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 =8;
end
% There are a total of 3 entries in each of the rate and state variable arrays.
% There are a total of 10 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 (second)');
LEGEND_CONSTANTS(:,1) = strpad('C_m in component environment (fF)');
LEGEND_CONSTANTS(:,2) = strpad('w_i in component environment (pL)');
LEGEND_CONSTANTS(:,3) = strpad('w_o in component environment (pL)');
LEGEND_STATES(:,1) = strpad('q_mem in component environment (fC)');
LEGEND_CONSTANTS(:,4) = strpad('R in component environment (J_per_K_per_mol)');
LEGEND_CONSTANTS(:,5) = strpad('T in component environment (kelvin)');
LEGEND_CONSTANTS(:,6) = strpad('F in component environment (C_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('v_CaB in component CaB (fmol_per_sec)');
LEGEND_STATES(:,2) = strpad('q_Ca_o in component environment (fmol)');
LEGEND_STATES(:,3) = strpad('q_Ca_i in component environment (fmol)');
LEGEND_ALGEBRAIC(:,1) = strpad('V_mem in component environment (J_per_C)');
LEGEND_ALGEBRAIC(:,8) = strpad('I_mem_CaB in component CaB (fA)');
LEGEND_CONSTANTS(:,7) = strpad('kappa_CaB in component CaB_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,8) = strpad('K_Ca_i in component CaB_parameters (per_fmol)');
LEGEND_CONSTANTS(:,9) = strpad('K_Ca_o in component CaB_parameters (per_fmol)');
LEGEND_CONSTANTS(:,10) = strpad('zCa in component CaB_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('mu_Ca_i in component CaB (J_per_mol)');
LEGEND_ALGEBRAIC(:,3) = strpad('mu_Ca_o in component CaB (J_per_mol)');
LEGEND_ALGEBRAIC(:,4) = strpad('Af_CaB in component CaB (J_per_mol)');
LEGEND_ALGEBRAIC(:,5) = strpad('Ar_CaB in component CaB (J_per_mol)');
LEGEND_ALGEBRAIC(:,6) = strpad('Am_CaB in component CaB (J_per_mol)');
LEGEND_RATES(:,3) = strpad('d/dt q_Ca_i in component environment (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_Ca_o in component environment (fmol)');
LEGEND_RATES(:,1) = strpad('d/dt q_mem in component environment (fC)');
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) = 1e6;
CONSTANTS(:,2) = 25.8;
CONSTANTS(:,3) = 3.52;
STATES(:,1) = -8.5e4;
CONSTANTS(:,4) = 8.31;
CONSTANTS(:,5) = 310;
CONSTANTS(:,6) = 96500;
STATES(:,2) = 9.3276;
STATES(:,3) = 0.00456;
CONSTANTS(:,7) = 2.73233e-05;
CONSTANTS(:,8) = 0.000151953;
CONSTANTS(:,9) = 0.00100872;
CONSTANTS(:,10) = 2;
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(:,1) = STATES(:,1)./CONSTANTS(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,4).*CONSTANTS(:,5).*log( CONSTANTS(:,8).*STATES(:,3));
ALGEBRAIC(:,4) = ALGEBRAIC(:,2)+ CONSTANTS(:,10).*CONSTANTS(:,6).*ALGEBRAIC(:,1);
ALGEBRAIC(:,3) = CONSTANTS(:,4).*CONSTANTS(:,5).*log( CONSTANTS(:,9).*STATES(:,2));
ALGEBRAIC(:,5) = ALGEBRAIC(:,3);
ALGEBRAIC(:,6) = CONSTANTS(:,10).*CONSTANTS(:,6).*ALGEBRAIC(:,1);
ALGEBRAIC(:,7) = piecewise({ALGEBRAIC(:,6)==0.00000, CONSTANTS(:,7).*(exp(ALGEBRAIC(:,4)./( CONSTANTS(:,4).*CONSTANTS(:,5))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,4).*CONSTANTS(:,5)))) }, ((( CONSTANTS(:,7).*ALGEBRAIC(:,6))./( CONSTANTS(:,4).*CONSTANTS(:,5)))./(exp(ALGEBRAIC(:,6)./( CONSTANTS(:,4).*CONSTANTS(:,5))) - 1.00000)).*(exp(ALGEBRAIC(:,4)./( CONSTANTS(:,4).*CONSTANTS(:,5))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,4).*CONSTANTS(:,5)))));
RATES(:,3) = - ALGEBRAIC(:,7);
RATES(:,2) = ALGEBRAIC(:,7);
ALGEBRAIC(:,8) = - CONSTANTS(:,10).*CONSTANTS(:,6).*ALGEBRAIC(:,7);
RATES(:,1) = ALGEBRAIC(:,8);
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(:,1) = STATES(:,1)./CONSTANTS(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,4).*CONSTANTS(:,5).*log( CONSTANTS(:,8).*STATES(:,3));
ALGEBRAIC(:,4) = ALGEBRAIC(:,2)+ CONSTANTS(:,10).*CONSTANTS(:,6).*ALGEBRAIC(:,1);
ALGEBRAIC(:,3) = CONSTANTS(:,4).*CONSTANTS(:,5).*log( CONSTANTS(:,9).*STATES(:,2));
ALGEBRAIC(:,5) = ALGEBRAIC(:,3);
ALGEBRAIC(:,6) = CONSTANTS(:,10).*CONSTANTS(:,6).*ALGEBRAIC(:,1);
ALGEBRAIC(:,7) = piecewise({ALGEBRAIC(:,6)==0.00000, CONSTANTS(:,7).*(exp(ALGEBRAIC(:,4)./( CONSTANTS(:,4).*CONSTANTS(:,5))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,4).*CONSTANTS(:,5)))) }, ((( CONSTANTS(:,7).*ALGEBRAIC(:,6))./( CONSTANTS(:,4).*CONSTANTS(:,5)))./(exp(ALGEBRAIC(:,6)./( CONSTANTS(:,4).*CONSTANTS(:,5))) - 1.00000)).*(exp(ALGEBRAIC(:,4)./( CONSTANTS(:,4).*CONSTANTS(:,5))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,4).*CONSTANTS(:,5)))));
ALGEBRAIC(:,8) = - CONSTANTS(:,10).*CONSTANTS(:,6).*ALGEBRAIC(:,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