTS(:,14)./(CONSTANTS(:,14)+STATES(:,16)./1.00000);
ALGEBRAIC(:,4) = arbitrary_log(STATES(:,15)./1.00000, 10);
ALGEBRAIC(:,6) = STATES(:,12)+STATES(:,13);
ALGEBRAIC(:,8) = ALGEBRAIC(:,2)+ALGEBRAIC(:,6);
ALGEBRAIC(:,9) = arbitrary_log(ALGEBRAIC(:,8)./1.00000+1.00000e-12, 10);
end
% Compute a logarithm to any base" +
function x = arbitrary_log(a, base)
x = log(a) ./ log(base);
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