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 =11;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 23 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 (millisecond)');
LEGEND_STATES(:,1) = strpad('V in component membrane (millivolt)');
LEGEND_CONSTANTS(:,1) = strpad('C in component membrane (picofarad)');
LEGEND_ALGEBRAIC(:,6) = strpad('I_Ca in component I_Ca (picoampere)');
LEGEND_ALGEBRAIC(:,1) = strpad('I_K in component I_K (picoampere)');
LEGEND_ALGEBRAIC(:,8) = strpad('I_SK in component I_SK (picoampere)');
LEGEND_ALGEBRAIC(:,11) = strpad('I_DA in component I_DA (picoampere)');
LEGEND_CONSTANTS(:,2) = strpad('gK in component I_K (nanosiemens)');
LEGEND_CONSTANTS(:,3) = strpad('VK in component model_parameters (millivolt)');
LEGEND_STATES(:,2) = strpad('n in component n (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('n_infinity in component n (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('lambda in component n (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('tau_n in component n (millisecond)');
LEGEND_CONSTANTS(:,6) = strpad('vn in component n (millivolt)');
LEGEND_CONSTANTS(:,7) = strpad('sn in component n (millivolt)');
LEGEND_CONSTANTS(:,8) = strpad('gCa in component I_Ca (nanosiemens)');
LEGEND_CONSTANTS(:,9) = strpad('VCa in component model_parameters (millivolt)');
LEGEND_ALGEBRAIC(:,5) = strpad('m_infinity in component m (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('vm in component m (millivolt)');
LEGEND_CONSTANTS(:,11) = strpad('sm in component m (millivolt)');
LEGEND_CONSTANTS(:,12) = strpad('gSK in component I_SK (nanosiemens)');
LEGEND_ALGEBRAIC(:,7) = strpad('s_infinity in component I_SK (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('ks in component I_SK (micromolar)');
LEGEND_STATES(:,3) = strpad('Ca in component Ca (micromolar)');
LEGEND_ALGEBRAIC(:,10) = strpad('I_A in component I_DA (picoampere)');
LEGEND_CONSTANTS(:,14) = strpad('gA in component I_DA (nanosiemens)');
LEGEND_ALGEBRAIC(:,9) = strpad('a_infinity in component a (dimensionless)');
LEGEND_STATES(:,4) = strpad('h in component h (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('va in component a (millivolt)');
LEGEND_CONSTANTS(:,16) = strpad('sa in component a (millivolt)');
LEGEND_ALGEBRAIC(:,3) = strpad('h_infinity in component h (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('tau_h in component h (millisecond)');
LEGEND_CONSTANTS(:,18) = strpad('vh in component h (millivolt)');
LEGEND_CONSTANTS(:,19) = strpad('sh in component h (millivolt)');
LEGEND_CONSTANTS(:,20) = strpad('fc in component Ca (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('alpha in component Ca (micromolar_femtocoulomb)');
LEGEND_CONSTANTS(:,22) = strpad('kc in component Ca (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('PRL in component PRL (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('kPRL in component PRL (micromolar_4)');
LEGEND_RATES(:,1) = strpad('d/dt V in component membrane (millivolt)');
LEGEND_RATES(:,2) = strpad('d/dt n in component n (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt h in component h (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt Ca in component Ca (micromolar)');
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 = [];
STATES(:,1) = -60;
CONSTANTS(:,1) = 10;
CONSTANTS(:,2) = 4;
CONSTANTS(:,3) = -75;
STATES(:,2) = 0.1;
CONSTANTS(:,4) = 0.7;
CONSTANTS(:,5) = 30;
CONSTANTS(:,6) = -5;
CONSTANTS(:,7) = 10;
CONSTANTS(:,8) = 2;
CONSTANTS(:,9) = 50;
CONSTANTS(:,10) = -20;
CONSTANTS(:,11) = 12;
CONSTANTS(:,12) = 1.7;
CONSTANTS(:,13) = 0.5;
STATES(:,3) = 0.1;
CONSTANTS(:,14) = 25;
STATES(:,4) = 0.1;
CONSTANTS(:,15) = -20;
CONSTANTS(:,16) = 10;
CONSTANTS(:,17) = 20;
CONSTANTS(:,18) = -60;
CONSTANTS(:,19) = 5;
CONSTANTS(:,20) = 0.01;
CONSTANTS(:,21) = 0.0015;
CONSTANTS(:,22) = 0.16;
CONSTANTS(:,23) = 1;
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(:,2) = 1.00000./(1.00000+exp((CONSTANTS(:,6) - STATES(:,1))./CONSTANTS(:,7)));
RATES(:,2) = ( CONSTANTS(:,4).*(ALGEBRAIC(:,2) - STATES(:,2)))./CONSTANTS(:,5);
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,18))./CONSTANTS(:,19)));
RATES(:,4) = (ALGEBRAIC(:,3) - STATES(:,4))./CONSTANTS(:,17);
ALGEBRAIC(:,5) = 1.00000./(1.00000+exp((CONSTANTS(:,10) - STATES(:,1))./CONSTANTS(:,11)));
ALGEBRAIC(:,6) = CONSTANTS(:,8).*ALGEBRAIC(:,5).*(STATES(:,1) - CONSTANTS(:,9));
RATES(:,3) = - CONSTANTS(:,20).*( CONSTANTS(:,21).*ALGEBRAIC(:,6)+ CONSTANTS(:,22).*STATES(:,3));
ALGEBRAIC(:,1) = CONSTANTS(:,2).*STATES(:,2).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,7) = power(STATES(:,3), 2.00000)./(power(STATES(:,3), 2.00000)+power(CONSTANTS(:,13), 2.00000));
ALGEBRAIC(:,8) = CONSTANTS(:,12).*ALGEBRAIC(:,7).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,9) = 1.00000./(1.00000+exp((CONSTANTS(:,15) - STATES(:,1))./CONSTANTS(:,16)));
ALGEBRAIC(:,10) = CONSTANTS(:,14).*ALGEBRAIC(:,9).*STATES(:,4).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,11) = ALGEBRAIC(:,10);
RATES(:,1) = - (ALGEBRAIC(:,6)+ALGEBRAIC(:,1)+ALGEBRAIC(:,8)+ALGEBRAIC(:,11))./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(:,2) = 1.00000./(1.00000+exp((CONSTANTS(:,6) - STATES(:,1))./CONSTANTS(:,7)));
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,18))./CONSTANTS(:,19)));
ALGEBRAIC(:,5) = 1.00000./(1.00000+exp((CONSTANTS(:,10) - STATES(:,1))./CONSTANTS(:,11)));
ALGEBRAIC(:,6) = CONSTANTS(:,8).*ALGEBRAIC(:,5).*(STATES(:,1) - CONSTANTS(:,9));
ALGEBRAIC(:,1) = CONSTANTS(:,2).*STATES(:,2).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,7) = power(STATES(:,3), 2.00000)./(power(STATES(:,3), 2.00000)+power(CONSTANTS(:,13), 2.00000));
ALGEBRAIC(:,8) = CONSTANTS(:,12).*ALGEBRAIC(:,7).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,9) = 1.00000./(1.00000+exp((CONSTANTS(:,15) - STATES(:,1))./CONSTANTS(:,16)));
ALGEBRAIC(:,10) = CONSTANTS(:,14).*ALGEBRAIC(:,9).*STATES(:,4).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,11) = ALGEBRAIC(:,10);
ALGEBRAIC(:,4) = CONSTANTS(:,23).*power(STATES(:,3), 4.00000);
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