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 5 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_VOI = strpad('time in component environment (millisecond)');
LEGEND_CONSTANTS(:,1) = strpad('alpha in component model_constants (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('lamda in component model_constants (dimensionless)');
LEGEND_STATES(:,1) = strpad('V in component membrane (millivolt)');
LEGEND_CONSTANTS(:,3) = strpad('Cm in component membrane (microF_per_cm2)');
LEGEND_ALGEBRAIC(:,9) = strpad('i_Ca_T in component T_type_calcium_current (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,10) = strpad('i_Ca_L in component L_type_calcium_current (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,12) = strpad('i_Ca_K in component calcium_activated_potassium_current (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,11) = strpad('i_K in component potassium_current (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,13) = strpad('i_Cl in component leak_chloride_current (microA_per_cm2)');
LEGEND_ALGEBRAIC(:,1) = strpad('V_tilde in component gate_voltage (millivolt)');
LEGEND_CONSTANTS(:,4) = strpad('E_Ca in component T_type_calcium_current (millivolt)');
LEGEND_CONSTANTS(:,5) = strpad('g_Ca_T in component T_type_calcium_current (milliS_per_cm2)');
LEGEND_ALGEBRAIC(:,8) = strpad('m in component T_type_calcium_current_m_gate (dimensionless)');
LEGEND_STATES(:,2) = strpad('h in component T_type_calcium_current_h_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('alpha_m in component T_type_calcium_current_m_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,5) = strpad('beta_m in component T_type_calcium_current_m_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,3) = strpad('alpha_h in component T_type_calcium_current_h_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,6) = strpad('beta_h in component T_type_calcium_current_h_gate (per_millisecond)');
LEGEND_CONSTANTS(:,6) = strpad('g_Ca_L in component L_type_calcium_current (milliS_per_cm2)');
LEGEND_STATES(:,3) = strpad('x_Ca in component L_type_calcium_current_x_Ca_gate (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('tau_x_Ca in component L_type_calcium_current_x_Ca_gate (millisecond)');
LEGEND_CONSTANTS(:,8) = strpad('E_K in component potassium_current (millivolt)');
LEGEND_CONSTANTS(:,9) = strpad('g_K in component potassium_current (milliS_per_cm2)');
LEGEND_STATES(:,4) = strpad('n in component potassium_current_n_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('alpha_n in component potassium_current_n_gate (per_millisecond)');
LEGEND_ALGEBRAIC(:,7) = strpad('beta_n in component potassium_current_n_gate (per_millisecond)');
LEGEND_STATES(:,5) = strpad('Ca in component calcium_activated_potassium_current (millimolar)');
LEGEND_CONSTANTS(:,10) = strpad('g_Ca_K in component calcium_activated_potassium_current (milliS_per_cm2)');
LEGEND_CONSTANTS(:,11) = strpad('rho in component calcium_activated_potassium_current (per_millisecond)');
LEGEND_CONSTANTS(:,12) = strpad('K_c in component calcium_activated_potassium_current (millimolar_per_millivolt)');
LEGEND_CONSTANTS(:,13) = strpad('g_Cl in component leak_chloride_current (milliS_per_cm2)');
LEGEND_CONSTANTS(:,14) = strpad('E_Cl in component leak_chloride_current (millivolt)');
LEGEND_RATES(:,1) = strpad('d/dt V in component membrane (millivolt)');
LEGEND_RATES(:,2) = strpad('d/dt h in component T_type_calcium_current_h_gate (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt x_Ca in component L_type_calcium_current_x_Ca_gate (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt n in component potassium_current_n_gate (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt Ca in component calcium_activated_potassium_current (millimolar)');
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) = 0.12;
CONSTANTS(:,2) = 12.5;
STATES(:,1) = -55.0;
CONSTANTS(:,3) = 2.5;
CONSTANTS(:,4) = 80.0;
CONSTANTS(:,5) = 0.51;
STATES(:,2) = 0.01;
CONSTANTS(:,6) = 0.004;
STATES(:,3) = 0.01;
CONSTANTS(:,7) = 500.0;
CONSTANTS(:,8) = -75.0;
CONSTANTS(:,9) = 0.3;
STATES(:,4) = 0.01;
STATES(:,5) = 1E-4;
CONSTANTS(:,10) = 0.03;
CONSTANTS(:,11) = 0.125E3;
CONSTANTS(:,12) = 425.0E-5;
CONSTANTS(:,13) = 0.003;
CONSTANTS(:,14) = -40.0;
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
RATES(:,5) = (CONSTANTS(:,11)./CONSTANTS(:,1)).*( CONSTANTS(:,12).*STATES(:,3).*(CONSTANTS(:,4) - STATES(:,1)) - STATES(:,5));
ALGEBRAIC(:,1) = ( 127.000.*STATES(:,1)+8265.00)./105.000;
RATES(:,3) = (1.00000./(1.00000+exp( 0.150000.*( - ALGEBRAIC(:,1) - 50.0000))) - STATES(:,3))./( CONSTANTS(:,1).*CONSTANTS(:,7));
ALGEBRAIC(:,3) = 0.0700000.*exp((25.0000 - ALGEBRAIC(:,1))./20.0000);
ALGEBRAIC(:,6) = 1.00000./(1.00000+exp(5.50000 - ALGEBRAIC(:,1).*0.100000));
RATES(:,2) = ( ALGEBRAIC(:,3).*(1.00000 - STATES(:,2)) - ALGEBRAIC(:,6).*STATES(:,2))./( CONSTANTS(:,1).*CONSTANTS(:,2));
ALGEBRAIC(:,4) = ( 0.0100000.*(55.0000 - ALGEBRAIC(:,1)))./(exp((55.0000 - ALGEBRAIC(:,1))./10.0000) - 1.00000);
ALGEBRAIC(:,7) = 0.125000.*exp((45.0000 - ALGEBRAIC(:,1))./80.0000);
RATES(:,4) = ( ALGEBRAIC(:,4).*(1.00000 - STATES(:,4)) - ALGEBRAIC(:,7).*STATES(:,4))./( CONSTANTS(:,1).*CONSTANTS(:,2));
ALGEBRAIC(:,2) = ( 0.100000.*(50.0000 - ALGEBRAIC(:,1)))./(exp(5.00000 - ALGEBRAIC(:,1).*0.100000) - 1.00000);
ALGEBRAIC(:,5) = 4.00000.*exp((25.0000 - ALGEBRAIC(:,1))./18.0000);
ALGEBRAIC(:,8) = ALGEBRAIC(:,2)./(ALGEBRAIC(:,2)+ALGEBRAIC(:,5));
ALGEBRAIC(:,9) = CONSTANTS(:,5).*power(ALGEBRAIC(:,8), 3.00000).*STATES(:,2).*(STATES(:,1) - CONSTANTS(:,4));
ALGEBRAIC(:,10) = CONSTANTS(:,6).*STATES(:,3).*(STATES(:,1) - CONSTANTS(:,4));
ALGEBRAIC(:,12) = ( CONSTANTS(:,10).*STATES(:,5).*(STATES(:,1) - CONSTANTS(:,8)))./(0.500000+STATES(:,5));
ALGEBRAIC(:,11) = CONSTANTS(:,9).*power(STATES(:,4), 4.00000).*(STATES(:,1) - CONSTANTS(:,8));
ALGEBRAIC(:,13) = CONSTANTS(:,13).*(STATES(:,1) - CONSTANTS(:,14));
RATES(:,1) = - (1.00000./( CONSTANTS(:,3).*CONSTANTS(:,1))).*(ALGEBRAIC(:,9)+ALGEBRAIC(:,10)+ALGEBRAIC(:,12)+ALGEBRAIC(:,11)+ALGEBRAIC(:,13));
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) = ( 127.000.*STATES(:,1)+8265.00)./105.000;
ALGEBRAIC(:,3) = 0.0700000.*exp((25.0000 - ALGEBRAIC(:,1))./20.0000);
ALGEBRAIC(:,6) = 1.00000./(1.00000+exp(5.50000 - ALGEBRAIC(:,1).*0.100000));
ALGEBRAIC(:,4) = ( 0.0100000.*(55.0000 - ALGEBRAIC(:,1)))./(exp((55.0000 - ALGEBRAIC(:,1))./10.0000) - 1.00000);
ALGEBRAIC(:,7) = 0.125000.*exp((45.0000 - ALGEBRAIC(:,1))./80.0000);
ALGEBRAIC(:,2) = ( 0.100000.*(50.0000 - ALGEBRAIC(:,1)))./(exp(5.00000 - ALGEBRAIC(:,1).*0.100000) - 1.00000);
ALGEBRAIC(:,5) = 4.00000.*exp((25.0000 - ALGEBRAIC(:,1))./18.0000);
ALGEBRAIC(:,8) = ALGEBRAIC(:,2)./(ALGEBRAIC(:,2)+ALGEBRAIC(:,5));
ALGEBRAIC(:,9) = CONSTANTS(:,5).*power(ALGEBRAIC(:,8), 3.00000).*STATES(:,2).*(STATES(:,1) - CONSTANTS(:,4));
ALGEBRAIC(:,10) = CONSTANTS(:,6).*STATES(:,3).*(STATES(:,1) - CONSTANTS(:,4));
ALGEBRAIC(:,12) = ( CONSTANTS(:,10).*STATES(:,5).*(STATES(:,1) - CONSTANTS(:,8)))./(0.500000+STATES(:,5));
ALGEBRAIC(:,11) = CONSTANTS(:,9).*power(STATES(:,4), 4.00000).*(STATES(:,1) - CONSTANTS(:,8));
ALGEBRAIC(:,13) = CONSTANTS(:,13).*(STATES(:,1) - CONSTANTS(:,14));
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