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 =17;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 1 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('Cm in component membrane (microF_per_cm2)');
LEGEND_ALGEBRAIC(:,1) = strpad('i_Na in component sodium_channel (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,8) = strpad('i_K in component potassium_channel (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,15) = strpad('i_Leak in component leakage_current (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,16) = strpad('i_s in component calcium_channel (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,17) = strpad('i_h in component hyperpolarization_activated_channel (microA_per_cm2)');
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_millisecond)');
LEGEND_ALGEBRAIC(:,9) = strpad('beta_m in component sodium_channel_m_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,3) = strpad('alpha_h in component sodium_channel_h_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,10) = strpad('beta_h in component sodium_channel_h_gate (per_millisecond)');
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_millisecond)');
LEGEND_ALGEBRAIC(:,11) = strpad('beta_n in component potassium_channel_n_gate (per_millisecond)');
LEGEND_STATES(:,5) = strpad('d in component calcium_channel_d_gate (dimensionless)');
LEGEND_STATES(:,6) = strpad('f in component calcium_channel_f_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('alpha_d in component calcium_channel_d_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,12) = strpad('beta_d in component calcium_channel_d_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,6) = strpad('alpha_f in component calcium_channel_f_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,13) = strpad('beta_f in component calcium_channel_f_gate (per_millisecond)');
LEGEND_STATES(:,7) = strpad('q in component hyperpolarization_activated_channel_q_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('alpha_q in component hyperpolarization_activated_channel_q_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,14) = strpad('beta_q in component hyperpolarization_activated_channel_q_gate (per_millisecond)');
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_RATES(:,5) = strpad('d/dt d in component calcium_channel_d_gate (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt f in component calcium_channel_f_gate (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt q in component hyperpolarization_activated_channel_q_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) = -62.83;
CONSTANTS(:,1) = 1;
STATES(:,2) = 0.047938;
STATES(:,3) = 0.95994;
STATES(:,4) = 0.509494;
STATES(:,5) = 0.000032;
STATES(:,6) = 1;
STATES(:,7) = 0.010759;
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.*(STATES(:,1)+37.0000))./( - exp((STATES(:,1)+37.0000)./ - 10.0000)+1.00000);
ALGEBRAIC(:,9) = 40.0000.*exp((STATES(:,1)+62.0000)./ - 17.8000);
RATES(:,2) = ALGEBRAIC(:,2).*(1.00000 - STATES(:,2)) - ALGEBRAIC(:,9).*STATES(:,2);
ALGEBRAIC(:,3) = 0.00120900.*exp((STATES(:,1)+20.0000)./ - 6.53400);
ALGEBRAIC(:,10) = 1.00000./(1.00000+exp((STATES(:,1)+30.0000)./ - 10.0000));
RATES(:,3) = ALGEBRAIC(:,3).*(1.00000 - STATES(:,3)) - ALGEBRAIC(:,10).*STATES(:,3);
ALGEBRAIC(:,4) = ( 0.00900000.*1.00000)./(1.00000+exp( - (STATES(:,1)+3.80000)./9.71000))+0.000600000;
ALGEBRAIC(:,11) = ( - 0.000225000.*(STATES(:,1)+40.0000))./(1.00000 - exp((STATES(:,1)+40.0000)./13.3000));
RATES(:,4) = ALGEBRAIC(:,4).*(1.00000 - STATES(:,4)) - ALGEBRAIC(:,11).*STATES(:,4);
ALGEBRAIC(:,5) = ( 0.0145000.*(STATES(:,1)+35.0000))./(1.00000 - exp( - (STATES(:,1)+35.0000)./2.50000))+( 0.0312500.*STATES(:,1))./(1.00000 - exp( - STATES(:,1)./4.80000));
ALGEBRAIC(:,12) = ( - 0.00421000.*(STATES(:,1) - 5.00000))./( - exp((STATES(:,1) - 5.00000)./2.50000)+1.00000);
RATES(:,5) = ALGEBRAIC(:,5).*(1.00000 - STATES(:,5)) - ALGEBRAIC(:,12).*STATES(:,5);
ALGEBRAIC(:,6) = ( - 0.000355000.*(STATES(:,1)+20.0000))./( - exp((STATES(:,1)+20.0000)./5.63300)+1.00000);
ALGEBRAIC(:,13) = ( 0.000944000.*(STATES(:,1)+60.0000))./(1.00000+exp( - (STATES(:,1)+29.5000)./4.16000));
RATES(:,6) = ALGEBRAIC(:,6).*(1.00000 - STATES(:,6)) - ALGEBRAIC(:,13).*STATES(:,6);
ALGEBRAIC(:,7) = ( 0.000340000.*(STATES(:,1)+100.000))./(exp((STATES(:,1)+100.000)./4.40000) - 1.00000)+4.95000e-05;
ALGEBRAIC(:,14) = ( 0.000500000.*(STATES(:,1)+40.0000))./(1.00000 - exp( - (STATES(:,1)+40.0000)./6.00000))+8.45000e-05;
RATES(:,7) = ALGEBRAIC(:,7).*(1.00000 - STATES(:,7)) - ALGEBRAIC(:,14).*STATES(:,7);
ALGEBRAIC(:,1) = 0.500000.*power(STATES(:,2), 3.00000).*STATES(:,3).*(STATES(:,1) - 30.0000);
ALGEBRAIC(:,8) = ( 0.700000.*STATES(:,4).*(exp( 0.0277000.*(STATES(:,1)+90.0000)) - 1.00000))./exp( 0.0277000.*(STATES(:,1)+40.0000));
ALGEBRAIC(:,15) = 0.800000.*(1.00000 - exp( - (STATES(:,1)+60.0000)./20.0000));
ALGEBRAIC(:,16) = 12.5000.*( 0.950000.*STATES(:,5)+0.0500000).*( 0.950000.*STATES(:,6)+0.0500000).*(exp((STATES(:,1) - 10.0000)./15.0000) - 1.00000);
ALGEBRAIC(:,17) = 0.400000.*STATES(:,7).*(STATES(:,1)+45.0000);
RATES(:,1) = - (ALGEBRAIC(:,1)+ALGEBRAIC(:,8)+ALGEBRAIC(:,15)+ALGEBRAIC(:,16)+ALGEBRAIC(:,17))./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.*(STATES(:,1)+37.0000))./( - exp((STATES(:,1)+37.0000)./ - 10.0000)+1.00000);
ALGEBRAIC(:,9) = 40.0000.*exp((STATES(:,1)+62.0000)./ - 17.8000);
ALGEBRAIC(:,3) = 0.00120900.*exp((STATES(:,1)+20.0000)./ - 6.53400);
ALGEBRAIC(:,10) = 1.00000./(1.00000+exp((STATES(:,1)+30.0000)./ - 10.0000));
ALGEBRAIC(:,4) = ( 0.00900000.*1.00000)./(1.00000+exp( - (STATES(:,1)+3.80000)./9.71000))+0.000600000;
ALGEBRAIC(:,11) = ( - 0.000225000.*(STATES(:,1)+40.0000))./(1.00000 - exp((STATES(:,1)+40.0000)./13.3000));
ALGEBRAIC(:,5) = ( 0.0145000.*(STATES(:,1)+35.0000))./(1.00000 - exp( - (STATES(:,1)+35.0000)./2.50000))+( 0.0312500.*STATES(:,1))./(1.00000 - exp( - STATES(:,1)./4.80000));
ALGEBRAIC(:,12) = ( - 0.00421000.*(STATES(:,1) - 5.00000))./( - exp((STATES(:,1) - 5.00000)./2.50000)+1.00000);
ALGEBRAIC(:,6) = ( - 0.000355000.*(STATES(:,1)+20.0000))./( - exp((STATES(:,1)+20.0000)./5.63300)+1.00000);
ALGEBRAIC(:,13) = ( 0.000944000.*(STATES(:,1)+60.0000))./(1.00000+exp( - (STATES(:,1)+29.5000)./4.16000));
ALGEBRAIC(:,7) = ( 0.000340000.*(STATES(:,1)+100.000))./(exp((STATES(:,1)+100.000)./4.40000) - 1.00000)+4.95000e-05;
ALGEBRAIC(:,14) = ( 0.000500000.*(STATES(:,1)+40.0000))./(1.00000 - exp( - (STATES(:,1)+40.0000)./6.00000))+8.45000e-05;
ALGEBRAIC(:,1) = 0.500000.*power(STATES(:,2), 3.00000).*STATES(:,3).*(STATES(:,1) - 30.0000);
ALGEBRAIC(:,8) = ( 0.700000.*STATES(:,4).*(exp( 0.0277000.*(STATES(:,1)+90.0000)) - 1.00000))./exp( 0.0277000.*(STATES(:,1)+40.0000));
ALGEBRAIC(:,15) = 0.800000.*(1.00000 - exp( - (STATES(:,1)+60.0000)./20.0000));
ALGEBRAIC(:,16) = 12.5000.*( 0.950000.*STATES(:,5)+0.0500000).*( 0.950000.*STATES(:,6)+0.0500000).*(exp((STATES(:,1) - 10.0000)./15.0000) - 1.00000);
ALGEBRAIC(:,17) = 0.400000.*STATES(:,7).*(STATES(:,1)+45.0000);
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