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 =14;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 24 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('Vm in component membrane (millivolt)');
LEGEND_CONSTANTS(:,1) = strpad('Cm in component membrane (microfarad)');
LEGEND_ALGEBRAIC(:,12) = strpad('I_b in component I_b (nanoampere)');
LEGEND_ALGEBRAIC(:,3) = strpad('I_Kir in component I_Kir (nanoampere)');
LEGEND_ALGEBRAIC(:,10) = strpad('I_Shkr in component I_Shkr (nanoampere)');
LEGEND_ALGEBRAIC(:,14) = strpad('I_stim in component I_stim (nanoampere)');
LEGEND_STATES(:,1) = strpad('VmReal in component membrane (millivolt)');
LEGEND_CONSTANTS(:,2) = strpad('GKir in component I_Kir (microsiemens)');
LEGEND_CONSTANTS(:,3) = strpad('aKir in component I_Kir (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('bKir in component I_Kir (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('EK in component I_Kir (millivolt)');
LEGEND_ALGEBRAIC(:,2) = strpad('OKir in component I_Kir (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('R in component model_parameters (millijoule_per_kelvin_mole)');
LEGEND_CONSTANTS(:,6) = strpad('T in component model_parameters (kelvin)');
LEGEND_CONSTANTS(:,7) = strpad('F in component model_parameters (coulomb_per_mole)');
LEGEND_CONSTANTS(:,8) = strpad('Ko in component model_parameters (millimolar)');
LEGEND_CONSTANTS(:,9) = strpad('Ki in component model_parameters (millimolar)');
LEGEND_CONSTANTS(:,10) = strpad('PShkr in component I_Shkr (microlitre_per_second)');
LEGEND_STATES(:,2) = strpad('C0ShkrReal in component I_Shkr (dimensionless)');
LEGEND_STATES(:,3) = strpad('C1ShkrReal in component I_Shkr (dimensionless)');
LEGEND_STATES(:,4) = strpad('C2ShkrReal in component I_Shkr (dimensionless)');
LEGEND_STATES(:,5) = strpad('C3ShkrReal in component I_Shkr (dimensionless)');
LEGEND_STATES(:,6) = strpad('C4ShkrReal in component I_Shkr (dimensionless)');
LEGEND_STATES(:,7) = strpad('OShkrReal in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('C0Shkr in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('C1Shkr in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('C2Shkr in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('C3Shkr in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('C4Shkr in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,9) = strpad('OShkr in component I_Shkr (dimensionless)');
LEGEND_ALGEBRAIC(:,11) = strpad('kv in component I_Shkr (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,13) = strpad('k_v in component I_Shkr (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('kv0 in component I_Shkr (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('zv in component I_Shkr (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('k_v0 in component I_Shkr (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('z_v in component I_Shkr (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('ko in component I_Shkr (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('k_o in component I_Shkr (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('Gb in component I_b (microsiemens)');
LEGEND_CONSTANTS(:,18) = strpad('Eb in component I_b (millivolt)');
LEGEND_CONSTANTS(:,19) = strpad('stim_start in component I_stim (second)');
LEGEND_CONSTANTS(:,20) = strpad('stim_end in component I_stim (second)');
LEGEND_CONSTANTS(:,21) = strpad('stim_period in component I_stim (second)');
LEGEND_CONSTANTS(:,22) = strpad('stim_duration in component I_stim (second)');
LEGEND_CONSTANTS(:,23) = strpad('stim_amplitude in component I_stim (nanoampere)');
LEGEND_RATES(:,1) = strpad('d/dt VmReal in component membrane (millivolt)');
LEGEND_RATES(:,2) = strpad('d/dt C0ShkrReal in component I_Shkr (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt C1ShkrReal in component I_Shkr (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt C2ShkrReal in component I_Shkr (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt C3ShkrReal in component I_Shkr (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt C4ShkrReal in component I_Shkr (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt OShkrReal in component I_Shkr (dimensionless)');
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) = 4.5e-6;
STATES(:,1) = -58.00;
CONSTANTS(:,2) = 1e-3;
CONSTANTS(:,3) = 0.94;
CONSTANTS(:,4) = 1.26;
CONSTANTS(:,5) = 8310;
CONSTANTS(:,6) = 295;
CONSTANTS(:,7) = 9.65e4;
CONSTANTS(:,8) = 5;
CONSTANTS(:,9) = 140;
CONSTANTS(:,10) = 5.4e-9;
STATES(:,2) = 9.11e-1;
STATES(:,3) = 8.57e-2;
STATES(:,4) = 3.02e-3;
STATES(:,5) = 4.74e-5;
STATES(:,6) = 2.79e-7;
STATES(:,7) = 0;
CONSTANTS(:,11) = 30;
CONSTANTS(:,12) = 1.28;
CONSTANTS(:,13) = 2;
CONSTANTS(:,14) = -1.53;
CONSTANTS(:,15) = 77;
CONSTANTS(:,16) = 18;
CONSTANTS(:,17) = 6.9e-6;
CONSTANTS(:,18) = 0;
CONSTANTS(:,19) = 0.1;
CONSTANTS(:,20) = 10;
CONSTANTS(:,21) = 1;
CONSTANTS(:,22) = 0.001;
CONSTANTS(:,23) = 0.1;
CONSTANTS(:,24) = (( CONSTANTS(:,5).*CONSTANTS(:,6))./CONSTANTS(:,7)).*log(CONSTANTS(:,8)./CONSTANTS(:,9));
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(:,8) = piecewise({STATES(:,6)<0.00000, 0.00000 , STATES(:,6)>1.00000, 1.00000 }, STATES(:,6));
ALGEBRAIC(:,9) = piecewise({STATES(:,7)<0.00000, 0.00000 , STATES(:,7)>1.00000, 1.00000 }, STATES(:,7));
RATES(:,7) = CONSTANTS(:,15).*ALGEBRAIC(:,8) - CONSTANTS(:,16).*ALGEBRAIC(:,9);
ALGEBRAIC(:,4) = piecewise({STATES(:,2)<0.00000, 0.00000 , STATES(:,2)>1.00000, 1.00000 }, STATES(:,2));
ALGEBRAIC(:,5) = piecewise({STATES(:,3)<0.00000, 0.00000 , STATES(:,3)>1.00000, 1.00000 }, STATES(:,3));
ALGEBRAIC(:,1) = piecewise({abs(STATES(:,1))<1.00000e-07, 1.00000e-07 }, STATES(:,1));
ALGEBRAIC(:,11) = CONSTANTS(:,11).*exp(( ALGEBRAIC(:,1).*CONSTANTS(:,12).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6)));
ALGEBRAIC(:,13) = CONSTANTS(:,13).*exp(( ALGEBRAIC(:,1).*CONSTANTS(:,14).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6)));
RATES(:,2) = ALGEBRAIC(:,13).*ALGEBRAIC(:,5) - 4.00000.*ALGEBRAIC(:,11).*ALGEBRAIC(:,4);
ALGEBRAIC(:,6) = piecewise({STATES(:,4)<0.00000, 0.00000 , STATES(:,4)>1.00000, 1.00000 }, STATES(:,4));
RATES(:,3) = ( 2.00000.*ALGEBRAIC(:,13).*ALGEBRAIC(:,6)+ 4.00000.*ALGEBRAIC(:,11).*ALGEBRAIC(:,4)) - ( 3.00000.*ALGEBRAIC(:,11)+ALGEBRAIC(:,13)).*ALGEBRAIC(:,5);
ALGEBRAIC(:,7) = piecewise({STATES(:,5)<0.00000, 0.00000 , STATES(:,5)>1.00000, 1.00000 }, STATES(:,5));
RATES(:,4) = ( 3.00000.*ALGEBRAIC(:,13).*ALGEBRAIC(:,7)+ 3.00000.*ALGEBRAIC(:,11).*ALGEBRAIC(:,5)) - ( 2.00000.*ALGEBRAIC(:,11)+ 2.00000.*ALGEBRAIC(:,13)).*ALGEBRAIC(:,6);
RATES(:,5) = ( 4.00000.*ALGEBRAIC(:,13).*ALGEBRAIC(:,8)+ 2.00000.*ALGEBRAIC(:,11).*ALGEBRAIC(:,6)) - (ALGEBRAIC(:,11)+ 3.00000.*ALGEBRAIC(:,13)).*ALGEBRAIC(:,7);
RATES(:,6) = ( CONSTANTS(:,16).*ALGEBRAIC(:,9)+ ALGEBRAIC(:,11).*ALGEBRAIC(:,7)) - (CONSTANTS(:,15)+ 4.00000.*ALGEBRAIC(:,13)).*ALGEBRAIC(:,8);
ALGEBRAIC(:,12) = CONSTANTS(:,17).*(ALGEBRAIC(:,1) - CONSTANTS(:,18));
ALGEBRAIC(:,2) = 1.00000./(CONSTANTS(:,3)+exp(( CONSTANTS(:,4).*(ALGEBRAIC(:,1) - CONSTANTS(:,24)).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6))));
ALGEBRAIC(:,3) = CONSTANTS(:,2).*ALGEBRAIC(:,2).*power(( CONSTANTS(:,8).*0.00100000), 1.0 ./ 2).*(ALGEBRAIC(:,1) - CONSTANTS(:,24));
ALGEBRAIC(:,10) = ( (( CONSTANTS(:,10).*ALGEBRAIC(:,9).*ALGEBRAIC(:,1).*power(CONSTANTS(:,7), 2.00000))./( CONSTANTS(:,5).*CONSTANTS(:,6))).*(CONSTANTS(:,9) - CONSTANTS(:,8).*exp(( - ALGEBRAIC(:,1).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6)))))./(1.00000 - exp(( - ALGEBRAIC(:,1).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6))));
ALGEBRAIC(:,14) = piecewise({VOI>=CONSTANTS(:,19)&(VOI<=CONSTANTS(:,20)&(VOI - CONSTANTS(:,19)) - floor((VOI - CONSTANTS(:,19))./CONSTANTS(:,21)).*CONSTANTS(:,21)<=CONSTANTS(:,22)), CONSTANTS(:,23) }, 0.00000);
RATES(:,1) = - ((ALGEBRAIC(:,3)+ALGEBRAIC(:,10)+ALGEBRAIC(:,12)) - ALGEBRAIC(:,14))./CONSTANTS(:,1);
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(:,8) = piecewise({STATES(:,6)<0.00000, 0.00000 , STATES(:,6)>1.00000, 1.00000 }, STATES(:,6));
ALGEBRAIC(:,9) = piecewise({STATES(:,7)<0.00000, 0.00000 , STATES(:,7)>1.00000, 1.00000 }, STATES(:,7));
ALGEBRAIC(:,4) = piecewise({STATES(:,2)<0.00000, 0.00000 , STATES(:,2)>1.00000, 1.00000 }, STATES(:,2));
ALGEBRAIC(:,5) = piecewise({STATES(:,3)<0.00000, 0.00000 , STATES(:,3)>1.00000, 1.00000 }, STATES(:,3));
ALGEBRAIC(:,1) = piecewise({abs(STATES(:,1))<1.00000e-07, 1.00000e-07 }, STATES(:,1));
ALGEBRAIC(:,11) = CONSTANTS(:,11).*exp(( ALGEBRAIC(:,1).*CONSTANTS(:,12).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6)));
ALGEBRAIC(:,13) = CONSTANTS(:,13).*exp(( ALGEBRAIC(:,1).*CONSTANTS(:,14).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6)));
ALGEBRAIC(:,6) = piecewise({STATES(:,4)<0.00000, 0.00000 , STATES(:,4)>1.00000, 1.00000 }, STATES(:,4));
ALGEBRAIC(:,7) = piecewise({STATES(:,5)<0.00000, 0.00000 , STATES(:,5)>1.00000, 1.00000 }, STATES(:,5));
ALGEBRAIC(:,12) = CONSTANTS(:,17).*(ALGEBRAIC(:,1) - CONSTANTS(:,18));
ALGEBRAIC(:,2) = 1.00000./(CONSTANTS(:,3)+exp(( CONSTANTS(:,4).*(ALGEBRAIC(:,1) - CONSTANTS(:,24)).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6))));
ALGEBRAIC(:,3) = CONSTANTS(:,2).*ALGEBRAIC(:,2).*power(( CONSTANTS(:,8).*0.00100000), 1.0 ./ 2).*(ALGEBRAIC(:,1) - CONSTANTS(:,24));
ALGEBRAIC(:,10) = ( (( CONSTANTS(:,10).*ALGEBRAIC(:,9).*ALGEBRAIC(:,1).*power(CONSTANTS(:,7), 2.00000))./( CONSTANTS(:,5).*CONSTANTS(:,6))).*(CONSTANTS(:,9) - CONSTANTS(:,8).*exp(( - ALGEBRAIC(:,1).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6)))))./(1.00000 - exp(( - ALGEBRAIC(:,1).*CONSTANTS(:,7))./( CONSTANTS(:,5).*CONSTANTS(:,6))));
ALGEBRAIC(:,14) = piecewise({VOI>=CONSTANTS(:,19)&(VOI<=CONSTANTS(:,20)&(VOI - CONSTANTS(:,19)) - floor((VOI - CONSTANTS(:,19))./CONSTANTS(:,21)).*CONSTANTS(:,21)<=CONSTANTS(:,22)), CONSTANTS(:,23) }, 0.00000);
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
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