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 =13;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 39 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_CONSTANTS(:,1) = strpad('t_ss in component Vstim_para (second)');
LEGEND_CONSTANTS(:,2) = strpad('V_actHolding in component Vstim_para (mV)');
LEGEND_CONSTANTS(:,3) = strpad('t_act in component Vstim_para (second)');
LEGEND_CONSTANTS(:,4) = strpad('V_actTest in component Vstim_para (mV)');
LEGEND_CONSTANTS(:,5) = strpad('Nai in component control_para (mM)');
LEGEND_CONSTANTS(:,6) = strpad('Cai_init in component control_para (mM)');
LEGEND_CONSTANTS(:,7) = strpad('inhPump in component control_para (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('K_Cahalf in component control_para (mV)');
LEGEND_VOI = strpad('time in component time_s (second)');
LEGEND_ALGEBRAIC(:,3) = strpad('V in component sPulse_protocol_s (mV)');
LEGEND_STATES(:,1) = strpad('Cai in component Cai (mM)');
LEGEND_ALGEBRAIC(:,13) = strpad('J_VOCC in component J_VOCC (mM_per_s)');
LEGEND_ALGEBRAIC(:,7) = strpad('J_CaPump in component J_CaPump (mM_per_s)');
LEGEND_ALGEBRAIC(:,11) = strpad('J_NaCa in component J_NaCa (mM_per_s)');
LEGEND_ALGEBRAIC(:,1) = strpad('stress in component CB4HM (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('phosphorylation in component CB4HM (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('R in component constants (J_per_K_mol)');
LEGEND_CONSTANTS(:,10) = strpad('F in component constants (C_per_mmol)');
LEGEND_CONSTANTS(:,11) = strpad('T in component model_para (kelvin)');
LEGEND_CONSTANTS(:,12) = strpad('Nao in component model_para (mM)');
LEGEND_CONSTANTS(:,13) = strpad('Cao in component model_para (mM)');
LEGEND_CONSTANTS(:,14) = strpad('V_cell in component model_para (fm3)');
LEGEND_CONSTANTS(:,15) = strpad('V_Cahalf in component model_para (mV)');
LEGEND_CONSTANTS(:,16) = strpad('g_mCa in component model_para (nS)');
LEGEND_CONSTANTS(:,17) = strpad('V_pmax in component model_para (mM_per_s)');
LEGEND_CONSTANTS(:,18) = strpad('n in component model_para (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('K_ph in component model_para (mM)');
LEGEND_CONSTANTS(:,20) = strpad('K_NaCa in component model_para (mM)');
LEGEND_CONSTANTS(:,21) = strpad('G_NaCa in component model_para (mM_per_s_mV)');
LEGEND_CONSTANTS(:,22) = strpad('n_M in component model_para (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('Ca_halfMLCK in component model_para (mM)');
LEGEND_CONSTANTS(:,24) = strpad('M_init in component initials (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('Mp_init in component initials (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('AM_init in component initials (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('AMp_init in component initials (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('K_7 in component model_para (per_s)');
LEGEND_CONSTANTS(:,29) = strpad('K_2 in component model_para (per_s)');
LEGEND_CONSTANTS(:,30) = strpad('K_3 in component model_para (per_s)');
LEGEND_ALGEBRAIC(:,5) = strpad('rho_vCa in component J_VOCC (dimensionless)');
LEGEND_CONSTANTS(:,31) = strpad('Nai in component model_para (mM)');
LEGEND_CONSTANTS(:,32) = strpad('K_Cahalf in component model_para (mV)');
LEGEND_CONSTANTS(:,33) = strpad('inhPump in component model_para (dimensionless)');
LEGEND_CONSTANTS(:,34) = strpad('Cai_init in component initials (mM)');
LEGEND_CONSTANTS(:,35) = strpad('z_Ca in component E_Ca (dimensionless)');
LEGEND_ALGEBRAIC(:,9) = strpad('E in component Nernst_potential (mV)');
LEGEND_CONSTANTS(:,36) = strpad('z_Na in component E_Na (dimensionless)');
LEGEND_CONSTANTS(:,37) = strpad('E in component Nernst_potential (mV)');
LEGEND_ALGEBRAIC(:,12) = strpad('I in component Ionic_currents (pA)');
LEGEND_ALGEBRAIC(:,10) = strpad('V_mNaCa in component J_NaCa (mV)');
LEGEND_ALGEBRAIC(:,6) = strpad('K_1 in component K_1 (per_s)');
LEGEND_CONSTANTS(:,38) = strpad('K_4 in component CB4HM (per_s)');
LEGEND_CONSTANTS(:,39) = strpad('K_5 in component CB4HM (per_s)');
LEGEND_ALGEBRAIC(:,8) = strpad('K_6 in component CB4HM (per_s)');
LEGEND_ALGEBRAIC(:,4) = strpad('norm in component CB4HM (dimensionless)');
LEGEND_STATES(:,2) = strpad('M in component CB4HM (dimensionless)');
LEGEND_STATES(:,3) = strpad('Mp in component CB4HM (dimensionless)');
LEGEND_STATES(:,4) = strpad('AM in component CB4HM (dimensionless)');
LEGEND_STATES(:,5) = strpad('AMp in component CB4HM (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt Cai in component Cai (mM)');
LEGEND_RATES(:,2) = strpad('d/dt M in component CB4HM (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt Mp in component CB4HM (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt AM in component CB4HM (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt AMp in component CB4HM (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) = 0;
CONSTANTS(:,2) = -80;
CONSTANTS(:,3) = 1;
CONSTANTS(:,4) = 0;
CONSTANTS(:,5) = 16.55;
CONSTANTS(:,6) = 0.1e-3;
CONSTANTS(:,7) = 1;
CONSTANTS(:,8) = 11;
CONSTANTS(:,9) = 8.314;
CONSTANTS(:,10) = 96.48534;
CONSTANTS(:,11) = 310;
CONSTANTS(:,12) = 140;
CONSTANTS(:,13) = 2;
CONSTANTS(:,14) = 21;
CONSTANTS(:,15) = -27;
CONSTANTS(:,16) = 0.046842;
CONSTANTS(:,17) = 5.1449e-4;
CONSTANTS(:,18) = 1.9015;
CONSTANTS(:,19) = 0.6e-3;
CONSTANTS(:,20) = 7e-3;
CONSTANTS(:,21) = 5.7297e-5;
CONSTANTS(:,22) = 8.7613;
CONSTANTS(:,23) = 256.98e-6;
CONSTANTS(:,24) = 1;
CONSTANTS(:,25) = 0;
CONSTANTS(:,26) = 0;
CONSTANTS(:,27) = 0;
CONSTANTS(:,28) = 0.0378;
CONSTANTS(:,29) = 1.2387;
CONSTANTS(:,30) = 0.1419;
CONSTANTS(:,31) = 2.9836;
CONSTANTS(:,32) = 11;
CONSTANTS(:,33) = 1;
CONSTANTS(:,34) = 0.1e-6;
CONSTANTS(:,35) = 2;
CONSTANTS(:,36) = 1;
CONSTANTS(:,37) = (( CONSTANTS(:,9).*CONSTANTS(:,11))./( CONSTANTS(:,36).*CONSTANTS(:,10))).*log(CONSTANTS(:,12)./CONSTANTS(:,5));
CONSTANTS(:,38) = CONSTANTS(:,30)./4.00000;
CONSTANTS(:,39) = CONSTANTS(:,29);
STATES(:,1) = CONSTANTS(:,6);
STATES(:,2) = CONSTANTS(:,24);
STATES(:,3) = CONSTANTS(:,25);
STATES(:,4) = CONSTANTS(:,26);
STATES(:,5) = CONSTANTS(:,27);
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(:,6) = (power(STATES(:,1), CONSTANTS(:,22))./(power(CONSTANTS(:,23), CONSTANTS(:,22))+power(STATES(:,1), CONSTANTS(:,22)))).*1.00000;
ALGEBRAIC(:,4) = STATES(:,2)+STATES(:,3)+STATES(:,4)+STATES(:,5);
RATES(:,2) = ( - ALGEBRAIC(:,6).*STATES(:,2))./ALGEBRAIC(:,4)+( CONSTANTS(:,29).*STATES(:,3))./ALGEBRAIC(:,4)+( CONSTANTS(:,28).*STATES(:,4))./ALGEBRAIC(:,4);
RATES(:,3) = (( CONSTANTS(:,38).*STATES(:,5))./ALGEBRAIC(:,4)+( ALGEBRAIC(:,6).*STATES(:,2))./ALGEBRAIC(:,4)) - ( (CONSTANTS(:,29)+CONSTANTS(:,30)).*STATES(:,3))./ALGEBRAIC(:,4);
ALGEBRAIC(:,8) = ALGEBRAIC(:,6);
RATES(:,4) = ( CONSTANTS(:,39).*STATES(:,5))./ALGEBRAIC(:,4) - ( (ALGEBRAIC(:,8)+CONSTANTS(:,28)).*STATES(:,4))./ALGEBRAIC(:,4);
RATES(:,5) = (( CONSTANTS(:,30).*STATES(:,3))./ALGEBRAIC(:,4)+( ALGEBRAIC(:,8).*STATES(:,4))./ALGEBRAIC(:,4)) - ( (CONSTANTS(:,38)+CONSTANTS(:,39)).*STATES(:,5))./ALGEBRAIC(:,4);
ALGEBRAIC(:,3) = piecewise({VOI<CONSTANTS(:,1), CONSTANTS(:,2) , VOI>=CONSTANTS(:,1)&VOI<CONSTANTS(:,3)+CONSTANTS(:,1), CONSTANTS(:,4) }, CONSTANTS(:,2));
ALGEBRAIC(:,5) = 1.00000./(1.00000+exp((CONSTANTS(:,15) - ALGEBRAIC(:,3))./CONSTANTS(:,8)));
ALGEBRAIC(:,9) = (( CONSTANTS(:,9).*CONSTANTS(:,11))./( CONSTANTS(:,35).*CONSTANTS(:,10))).*log(CONSTANTS(:,13)./STATES(:,1));
ALGEBRAIC(:,12) = CONSTANTS(:,16).*ALGEBRAIC(:,5).*(ALGEBRAIC(:,3) - ALGEBRAIC(:,9));
ALGEBRAIC(:,13) = - ALGEBRAIC(:,12)./( 2.00000.*CONSTANTS(:,14).*CONSTANTS(:,10));
ALGEBRAIC(:,7) = ( - CONSTANTS(:,17).*power(STATES(:,1), CONSTANTS(:,18)))./(power(CONSTANTS(:,19), CONSTANTS(:,18))+power(STATES(:,1), CONSTANTS(:,18)));
ALGEBRAIC(:,10) = 3.00000.*CONSTANTS(:,37) - 2.00000.*ALGEBRAIC(:,9);
ALGEBRAIC(:,11) = (( CONSTANTS(:,21).*STATES(:,1))./(STATES(:,1)+CONSTANTS(:,20))).*(ALGEBRAIC(:,3) - ALGEBRAIC(:,10));
RATES(:,1) = ALGEBRAIC(:,13)+ CONSTANTS(:,7).*ALGEBRAIC(:,7)+ALGEBRAIC(:,11);
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(:,6) = (power(STATES(:,1), CONSTANTS(:,22))./(power(CONSTANTS(:,23), CONSTANTS(:,22))+power(STATES(:,1), CONSTANTS(:,22)))).*1.00000;
ALGEBRAIC(:,4) = STATES(:,2)+STATES(:,3)+STATES(:,4)+STATES(:,5);
ALGEBRAIC(:,8) = ALGEBRAIC(:,6);
ALGEBRAIC(:,3) = piecewise({VOI<CONSTANTS(:,1), CONSTANTS(:,2) , VOI>=CONSTANTS(:,1)&VOI<CONSTANTS(:,3)+CONSTANTS(:,1), CONSTANTS(:,4) }, CONSTANTS(:,2));
ALGEBRAIC(:,5) = 1.00000./(1.00000+exp((CONSTANTS(:,15) - ALGEBRAIC(:,3))./CONSTANTS(:,8)));
ALGEBRAIC(:,9) = (( CONSTANTS(:,9).*CONSTANTS(:,11))./( CONSTANTS(:,35).*CONSTANTS(:,10))).*log(CONSTANTS(:,13)./STATES(:,1));
ALGEBRAIC(:,12) = CONSTANTS(:,16).*ALGEBRAIC(:,5).*(ALGEBRAIC(:,3) - ALGEBRAIC(:,9));
ALGEBRAIC(:,13) = - ALGEBRAIC(:,12)./( 2.00000.*CONSTANTS(:,14).*CONSTANTS(:,10));
ALGEBRAIC(:,7) = ( - CONSTANTS(:,17).*power(STATES(:,1), CONSTANTS(:,18)))./(power(CONSTANTS(:,19), CONSTANTS(:,18))+power(STATES(:,1), CONSTANTS(:,18)));
ALGEBRAIC(:,10) = 3.00000.*CONSTANTS(:,37) - 2.00000.*ALGEBRAIC(:,9);
ALGEBRAIC(:,11) = (( CONSTANTS(:,21).*STATES(:,1))./(STATES(:,1)+CONSTANTS(:,20))).*(ALGEBRAIC(:,3) - ALGEBRAIC(:,10));
ALGEBRAIC(:,1) = STATES(:,5)+STATES(:,4);
ALGEBRAIC(:,2) = STATES(:,5)+STATES(:,3);
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