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 16 entries in each of the rate and state variable arrays.
% There are a total of 21 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('kM2T2_on in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('kM2T2_off in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('kM2T2_iso in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('kM2T2_negativeiso in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('kM2C1_on in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('kM2C1_off in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('kM2C1_cat in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('kMT1T2_on in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('kMT1T2_off in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('kMT1T2M2pro_on in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('kMT1T2M2pro_off in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('kM2_act in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('kMT1_shedeff in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('kMT1C1_cat in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('kMT1C1_on in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('kMT1C1_off in component Model (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('kMT1T2M2proMT1_on in component Model (second_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('kMT1T2M2proMT1_off in component Model (first_order_rate_constant)');
LEGEND_STATES(:,1) = strpad('M2T2 in component Model (M)');
LEGEND_STATES(:,2) = strpad('M2C1 in component Model (M)');
LEGEND_STATES(:,3) = strpad('MT1T2 in component Model (M)');
LEGEND_STATES(:,4) = strpad('MT1T2M2proMT1 in component Model (M)');
LEGEND_STATES(:,5) = strpad('MT1C1 in component Model (M)');
LEGEND_STATES(:,6) = strpad('M2 in component Model (M)');
LEGEND_STATES(:,7) = strpad('MT1 in component Model (M)');
LEGEND_STATES(:,8) = strpad('M2_p in component Model (M)');
LEGEND_STATES(:,9) = strpad('T2 in component Model (M)');
LEGEND_STATES(:,10) = strpad('C1_D in component Model (M)');
LEGEND_STATES(:,11) = strpad('C1 in component Model (M)');
LEGEND_STATES(:,12) = strpad('MT1_cat in component Model (M)');
LEGEND_STATES(:,13) = strpad('MT1_t in component Model (M)');
LEGEND_STATES(:,14) = strpad('MT1T2M2pro in component Model (M)');
LEGEND_CONSTANTS(:,19) = strpad('qMT1 in component Model (flux)');
LEGEND_CONSTANTS(:,20) = strpad('qT2 in component Model (flux)');
LEGEND_CONSTANTS(:,21) = strpad('qpro in component Model (flux)');
LEGEND_STATES(:,15) = strpad('MT1T2_star in component Model (um)');
LEGEND_STATES(:,16) = strpad('M2T2_star in component Model (um)');
LEGEND_RATES(:,6) = strpad('d/dt M2 in component Model (M)');
LEGEND_RATES(:,7) = strpad('d/dt MT1 in component Model (M)');
LEGEND_RATES(:,13) = strpad('d/dt MT1_t in component Model (M)');
LEGEND_RATES(:,5) = strpad('d/dt MT1C1 in component Model (M)');
LEGEND_RATES(:,3) = strpad('d/dt MT1T2 in component Model (M)');
LEGEND_RATES(:,14) = strpad('d/dt MT1T2M2pro in component Model (M)');
LEGEND_RATES(:,4) = strpad('d/dt MT1T2M2proMT1 in component Model (M)');
LEGEND_RATES(:,11) = strpad('d/dt C1 in component Model (M)');
LEGEND_RATES(:,10) = strpad('d/dt C1_D in component Model (M)');
LEGEND_RATES(:,12) = strpad('d/dt MT1_cat in component Model (M)');
LEGEND_RATES(:,9) = strpad('d/dt T2 in component Model (M)');
LEGEND_RATES(:,8) = strpad('d/dt M2_p in component Model (M)');
LEGEND_RATES(:,1) = strpad('d/dt M2T2 in component Model (M)');
LEGEND_RATES(:,16) = strpad('d/dt M2T2_star in component Model (um)');
LEGEND_RATES(:,2) = strpad('d/dt M2C1 in component Model (M)');
LEGEND_RATES(:,15) = strpad('d/dt MT1T2_star in component Model (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) = 5900000;
CONSTANTS(:,2) = 6.3;
CONSTANTS(:,3) = 33;
CONSTANTS(:,4) = 0.00000002;
CONSTANTS(:,5) = 2600;
CONSTANTS(:,6) = 0.0021;
CONSTANTS(:,7) = 0.0045;
CONSTANTS(:,8) = 2980000;
CONSTANTS(:,9) = 0.202;
CONSTANTS(:,10) = 140000;
CONSTANTS(:,11) = 0.0047;
CONSTANTS(:,12) = 0.02;
CONSTANTS(:,13) = 2800;
CONSTANTS(:,14) = 0.00197;
CONSTANTS(:,15) = 1000;
CONSTANTS(:,16) = 1;
CONSTANTS(:,17) = 3000;
CONSTANTS(:,18) = 0.0009;
STATES(:,1) = 0.0000000072;
STATES(:,2) = 0.0000085;
STATES(:,3) = 0.00000000139;
STATES(:,4) = 0.00000000056;
STATES(:,5) = 0.0000029;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
STATES(:,10) = 0;
STATES(:,11) = 0;
STATES(:,12) = 0;
STATES(:,13) = 0;
STATES(:,14) = 0;
CONSTANTS(:,19) = 0;
CONSTANTS(:,20) = 0;
CONSTANTS(:,21) = 0;
STATES(:,15) = 0;
STATES(:,16) = 0;
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) = (( - CONSTANTS(:,1).*STATES(:,6).*STATES(:,9)+ CONSTANTS(:,2).*STATES(:,1)) - CONSTANTS(:,5).*STATES(:,6).*STATES(:,11))+ (CONSTANTS(:,6)+CONSTANTS(:,7)).*STATES(:,2)+ CONSTANTS(:,12).*STATES(:,4);
RATES(:,7) = ((((((CONSTANTS(:,19) - CONSTANTS(:,13).*STATES(:,7).*STATES(:,7)) - CONSTANTS(:,8).*STATES(:,7).*STATES(:,9))+ CONSTANTS(:,9).*STATES(:,3)) - CONSTANTS(:,15).*STATES(:,7).*STATES(:,11))+ (CONSTANTS(:,16)+CONSTANTS(:,14)).*STATES(:,5)) - CONSTANTS(:,17).*STATES(:,7).*STATES(:,14))+ CONSTANTS(:,18).*STATES(:,4)+ CONSTANTS(:,12).*STATES(:,4);
RATES(:,13) = CONSTANTS(:,13).*STATES(:,7).*STATES(:,7);
RATES(:,5) = CONSTANTS(:,15).*STATES(:,7).*STATES(:,11) - (CONSTANTS(:,16)+CONSTANTS(:,14)).*STATES(:,5);
RATES(:,3) = (( CONSTANTS(:,8).*STATES(:,7).*STATES(:,9) - CONSTANTS(:,9).*STATES(:,3)) - CONSTANTS(:,10).*STATES(:,3).*STATES(:,8))+ CONSTANTS(:,11).*STATES(:,14);
RATES(:,14) = (( CONSTANTS(:,10).*STATES(:,3).*STATES(:,8) - CONSTANTS(:,11).*STATES(:,14)) - CONSTANTS(:,17).*STATES(:,7).*STATES(:,14))+ CONSTANTS(:,18).*STATES(:,4);
RATES(:,4) = ( CONSTANTS(:,17).*STATES(:,7).*STATES(:,14) - CONSTANTS(:,18).*STATES(:,4)) - CONSTANTS(:,12).*STATES(:,4);
RATES(:,11) = (( - CONSTANTS(:,15).*STATES(:,7).*STATES(:,11)+ CONSTANTS(:,16).*STATES(:,5)) - CONSTANTS(:,5).*STATES(:,6).*STATES(:,11))+ CONSTANTS(:,6).*STATES(:,2);
RATES(:,10) = CONSTANTS(:,7).*STATES(:,2)+ CONSTANTS(:,14).*STATES(:,5);
RATES(:,12) = CONSTANTS(:,13).*STATES(:,7).*STATES(:,7);
RATES(:,9) = (( - CONSTANTS(:,1).*STATES(:,6).*STATES(:,9)+ CONSTANTS(:,2).*STATES(:,1)+CONSTANTS(:,20)) - CONSTANTS(:,8).*STATES(:,7).*STATES(:,9))+ CONSTANTS(:,9).*STATES(:,3);
RATES(:,8) = (CONSTANTS(:,21) - CONSTANTS(:,10).*STATES(:,3).*STATES(:,8))+ CONSTANTS(:,11).*STATES(:,14);
RATES(:,1) = (( CONSTANTS(:,1).*STATES(:,6).*STATES(:,9) - CONSTANTS(:,2).*STATES(:,1)) - CONSTANTS(:,3).*STATES(:,1))+ CONSTANTS(:,4).*STATES(:,16);
RATES(:,16) = CONSTANTS(:,3).*STATES(:,1) - CONSTANTS(:,4).*STATES(:,16);
RATES(:,2) = CONSTANTS(:,5).*STATES(:,6).*STATES(:,11) - (CONSTANTS(:,6)+CONSTANTS(:,7)).*STATES(:,2);
RATES(:,15) = CONSTANTS(:,12).*STATES(:,4);
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