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 =10;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 11 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_STATES(:,1) = strpad('q_mem in component environment (fC)');
LEGEND_CONSTANTS(:,2) = strpad('R in component environment (J_per_K_per_mol)');
LEGEND_CONSTANTS(:,3) = strpad('T in component environment (kelvin)');
LEGEND_CONSTANTS(:,4) = strpad('F in component environment (C_per_mol)');
LEGEND_ALGEBRAIC(:,8) = strpad('v_pCa_R1 in component pCa (fmol_per_sec)');
LEGEND_ALGEBRAIC(:,9) = strpad('v_pCa_R2 in component pCa (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_STATES(:,4) = strpad('q_pCa in component environment (fmol)');
LEGEND_STATES(:,5) = strpad('q_pCa_Ca in component environment (fmol)');
LEGEND_ALGEBRAIC(:,2) = strpad('V_mem in component environment (J_per_C)');
LEGEND_ALGEBRAIC(:,10) = strpad('I_mem_pCa in component pCa (fA)');
LEGEND_ALGEBRAIC(:,3) = strpad('Ca_T in component environment (fmol)');
LEGEND_ALGEBRAIC(:,4) = strpad('channel_T in component environment (fmol)');
LEGEND_CONSTANTS(:,5) = strpad('kappa_pCa_R1 in component pCa_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,6) = strpad('kappa_pCa_R2 in component pCa_parameters (fmol_per_sec)');
LEGEND_CONSTANTS(:,7) = strpad('K_Ca_i in component pCa_parameters (per_fmol)');
LEGEND_CONSTANTS(:,8) = strpad('K_Ca_o in component pCa_parameters (per_fmol)');
LEGEND_CONSTANTS(:,9) = strpad('K_pCa in component pCa_parameters (per_fmol)');
LEGEND_CONSTANTS(:,10) = strpad('K_pCa_Ca in component pCa_parameters (per_fmol)');
LEGEND_CONSTANTS(:,11) = strpad('zCa in component pCa_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('mu_Ca_i in component pCa (J_per_mol)');
LEGEND_ALGEBRAIC(:,5) = strpad('mu_Ca_o in component pCa (J_per_mol)');
LEGEND_ALGEBRAIC(:,6) = strpad('mu_pCa in component pCa (J_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('mu_pCa_Ca in component pCa (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(:,4) = strpad('d/dt q_pCa in component environment (fmol)');
LEGEND_RATES(:,5) = strpad('d/dt q_pCa_Ca 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) = 153400;
STATES(:,1) = -13039;
CONSTANTS(:,2) = 8.31;
CONSTANTS(:,3) = 310;
CONSTANTS(:,4) = 96500;
STATES(:,2) = 9.3276;
STATES(:,3) = 0.00456;
STATES(:,4) = 0.0032;
STATES(:,5) = 1e-9;
CONSTANTS(:,5) = 2647.75;
CONSTANTS(:,6) = 2.95771e-05;
CONSTANTS(:,7) = 26.4744;
CONSTANTS(:,8) = 8.78733e-05;
CONSTANTS(:,9) = 0.0120554;
CONSTANTS(:,10) = 0.00548953;
CONSTANTS(:,11) = 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) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,7).*STATES(:,3));
ALGEBRAIC(:,6) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,9).*STATES(:,4));
ALGEBRAIC(:,7) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,10).*STATES(:,5));
ALGEBRAIC(:,8) = CONSTANTS(:,5).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,6))./( CONSTANTS(:,2).*CONSTANTS(:,3))) - exp(ALGEBRAIC(:,7)./( CONSTANTS(:,2).*CONSTANTS(:,3))));
RATES(:,3) = - ALGEBRAIC(:,8);
ALGEBRAIC(:,5) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,8).*STATES(:,2));
ALGEBRAIC(:,9) = CONSTANTS(:,6).*(exp(ALGEBRAIC(:,7)./( CONSTANTS(:,2).*CONSTANTS(:,3))) - exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,6))./( CONSTANTS(:,2).*CONSTANTS(:,3))));
RATES(:,2) = ALGEBRAIC(:,9);
RATES(:,4) = - ALGEBRAIC(:,8)+ALGEBRAIC(:,9);
RATES(:,5) = ALGEBRAIC(:,8) - ALGEBRAIC(:,9);
ALGEBRAIC(:,10) = - CONSTANTS(:,11).*CONSTANTS(:,4).*ALGEBRAIC(:,9);
RATES(:,1) = ALGEBRAIC(:,10);
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) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,7).*STATES(:,3));
ALGEBRAIC(:,6) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,9).*STATES(:,4));
ALGEBRAIC(:,7) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,10).*STATES(:,5));
ALGEBRAIC(:,8) = CONSTANTS(:,5).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,6))./( CONSTANTS(:,2).*CONSTANTS(:,3))) - exp(ALGEBRAIC(:,7)./( CONSTANTS(:,2).*CONSTANTS(:,3))));
ALGEBRAIC(:,5) = CONSTANTS(:,2).*CONSTANTS(:,3).*log( CONSTANTS(:,8).*STATES(:,2));
ALGEBRAIC(:,9) = CONSTANTS(:,6).*(exp(ALGEBRAIC(:,7)./( CONSTANTS(:,2).*CONSTANTS(:,3))) - exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,6))./( CONSTANTS(:,2).*CONSTANTS(:,3))));
ALGEBRAIC(:,10) = - CONSTANTS(:,11).*CONSTANTS(:,4).*ALGEBRAIC(:,9);
ALGEBRAIC(:,2) = STATES(:,1)./CONSTANTS(:,1);
ALGEBRAIC(:,3) = STATES(:,3)+STATES(:,2)+STATES(:,5);
ALGEBRAIC(:,4) = STATES(:,4)+STATES(:,5);
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