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 13 entries in each of the rate and state variable arrays.
% There are a total of 15 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 (second)');
LEGEND_ALGEBRAIC(:,1) = strpad('v1 in component main (flux)');
LEGEND_ALGEBRAIC(:,2) = strpad('v2 in component main (flux)');
LEGEND_ALGEBRAIC(:,3) = strpad('v3 in component main (flux)');
LEGEND_ALGEBRAIC(:,4) = strpad('v4 in component main (flux)');
LEGEND_ALGEBRAIC(:,5) = strpad('v5 in component main (flux)');
LEGEND_ALGEBRAIC(:,6) = strpad('v6 in component main (flux)');
LEGEND_ALGEBRAIC(:,7) = strpad('v7 in component main (flux)');
LEGEND_ALGEBRAIC(:,8) = strpad('v8 in component main (flux)');
LEGEND_ALGEBRAIC(:,9) = strpad('v9 in component main (flux)');
LEGEND_STATES(:,1) = strpad('MT1 in component main (molar)');
LEGEND_STATES(:,2) = strpad('MT1cat in component main (molar)');
LEGEND_STATES(:,3) = strpad('MT1T2 in component main (molar)');
LEGEND_STATES(:,4) = strpad('MT1T2M2P in component main (molar)');
LEGEND_STATES(:,5) = strpad('M2P in component main (molar)');
LEGEND_STATES(:,6) = strpad('M2 in component main (molar)');
LEGEND_STATES(:,7) = strpad('M2T2 in component main (molar)');
LEGEND_STATES(:,8) = strpad('M2T2star in component main (molar)');
LEGEND_STATES(:,9) = strpad('M2C1 in component main (molar)');
LEGEND_STATES(:,10) = strpad('C1 in component main (molar)');
LEGEND_STATES(:,11) = strpad('C1dmt1 in component main (molar)');
LEGEND_STATES(:,12) = strpad('C1dm2 in component main (molar)');
LEGEND_STATES(:,13) = strpad('T2 in component main (molar)');
LEGEND_CONSTANTS(:,1) = strpad('kshed_eff in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('kon_MT1T2 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('ki_MT1T2 in component model_parameters (molar)');
LEGEND_CONSTANTS(:,4) = strpad('kon_MT1T2M2P in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('koff_MT1T2M2P in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('kact_eff_m2 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('kon_M2T2 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('ki_M2T2 in component model_parameters (molar)');
LEGEND_CONSTANTS(:,9) = strpad('kiso_M2T2 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k_iso_M2T2 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('kon_M2C1 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('koff_M2C1 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('kcat_M2C1 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('kcat_MT1C1 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('km_MT1C1 in component model_parameters (molar)');
LEGEND_RATES(:,1) = strpad('d/dt MT1 in component main (molar)');
LEGEND_RATES(:,2) = strpad('d/dt MT1cat in component main (molar)');
LEGEND_RATES(:,3) = strpad('d/dt MT1T2 in component main (molar)');
LEGEND_RATES(:,4) = strpad('d/dt MT1T2M2P in component main (molar)');
LEGEND_RATES(:,5) = strpad('d/dt M2P in component main (molar)');
LEGEND_RATES(:,6) = strpad('d/dt M2 in component main (molar)');
LEGEND_RATES(:,7) = strpad('d/dt M2T2 in component main (molar)');
LEGEND_RATES(:,8) = strpad('d/dt M2T2star in component main (molar)');
LEGEND_RATES(:,9) = strpad('d/dt M2C1 in component main (molar)');
LEGEND_RATES(:,10) = strpad('d/dt C1 in component main (molar)');
LEGEND_RATES(:,11) = strpad('d/dt C1dmt1 in component main (molar)');
LEGEND_RATES(:,12) = strpad('d/dt C1dm2 in component main (molar)');
LEGEND_RATES(:,13) = strpad('d/dt T2 in component main (molar)');
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) = 100e-9;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 50e-9;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
STATES(:,10) = 1e-6;
STATES(:,11) = 0;
STATES(:,12) = 0;
STATES(:,13) = 50e-9;
CONSTANTS(:,1) = 2.8e3;
CONSTANTS(:,2) = 3.54e6;
CONSTANTS(:,3) = 4.9e-9;
CONSTANTS(:,4) = 0.14e6;
CONSTANTS(:,5) = 4.7e-3;
CONSTANTS(:,6) = 2.8e3;
CONSTANTS(:,7) = 5.9e6;
CONSTANTS(:,8) = 1.07e-6;
CONSTANTS(:,9) = 33;
CONSTANTS(:,10) = 2e-8;
CONSTANTS(:,11) = 2.6e3;
CONSTANTS(:,12) = 2.1e-3;
CONSTANTS(:,13) = 4.5e-3;
CONSTANTS(:,14) = 1.97e-3;
CONSTANTS(:,15) = 2.9e-6;
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
ALGEBRAIC(:,1) = CONSTANTS(:,1).*STATES(:,1).*STATES(:,1);
RATES(:,2) = ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,2).*STATES(:,1).*STATES(:,13) - CONSTANTS(:,3).*CONSTANTS(:,2).*STATES(:,3);
RATES(:,1) = - ALGEBRAIC(:,1) - ALGEBRAIC(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,4).*STATES(:,3).*STATES(:,5) - CONSTANTS(:,5).*STATES(:,4);
RATES(:,3) = ALGEBRAIC(:,2) - ALGEBRAIC(:,3);
RATES(:,5) = - ALGEBRAIC(:,3);
ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,1).*STATES(:,4);
RATES(:,4) = ALGEBRAIC(:,3) - ALGEBRAIC(:,4);
ALGEBRAIC(:,5) = CONSTANTS(:,7).*STATES(:,6).*STATES(:,13) - CONSTANTS(:,7).*CONSTANTS(:,8).*STATES(:,7);
RATES(:,13) = - ALGEBRAIC(:,2) - ALGEBRAIC(:,5);
ALGEBRAIC(:,7) = CONSTANTS(:,11).*STATES(:,6).*STATES(:,10) - CONSTANTS(:,12).*STATES(:,9);
RATES(:,6) = (ALGEBRAIC(:,4) - ALGEBRAIC(:,5)) - ALGEBRAIC(:,7);
ALGEBRAIC(:,6) = CONSTANTS(:,9).*STATES(:,7) - CONSTANTS(:,10).*STATES(:,8);
RATES(:,7) = ALGEBRAIC(:,5) - ALGEBRAIC(:,6);
RATES(:,8) = ALGEBRAIC(:,6);
ALGEBRAIC(:,8) = CONSTANTS(:,13).*STATES(:,9);
RATES(:,9) = ALGEBRAIC(:,7) - ALGEBRAIC(:,8);
ALGEBRAIC(:,9) = (CONSTANTS(:,14)./CONSTANTS(:,15)).*STATES(:,1).*STATES(:,10);
RATES(:,10) = - ALGEBRAIC(:,7) - ALGEBRAIC(:,9);
RATES(:,11) = ALGEBRAIC(:,9);
RATES(:,12) = ALGEBRAIC(:,8);
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) = CONSTANTS(:,1).*STATES(:,1).*STATES(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,2).*STATES(:,1).*STATES(:,13) - CONSTANTS(:,3).*CONSTANTS(:,2).*STATES(:,3);
ALGEBRAIC(:,3) = CONSTANTS(:,4).*STATES(:,3).*STATES(:,5) - CONSTANTS(:,5).*STATES(:,4);
ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,1).*STATES(:,4);
ALGEBRAIC(:,5) = CONSTANTS(:,7).*STATES(:,6).*STATES(:,13) - CONSTANTS(:,7).*CONSTANTS(:,8).*STATES(:,7);
ALGEBRAIC(:,7) = CONSTANTS(:,11).*STATES(:,6).*STATES(:,10) - CONSTANTS(:,12).*STATES(:,9);
ALGEBRAIC(:,6) = CONSTANTS(:,9).*STATES(:,7) - CONSTANTS(:,10).*STATES(:,8);
ALGEBRAIC(:,8) = CONSTANTS(:,13).*STATES(:,9);
ALGEBRAIC(:,9) = (CONSTANTS(:,14)./CONSTANTS(:,15)).*STATES(:,1).*STATES(:,10);
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