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 =15;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 40 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_CONSTANTS(:,1) = strpad('cap in component parameters (nanofarad)');
LEGEND_CONSTANTS(:,2) = strpad('cc1lin in component parameters (per_second)');
LEGEND_CONSTANTS(:,3) = strpad('cc_2 in component parameters (per_second)');
LEGEND_CONSTANTS(:,4) = strpad('ck1lin in component parameters (per_second)');
LEGEND_CONSTANTS(:,5) = strpad('ck_2 in component parameters (per_second)');
LEGEND_CONSTANTS(:,6) = strpad('clmax in component parameters (nanosiemens)');
LEGEND_CONSTANTS(:,7) = strpad('cnmax in component parameters (nanosiemens)');
LEGEND_CONSTANTS(:,8) = strpad('cx1lin in component parameters (per_second)');
LEGEND_CONSTANTS(:,9) = strpad('cx2 in component parameters (per_second)');
LEGEND_CONSTANTS(:,10) = strpad('ef in component parameters (per_second)');
LEGEND_CONSTANTS(:,11) = strpad('gl in component parameters (nanosiemens)');
LEGEND_CONSTANTS(:,12) = strpad('hmc_1 in component parameters (uM)');
LEGEND_CONSTANTS(:,13) = strpad('hmc_2 in component parameters (uM)');
LEGEND_CONSTANTS(:,14) = strpad('inf in component parameters (uM_per_picocoulomb)');
LEGEND_CONSTANTS(:,15) = strpad('inhmax in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('k_1 in component parameters (per_uM_per_second)');
LEGEND_CONSTANTS(:,17) = strpad('k_2 in component parameters (per_second)');
LEGEND_CONSTANTS(:,18) = strpad('kI in component parameters (uM)');
LEGEND_CONSTANTS(:,19) = strpad('kinh in component parameters (uM)');
LEGEND_CONSTANTS(:,20) = strpad('kinhcng in component parameters (uM)');
LEGEND_CONSTANTS(:,21) = strpad('n_1 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('n_2 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('nI in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('ninh in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('ninhcng in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('pd in component parameters (per_second)');
LEGEND_CONSTANTS(:,27) = strpad('r_1 in component parameters (per_second)');
LEGEND_CONSTANTS(:,28) = strpad('r_2 in component parameters (per_second)');
LEGEND_CONSTANTS(:,29) = strpad('smax in component parameters (uM_per_second)');
LEGEND_CONSTANTS(:,30) = strpad('V_Cl in component parameters (millivolt)');
LEGEND_CONSTANTS(:,31) = strpad('V_cng in component parameters (millivolt)');
LEGEND_CONSTANTS(:,32) = strpad('V_l in component parameters (millivolt)');
LEGEND_CONSTANTS(:,40) = strpad('F_vol in component parameters (picocoulomb_per_uM)');
LEGEND_CONSTANTS(:,33) = strpad('F in component parameters (coulombs_per_mole)');
LEGEND_CONSTANTS(:,34) = strpad('C_vol in component parameters (liter)');
LEGEND_ALGEBRAIC(:,10) = strpad('O_stim in component O_stim (uM)');
LEGEND_CONSTANTS(:,35) = strpad('od in component O_stim (uM)');
LEGEND_CONSTANTS(:,36) = strpad('t_0 in component O_stim (second)');
LEGEND_CONSTANTS(:,37) = strpad('t_1 in component O_stim (second)');
LEGEND_ALGEBRAIC(:,1) = strpad('H_0 in component O_stim (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('H_1 in component O_stim (dimensionless)');
LEGEND_STATES(:,1) = strpad('bLR in component bLR (dimensionless)');
LEGEND_CONSTANTS(:,38) = strpad('R_tot in component bLR (dimensionless)');
LEGEND_STATES(:,2) = strpad('aG in component aG (dimensionless)');
LEGEND_CONSTANTS(:,39) = strpad('G_tot in component aG (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('k_G in component k_G (per_second)');
LEGEND_ALGEBRAIC(:,7) = strpad('r_G in component r_G (per_second)');
LEGEND_STATES(:,3) = strpad('cAMP in component cAMP (uM)');
LEGEND_ALGEBRAIC(:,3) = strpad('synth in component synth (uM_per_second)');
LEGEND_ALGEBRAIC(:,8) = strpad('degrad in component degrad (uM_per_second)');
LEGEND_STATES(:,4) = strpad('aCaMK in component aCaMK (uM)');
LEGEND_STATES(:,5) = strpad('Ca in component Ca (uM)');
LEGEND_ALGEBRAIC(:,11) = strpad('I_CNG in component I_CNG (nanoampere)');
LEGEND_ALGEBRAIC(:,13) = strpad('J_NCX in component J_NCX (uM_per_second)');
LEGEND_ALGEBRAIC(:,4) = strpad('cc_1 in component cc_1 (uM_per_second)');
LEGEND_STATES(:,6) = strpad('CaCaM in component CaCaM (uM)');
LEGEND_ALGEBRAIC(:,5) = strpad('ck_1 in component ck_1 (uM_per_second)');
LEGEND_STATES(:,7) = strpad('V in component V (millivolt)');
LEGEND_ALGEBRAIC(:,12) = strpad('I_ClCa in component I_ClCa (nanoampere)');
LEGEND_ALGEBRAIC(:,14) = strpad('I_NCX in component I_NCX (nanoampere)');
LEGEND_ALGEBRAIC(:,15) = strpad('I_other in component I_other (nanoampere)');
LEGEND_ALGEBRAIC(:,9) = strpad('inhcng in component inhcng (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt bLR in component bLR (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt aG in component aG (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt cAMP in component cAMP (uM)');
LEGEND_RATES(:,5) = strpad('d/dt Ca in component Ca (uM)');
LEGEND_RATES(:,6) = strpad('d/dt CaCaM in component CaCaM (uM)');
LEGEND_RATES(:,4) = strpad('d/dt aCaMK in component aCaMK (uM)');
LEGEND_RATES(:,7) = strpad('d/dt V in component V (millivolt)');
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) = 0.004;
CONSTANTS(:,2) = 0.88;
CONSTANTS(:,3) = 26;
CONSTANTS(:,4) = 13;
CONSTANTS(:,5) = 0.9;
CONSTANTS(:,6) = 1;
CONSTANTS(:,7) = 1;
CONSTANTS(:,8) = 1;
CONSTANTS(:,9) = 13;
CONSTANTS(:,10) = 2;
CONSTANTS(:,11) = 6;
CONSTANTS(:,12) = 2;
CONSTANTS(:,13) = 3;
CONSTANTS(:,14) = 1.9;
CONSTANTS(:,15) = 5;
CONSTANTS(:,16) = 0.06;
CONSTANTS(:,17) = 20;
CONSTANTS(:,18) = 0.7;
CONSTANTS(:,19) = 2;
CONSTANTS(:,20) = 1;
CONSTANTS(:,21) = 2;
CONSTANTS(:,22) = 2;
CONSTANTS(:,23) = 2;
CONSTANTS(:,24) = 1.5;
CONSTANTS(:,25) = 1.3;
CONSTANTS(:,26) = 20;
CONSTANTS(:,27) = 10;
CONSTANTS(:,28) = 5;
CONSTANTS(:,29) = 71;
CONSTANTS(:,30) = -50;
CONSTANTS(:,31) = 0;
CONSTANTS(:,32) = -70;
CONSTANTS(:,33) = 9.649e4;
CONSTANTS(:,34) = 1e-13;
CONSTANTS(:,35) = 20;
CONSTANTS(:,36) = 0.5;
CONSTANTS(:,37) = 1.5;
STATES(:,1) = 0;
CONSTANTS(:,38) = 1;
STATES(:,2) = 0;
CONSTANTS(:,39) = 1;
STATES(:,3) = 1.35648992164649e-88;
STATES(:,4) = 6.60756525051462e-8;
STATES(:,5) = 5.09073088043779e-12;
STATES(:,6) = 1.86113118246926e-13;
STATES(:,7) = -70;
CONSTANTS(:,40) = (1.00000e+12./1.00000).*(1.00000./1000.00).*CONSTANTS(:,33).*CONSTANTS(:,34);
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(:,4) = CONSTANTS(:,2).*STATES(:,5);
RATES(:,6) = ALGEBRAIC(:,4) - CONSTANTS(:,3).*STATES(:,6);
ALGEBRAIC(:,5) = CONSTANTS(:,4).*STATES(:,6);
RATES(:,4) = ALGEBRAIC(:,5) - CONSTANTS(:,5).*STATES(:,4);
ALGEBRAIC(:,2) = CONSTANTS(:,17).*STATES(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,28).*STATES(:,2);
RATES(:,2) = ALGEBRAIC(:,2).*(CONSTANTS(:,39) - STATES(:,2)) - ALGEBRAIC(:,7);
ALGEBRAIC(:,3) = ( STATES(:,2).*CONSTANTS(:,29))./(1.00000+power(STATES(:,4)./CONSTANTS(:,19), CONSTANTS(:,24)));
ALGEBRAIC(:,8) = CONSTANTS(:,26).*STATES(:,3);
RATES(:,3) = ALGEBRAIC(:,3) - ALGEBRAIC(:,8);
ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,36), 0.00000 }, 1.00000);
ALGEBRAIC(:,6) = piecewise({VOI<CONSTANTS(:,37), 0.00000 }, 1.00000);
ALGEBRAIC(:,10) = CONSTANTS(:,35).*(ALGEBRAIC(:,1) - ALGEBRAIC(:,6));
RATES(:,1) = CONSTANTS(:,16).*ALGEBRAIC(:,10).*(CONSTANTS(:,38) - STATES(:,1)) - CONSTANTS(:,27).*STATES(:,1);
ALGEBRAIC(:,9) = 1.00000+( (CONSTANTS(:,15) - 1.00000).*power(STATES(:,6), CONSTANTS(:,25)))./(power(STATES(:,6), CONSTANTS(:,25))+power(CONSTANTS(:,20), CONSTANTS(:,25)));
ALGEBRAIC(:,11) = (( CONSTANTS(:,7).*power(STATES(:,3), CONSTANTS(:,21)))./(power(STATES(:,3), CONSTANTS(:,21))+power( ALGEBRAIC(:,9).*CONSTANTS(:,12), CONSTANTS(:,21)))).*(1.00000./1000.00).*(CONSTANTS(:,31) - STATES(:,7));
ALGEBRAIC(:,13) = CONSTANTS(:,10).*STATES(:,5);
RATES(:,5) = ( (1000.00./1.00000).*CONSTANTS(:,14).*ALGEBRAIC(:,11) - ALGEBRAIC(:,13)) - (ALGEBRAIC(:,4) - CONSTANTS(:,3).*STATES(:,6));
ALGEBRAIC(:,12) = (( CONSTANTS(:,6).*power(STATES(:,5), CONSTANTS(:,22)))./(power(STATES(:,5), CONSTANTS(:,22))+power(CONSTANTS(:,13), CONSTANTS(:,22)))).*(1.00000./1000.00).*(CONSTANTS(:,30) - STATES(:,7));
ALGEBRAIC(:,14) = (1.00000./1000.00).*CONSTANTS(:,40).*ALGEBRAIC(:,13);
ALGEBRAIC(:,15) = CONSTANTS(:,11).*(1.00000./1000.00).*(CONSTANTS(:,32) - STATES(:,7));
RATES(:,7) = (1000.00./1.00000).*(1.00000./CONSTANTS(:,1)).*(ALGEBRAIC(:,11)+ALGEBRAIC(:,12)+ALGEBRAIC(:,14)+ALGEBRAIC(:,15));
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(:,4) = CONSTANTS(:,2).*STATES(:,5);
ALGEBRAIC(:,5) = CONSTANTS(:,4).*STATES(:,6);
ALGEBRAIC(:,2) = CONSTANTS(:,17).*STATES(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,28).*STATES(:,2);
ALGEBRAIC(:,3) = ( STATES(:,2).*CONSTANTS(:,29))./(1.00000+power(STATES(:,4)./CONSTANTS(:,19), CONSTANTS(:,24)));
ALGEBRAIC(:,8) = CONSTANTS(:,26).*STATES(:,3);
ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,36), 0.00000 }, 1.00000);
ALGEBRAIC(:,6) = piecewise({VOI<CONSTANTS(:,37), 0.00000 }, 1.00000);
ALGEBRAIC(:,10) = CONSTANTS(:,35).*(ALGEBRAIC(:,1) - ALGEBRAIC(:,6));
ALGEBRAIC(:,9) = 1.00000+( (CONSTANTS(:,15) - 1.00000).*power(STATES(:,6), CONSTANTS(:,25)))./(power(STATES(:,6), CONSTANTS(:,25))+power(CONSTANTS(:,20), CONSTANTS(:,25)));
ALGEBRAIC(:,11) = (( CONSTANTS(:,7).*power(STATES(:,3), CONSTANTS(:,21)))./(power(STATES(:,3), CONSTANTS(:,21))+power( ALGEBRAIC(:,9).*CONSTANTS(:,12), CONSTANTS(:,21)))).*(1.00000./1000.00).*(CONSTANTS(:,31) - STATES(:,7));
ALGEBRAIC(:,13) = CONSTANTS(:,10).*STATES(:,5);
ALGEBRAIC(:,12) = (( CONSTANTS(:,6).*power(STATES(:,5), CONSTANTS(:,22)))./(power(STATES(:,5), CONSTANTS(:,22))+power(CONSTANTS(:,13), CONSTANTS(:,22)))).*(1.00000./1000.00).*(CONSTANTS(:,30) - STATES(:,7));
ALGEBRAIC(:,14) = (1.00000./1000.00).*CONSTANTS(:,40).*ALGEBRAIC(:,13);
ALGEBRAIC(:,15) = CONSTANTS(:,11).*(1.00000./1000.00).*(CONSTANTS(:,32) - STATES(:,7));
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