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 =12;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 5 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_STATES(:,1) = strpad('V in component membrane (millivolt)');
LEGEND_CONSTANTS(:,1) = strpad('Cm in component membrane (microF)');
LEGEND_ALGEBRAIC(:,5) = strpad('i_Na in component sodium_channel (nanoA)');
LEGEND_ALGEBRAIC(:,11) = strpad('i_K in component potassium_channel (nanoA)');
LEGEND_ALGEBRAIC(:,12) = strpad('i_Leak in component leakage_current (nanoA)');
LEGEND_CONSTANTS(:,2) = strpad('g_Na_max in component sodium_channel (microS)');
LEGEND_ALGEBRAIC(:,1) = strpad('g_Na in component sodium_channel (microS)');
LEGEND_CONSTANTS(:,3) = strpad('E_Na in component sodium_channel (millivolt)');
LEGEND_STATES(:,2) = strpad('m in component sodium_channel_m_gate (dimensionless)');
LEGEND_STATES(:,3) = strpad('h in component sodium_channel_h_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('alpha_m in component sodium_channel_m_gate (per_second)');
LEGEND_ALGEBRAIC(:,6) = strpad('beta_m in component sodium_channel_m_gate (per_second)');
LEGEND_ALGEBRAIC(:,3) = strpad('alpha_h in component sodium_channel_h_gate (per_second)');
LEGEND_ALGEBRAIC(:,7) = strpad('beta_h in component sodium_channel_h_gate (per_second)');
LEGEND_ALGEBRAIC(:,9) = strpad('g_K1 in component potassium_channel (microS)');
LEGEND_ALGEBRAIC(:,10) = strpad('g_K2 in component potassium_channel (microS)');
LEGEND_STATES(:,4) = strpad('n in component potassium_channel_n_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('alpha_n in component potassium_channel_n_gate (per_second)');
LEGEND_ALGEBRAIC(:,8) = strpad('beta_n in component potassium_channel_n_gate (per_second)');
LEGEND_CONSTANTS(:,4) = strpad('g_L in component leakage_current (microS)');
LEGEND_CONSTANTS(:,5) = strpad('E_L in component leakage_current (millivolt)');
LEGEND_RATES(:,1) = strpad('d/dt V in component membrane (millivolt)');
LEGEND_RATES(:,2) = strpad('d/dt m in component sodium_channel_m_gate (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt h in component sodium_channel_h_gate (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt n in component potassium_channel_n_gate (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 = [];
STATES(:,1) = -87;
CONSTANTS(:,1) = 12;
CONSTANTS(:,2) = 400000;
CONSTANTS(:,3) = 40;
STATES(:,2) = 0.01;
STATES(:,3) = 0.8;
STATES(:,4) = 0.01;
CONSTANTS(:,4) = 75;
CONSTANTS(:,5) = -60;
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) = ( 100.000.*( - STATES(:,1) - 48.0000))./(exp(( - STATES(:,1) - 48.0000)./15.0000) - 1.00000);
ALGEBRAIC(:,6) = ( 120.000.*(STATES(:,1)+8.00000))./(exp((STATES(:,1)+8.00000)./5.00000) - 1.00000);
RATES(:,2) = ALGEBRAIC(:,2).*(1.00000 - STATES(:,2)) - ALGEBRAIC(:,6).*STATES(:,2);
ALGEBRAIC(:,3) = 170.000.*exp(( - STATES(:,1) - 90.0000)./20.0000);
ALGEBRAIC(:,7) = 1000.00./(1.00000+exp(( - STATES(:,1) - 42.0000)./10.0000));
RATES(:,3) = ALGEBRAIC(:,3).*(1.00000 - STATES(:,3)) - ALGEBRAIC(:,7).*STATES(:,3);
ALGEBRAIC(:,4) = ( 0.100000.*( - STATES(:,1) - 50.0000))./(exp(( - STATES(:,1) - 50.0000)./10.0000) - 1.00000);
ALGEBRAIC(:,8) = 2.00000.*exp(( - STATES(:,1) - 90.0000)./80.0000);
RATES(:,4) = ALGEBRAIC(:,4).*(1.00000 - STATES(:,4)) - ALGEBRAIC(:,8).*STATES(:,4);
ALGEBRAIC(:,1) = power(STATES(:,2), 3.00000).*STATES(:,3).*CONSTANTS(:,2);
ALGEBRAIC(:,5) = (ALGEBRAIC(:,1)+140.000).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,9) = 1200.00.*exp(( - STATES(:,1) - 90.0000)./50.0000)+ 15.0000.*exp((STATES(:,1)+90.0000)./60.0000);
ALGEBRAIC(:,10) = 1200.00.*power(STATES(:,4), 4.00000);
ALGEBRAIC(:,11) = (ALGEBRAIC(:,9)+ALGEBRAIC(:,10)).*(STATES(:,1)+100.000);
ALGEBRAIC(:,12) = CONSTANTS(:,4).*(STATES(:,1) - CONSTANTS(:,5));
RATES(:,1) = - (ALGEBRAIC(:,5)+ALGEBRAIC(:,11)+ALGEBRAIC(:,12))./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) = ( 100.000.*( - STATES(:,1) - 48.0000))./(exp(( - STATES(:,1) - 48.0000)./15.0000) - 1.00000);
ALGEBRAIC(:,6) = ( 120.000.*(STATES(:,1)+8.00000))./(exp((STATES(:,1)+8.00000)./5.00000) - 1.00000);
ALGEBRAIC(:,3) = 170.000.*exp(( - STATES(:,1) - 90.0000)./20.0000);
ALGEBRAIC(:,7) = 1000.00./(1.00000+exp(( - STATES(:,1) - 42.0000)./10.0000));
ALGEBRAIC(:,4) = ( 0.100000.*( - STATES(:,1) - 50.0000))./(exp(( - STATES(:,1) - 50.0000)./10.0000) - 1.00000);
ALGEBRAIC(:,8) = 2.00000.*exp(( - STATES(:,1) - 90.0000)./80.0000);
ALGEBRAIC(:,1) = power(STATES(:,2), 3.00000).*STATES(:,3).*CONSTANTS(:,2);
ALGEBRAIC(:,5) = (ALGEBRAIC(:,1)+140.000).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,9) = 1200.00.*exp(( - STATES(:,1) - 90.0000)./50.0000)+ 15.0000.*exp((STATES(:,1)+90.0000)./60.0000);
ALGEBRAIC(:,10) = 1200.00.*power(STATES(:,4), 4.00000);
ALGEBRAIC(:,11) = (ALGEBRAIC(:,9)+ALGEBRAIC(:,10)).*(STATES(:,1)+100.000);
ALGEBRAIC(:,12) = CONSTANTS(:,4).*(STATES(:,1) - CONSTANTS(:,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