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 12 entries in each of the rate and state variable arrays.
% There are a total of 38 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_STATES(:,1) = strpad('E in component E (millimolar)');
LEGEND_CONSTANTS(:,1) = strpad('k23 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k24 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k17 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k18 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k1 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k2 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k3 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k4 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('ED in component ED (millimolar)');
LEGEND_STATES(:,3) = strpad('E_ in component E_ (millimolar)');
LEGEND_STATES(:,4) = strpad('ENa in component ENa (millimolar)');
LEGEND_STATES(:,5) = strpad('ECl in component ECl (millimolar)');
LEGEND_CONSTANTS(:,9) = strpad('D in component reaction_constants (millimolar)');
LEGEND_CONSTANTS(:,10) = strpad('Na in component reaction_constants (millimolar)');
LEGEND_CONSTANTS(:,11) = strpad('Cl in component reaction_constants (millimolar)');
LEGEND_CONSTANTS(:,12) = strpad('k29 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('k30 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('k11 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('k12 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('k9 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('k10 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,6) = strpad('ED_ in component ED_ (millimolar)');
LEGEND_STATES(:,7) = strpad('ENa_ in component ENa_ (millimolar)');
LEGEND_STATES(:,8) = strpad('ECl_ in component ECl_ (millimolar)');
LEGEND_CONSTANTS(:,18) = strpad('D_ in component reaction_constants (millimolar)');
LEGEND_CONSTANTS(:,19) = strpad('Na_ in component reaction_constants (millimolar)');
LEGEND_CONSTANTS(:,20) = strpad('Cl_ in component reaction_constants (millimolar)');
LEGEND_CONSTANTS(:,21) = strpad('k21 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,22) = strpad('k22 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,9) = strpad('ENaD in component ENaD (millimolar)');
LEGEND_CONSTANTS(:,23) = strpad('k27 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,24) = strpad('k28 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,10) = strpad('ENaD_ in component ENaD_ (millimolar)');
LEGEND_CONSTANTS(:,25) = strpad('k25 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,26) = strpad('k26 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,27) = strpad('k31 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,28) = strpad('k32 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,29) = strpad('k5 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,30) = strpad('k6 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,11) = strpad('ENaCl in component ENaCl (millimolar)');
LEGEND_CONSTANTS(:,31) = strpad('k13 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,32) = strpad('k14 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,12) = strpad('ENaCl_ in component ENaCl_ (millimolar)');
LEGEND_CONSTANTS(:,33) = strpad('k7 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,34) = strpad('k8 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,35) = strpad('k15 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,36) = strpad('k16 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,37) = strpad('k19 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,38) = strpad('k20 in component reaction_constants (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt E in component E (millimolar)');
LEGEND_RATES(:,3) = strpad('d/dt E_ in component E_ (millimolar)');
LEGEND_RATES(:,2) = strpad('d/dt ED in component ED (millimolar)');
LEGEND_RATES(:,6) = strpad('d/dt ED_ in component ED_ (millimolar)');
LEGEND_RATES(:,9) = strpad('d/dt ENaD in component ENaD (millimolar)');
LEGEND_RATES(:,10) = strpad('d/dt ENaD_ in component ENaD_ (millimolar)');
LEGEND_RATES(:,4) = strpad('d/dt ENa in component ENa (millimolar)');
LEGEND_RATES(:,7) = strpad('d/dt ENa_ in component ENa_ (millimolar)');
LEGEND_RATES(:,5) = strpad('d/dt ECl in component ECl (millimolar)');
LEGEND_RATES(:,8) = strpad('d/dt ECl_ in component ECl_ (millimolar)');
LEGEND_RATES(:,11) = strpad('d/dt ENaCl in component ENaCl (millimolar)');
LEGEND_RATES(:,12) = strpad('d/dt ENaCl_ in component ENaCl_ (millimolar)');
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) = 0.08333;
CONSTANTS(:,1) = 1.0E5;
CONSTANTS(:,2) = 3.192E1;
CONSTANTS(:,3) = 4.587E5;
CONSTANTS(:,4) = 1.0E5;
CONSTANTS(:,5) = 1.0E5;
CONSTANTS(:,6) = 4.183E5;
CONSTANTS(:,7) = 1.0E5;
CONSTANTS(:,8) = 4.928E6;
STATES(:,2) = 0.08333;
STATES(:,3) = 0.08333;
STATES(:,4) = 0.08333;
STATES(:,5) = 0.08333;
CONSTANTS(:,9) = 1.0E-6;
CONSTANTS(:,10) = 50.0;
CONSTANTS(:,11) = 96.0;
CONSTANTS(:,12) = 1.0E5;
CONSTANTS(:,13) = 3.514E-1;
CONSTANTS(:,14) = 1.0E5;
CONSTANTS(:,15) = 4.982E6;
CONSTANTS(:,16) = 1.0E5;
CONSTANTS(:,17) = 4.183E5;
STATES(:,6) = 0.08333;
STATES(:,7) = 0.08333;
STATES(:,8) = 0.08333;
CONSTANTS(:,18) = 1.0E-6;
CONSTANTS(:,19) = 10.0;
CONSTANTS(:,20) = 40.0;
CONSTANTS(:,21) = 1.0E5;
CONSTANTS(:,22) = 4.183E5;
STATES(:,9) = 0.08333;
CONSTANTS(:,23) = 1.0E5;
CONSTANTS(:,24) = 1.389E5;
STATES(:,10) = 0.08333;
CONSTANTS(:,25) = 1.0E5;
CONSTANTS(:,26) = 3.192E1;
CONSTANTS(:,27) = 1.0E5;
CONSTANTS(:,28) = 1.166E-1;
CONSTANTS(:,29) = 1.0E5;
CONSTANTS(:,30) = 1.065E6;
STATES(:,11) = 0.08333;
CONSTANTS(:,31) = 1.0E5;
CONSTANTS(:,32) = 1.065E6;
STATES(:,12) = 0.08333;
CONSTANTS(:,33) = 1.0E5;
CONSTANTS(:,34) = 8.940E4;
CONSTANTS(:,35) = 1.0E5;
CONSTANTS(:,36) = 8.940E4;
CONSTANTS(:,37) = 1.0E3;
CONSTANTS(:,38) = 2.180E2;
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(:,2).*STATES(:,2)+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,6).*STATES(:,4)+ CONSTANTS(:,8).*STATES(:,5)) - ( CONSTANTS(:,1).*CONSTANTS(:,9).*STATES(:,1)+ CONSTANTS(:,3).*STATES(:,1)+ CONSTANTS(:,5).*CONSTANTS(:,10).*STATES(:,1)+ CONSTANTS(:,7).*CONSTANTS(:,11).*STATES(:,1));
RATES(:,3) = ( CONSTANTS(:,13).*STATES(:,6)+ CONSTANTS(:,3).*STATES(:,1)+ CONSTANTS(:,17).*STATES(:,7)+ CONSTANTS(:,15).*STATES(:,8)) - ( CONSTANTS(:,12).*CONSTANTS(:,18).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,16).*CONSTANTS(:,19).*STATES(:,3)+ CONSTANTS(:,14).*CONSTANTS(:,20).*STATES(:,3));
RATES(:,2) = ( CONSTANTS(:,1).*STATES(:,1).*CONSTANTS(:,9)+ CONSTANTS(:,22).*STATES(:,9)) - ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,21).*CONSTANTS(:,10).*STATES(:,2));
RATES(:,6) = ( CONSTANTS(:,12).*STATES(:,3).*CONSTANTS(:,18)+ CONSTANTS(:,24).*STATES(:,10)) - ( CONSTANTS(:,13).*STATES(:,6)+ CONSTANTS(:,23).*CONSTANTS(:,19).*STATES(:,6));
RATES(:,9) = ( CONSTANTS(:,21).*CONSTANTS(:,10).*STATES(:,2)+ CONSTANTS(:,25).*CONSTANTS(:,9).*STATES(:,4)) - ( CONSTANTS(:,22).*STATES(:,9)+ CONSTANTS(:,26).*STATES(:,9));
RATES(:,10) = ( CONSTANTS(:,23).*CONSTANTS(:,19).*STATES(:,6)+ CONSTANTS(:,27).*CONSTANTS(:,18).*STATES(:,7)) - ( CONSTANTS(:,24).*STATES(:,10)+ CONSTANTS(:,28).*STATES(:,10));
RATES(:,4) = ( CONSTANTS(:,5).*CONSTANTS(:,10).*STATES(:,1)+ CONSTANTS(:,26).*STATES(:,9)+ CONSTANTS(:,30).*STATES(:,11)) - ( CONSTANTS(:,6).*STATES(:,4)+ CONSTANTS(:,29).*CONSTANTS(:,11).*STATES(:,4)+ CONSTANTS(:,25).*CONSTANTS(:,9).*STATES(:,4));
RATES(:,7) = ( CONSTANTS(:,16).*CONSTANTS(:,19).*STATES(:,3)+ CONSTANTS(:,28).*STATES(:,10)+ CONSTANTS(:,32).*STATES(:,12)) - ( CONSTANTS(:,17).*STATES(:,7)+ CONSTANTS(:,31).*CONSTANTS(:,20).*STATES(:,7)+ CONSTANTS(:,27).*CONSTANTS(:,18).*STATES(:,7));
RATES(:,5) = ( CONSTANTS(:,7).*CONSTANTS(:,11).*STATES(:,1)+ CONSTANTS(:,34).*STATES(:,11)) - ( CONSTANTS(:,33).*CONSTANTS(:,10).*STATES(:,5)+ CONSTANTS(:,8).*STATES(:,5));
RATES(:,8) = ( CONSTANTS(:,14).*CONSTANTS(:,20).*STATES(:,3)+ CONSTANTS(:,36).*STATES(:,12)) - ( CONSTANTS(:,35).*CONSTANTS(:,19).*STATES(:,8)+ CONSTANTS(:,15).*STATES(:,8));
RATES(:,11) = ( CONSTANTS(:,29).*CONSTANTS(:,11).*STATES(:,4)+ CONSTANTS(:,33).*CONSTANTS(:,10).*STATES(:,5)+ CONSTANTS(:,38).*STATES(:,12)) - ( CONSTANTS(:,30).*STATES(:,11)+ CONSTANTS(:,34).*STATES(:,11)+ CONSTANTS(:,37).*STATES(:,11));
RATES(:,12) = ( CONSTANTS(:,31).*CONSTANTS(:,20).*STATES(:,7)+ CONSTANTS(:,35).*CONSTANTS(:,19).*STATES(:,8)+ CONSTANTS(:,37).*STATES(:,11)) - ( CONSTANTS(:,32).*STATES(:,12)+ CONSTANTS(:,36).*STATES(:,12)+ CONSTANTS(:,38).*STATES(:,12));
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