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 =13;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 14 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_CONSTANTS(:,1) = strpad('stimPeriod in component stimulus_protocol_params (ms)');
LEGEND_CONSTANTS(:,2) = strpad('stimDuration in component stimulus_protocol_params (ms)');
LEGEND_CONSTANTS(:,3) = strpad('stimCurrent in component stimulus_protocol_params (uA_per_cmsq)');
LEGEND_VOI = strpad('time in component time (ms)');
LEGEND_ALGEBRAIC(:,10) = strpad('INa in component INa (uA_per_cmsq)');
LEGEND_ALGEBRAIC(:,12) = strpad('IK in component IK (uA_per_cmsq)');
LEGEND_ALGEBRAIC(:,13) = strpad('Ileak in component Ileak (uA_per_cmsq)');
LEGEND_STATES(:,1) = strpad('V in component action_potential (mV)');
LEGEND_ALGEBRAIC(:,1) = strpad('minus_V in component action_potential (mV)');
LEGEND_STATES(:,2) = strpad('X in component hh_gating_variable (dimensionless)');
LEGEND_STATES(:,3) = strpad('X in component hh_gating_variable (dimensionless)');
LEGEND_STATES(:,4) = strpad('X in component hh_gating_variable (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('V_initial in component initial_conditions (mV)');
LEGEND_CONSTANTS(:,5) = strpad('n_initial in component initial_conditions (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('m_initial in component initial_conditions (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('h_initial in component initial_conditions (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('IStim in component stimulus_protocol (uA_per_cmsq)');
LEGEND_CONSTANTS(:,8) = strpad('VNa in component parameters (mV)');
LEGEND_CONSTANTS(:,9) = strpad('VK in component parameters (mV)');
LEGEND_CONSTANTS(:,10) = strpad('Vleak in component parameters (mV)');
LEGEND_CONSTANTS(:,11) = strpad('gNa_max in component parameters (mS_per_cmsq)');
LEGEND_CONSTANTS(:,12) = strpad('gK_max in component parameters (mS_per_cmsq)');
LEGEND_CONSTANTS(:,13) = strpad('gleak_max in component parameters (mS_per_cmsq)');
LEGEND_CONSTANTS(:,14) = strpad('Cm in component parameters (uF_per_cmsq)');
LEGEND_ALGEBRAIC(:,6) = strpad('gNa in component INa (mS_per_cmsq)');
LEGEND_ALGEBRAIC(:,11) = strpad('gK in component IK (mS_per_cmsq)');
LEGEND_ALGEBRAIC(:,3) = strpad('alpha in component alpha_m (per_ms)');
LEGEND_ALGEBRAIC(:,7) = strpad('beta in component beta_m (per_ms)');
LEGEND_ALGEBRAIC(:,4) = strpad('alpha in component alpha_h (per_ms)');
LEGEND_ALGEBRAIC(:,8) = strpad('beta in component beta_h (per_ms)');
LEGEND_ALGEBRAIC(:,5) = strpad('alpha in component alpha_n (per_ms)');
LEGEND_ALGEBRAIC(:,9) = strpad('beta in component beta_n (per_ms)');
LEGEND_RATES(:,1) = strpad('d/dt V in component action_potential (mV)');
LEGEND_RATES(:,3) = strpad('d/dt X in component hh_gating_variable (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt X in component hh_gating_variable (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt X in component hh_gating_variable (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 = [];
CONSTANTS(:,1) = 50;
CONSTANTS(:,2) = 0.5;
CONSTANTS(:,3) = -10.0;
CONSTANTS(:,4) = 0.0;
CONSTANTS(:,5) = 0.315;
CONSTANTS(:,6) = 0.042;
CONSTANTS(:,7) = 0.608;
CONSTANTS(:,8) = -115.0;
CONSTANTS(:,9) = 12.0;
CONSTANTS(:,10) = -10.613;
CONSTANTS(:,11) = 120.0;
CONSTANTS(:,12) = 36.0;
CONSTANTS(:,13) = 0.3;
CONSTANTS(:,14) = 1.0;
STATES(:,1) = CONSTANTS(:,4);
STATES(:,2) = CONSTANTS(:,7);
STATES(:,3) = CONSTANTS(:,6);
STATES(:,4) = CONSTANTS(:,5);
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(:,3) = ( 0.100000.*(STATES(:,1)+25.0000))./(exp((STATES(:,1)+25.0000)./10.0000) - 1.00000);
ALGEBRAIC(:,7) = 4.00000.*exp(STATES(:,1)./18.0000);
RATES(:,3) = ALGEBRAIC(:,3).*(1.00000 - STATES(:,3)) - ALGEBRAIC(:,7).*STATES(:,3);
ALGEBRAIC(:,4) = 0.0700000.*exp(STATES(:,1)./20.0000);
ALGEBRAIC(:,8) = 1.00000./(exp((STATES(:,1)+30.0000)./10.0000)+1.00000);
RATES(:,2) = ALGEBRAIC(:,4).*(1.00000 - STATES(:,2)) - ALGEBRAIC(:,8).*STATES(:,2);
ALGEBRAIC(:,5) = ( 0.0100000.*(STATES(:,1)+10.0000))./(exp((STATES(:,1)+10.0000)./10.0000) - 1.00000);
ALGEBRAIC(:,9) = 0.125000.*exp(STATES(:,1)./80.0000);
RATES(:,4) = ALGEBRAIC(:,5).*(1.00000 - STATES(:,4)) - ALGEBRAIC(:,9).*STATES(:,4);
ALGEBRAIC(:,6) = CONSTANTS(:,11).*power(STATES(:,3), 3.00000).*STATES(:,2);
ALGEBRAIC(:,10) = ALGEBRAIC(:,6).*(STATES(:,1) - CONSTANTS(:,8));
ALGEBRAIC(:,11) = CONSTANTS(:,12).*power(STATES(:,4), 4.00000);
ALGEBRAIC(:,12) = ALGEBRAIC(:,11).*(STATES(:,1) - CONSTANTS(:,9));
ALGEBRAIC(:,13) = CONSTANTS(:,13).*(STATES(:,1) - CONSTANTS(:,10));
ALGEBRAIC(:,2) = piecewise({ rem(VOI, CONSTANTS(:,1))<CONSTANTS(:,2), CONSTANTS(:,3) }, 0.00000);
RATES(:,1) = (ALGEBRAIC(:,2) - (ALGEBRAIC(:,10)+ALGEBRAIC(:,12)+ALGEBRAIC(:,13)))./CONSTANTS(:,14);
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(:,3) = ( 0.100000.*(STATES(:,1)+25.0000))./(exp((STATES(:,1)+25.0000)./10.0000) - 1.00000);
ALGEBRAIC(:,7) = 4.00000.*exp(STATES(:,1)./18.0000);
ALGEBRAIC(:,4) = 0.0700000.*exp(STATES(:,1)./20.0000);
ALGEBRAIC(:,8) = 1.00000./(exp((STATES(:,1)+30.0000)./10.0000)+1.00000);
ALGEBRAIC(:,5) = ( 0.0100000.*(STATES(:,1)+10.0000))./(exp((STATES(:,1)+10.0000)./10.0000) - 1.00000);
ALGEBRAIC(:,9) = 0.125000.*exp(STATES(:,1)./80.0000);
ALGEBRAIC(:,6) = CONSTANTS(:,11).*power(STATES(:,3), 3.00000).*STATES(:,2);
ALGEBRAIC(:,10) = ALGEBRAIC(:,6).*(STATES(:,1) - CONSTANTS(:,8));
ALGEBRAIC(:,11) = CONSTANTS(:,12).*power(STATES(:,4), 4.00000);
ALGEBRAIC(:,12) = ALGEBRAIC(:,11).*(STATES(:,1) - CONSTANTS(:,9));
ALGEBRAIC(:,13) = CONSTANTS(:,13).*(STATES(:,1) - CONSTANTS(:,10));
ALGEBRAIC(:,2) = piecewise({ rem(VOI, CONSTANTS(:,1))<CONSTANTS(:,2), CONSTANTS(:,3) }, 0.00000);
ALGEBRAIC(:,1) = - STATES(:,1);
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