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 20 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_s in component soma_compartment (mV)');
LEGEND_CONSTANTS(:,1) = strpad('V_Na in component soma_compartment (mV)');
LEGEND_CONSTANTS(:,2) = strpad('V_K in component soma_compartment (mV)');
LEGEND_ALGEBRAIC(:,9) = strpad('I_Na in component soma_compartment (uA_per_cm2)');
LEGEND_ALGEBRAIC(:,1) = strpad('I_K_DR in component soma_compartment (uA_per_cm2)');
LEGEND_CONSTANTS(:,3) = strpad('g_K_DR in component soma_compartment (mS_per_cm2)');
LEGEND_CONSTANTS(:,4) = strpad('g_Na in component soma_compartment (mS_per_cm2)');
LEGEND_CONSTANTS(:,5) = strpad('g_c in component model_parameters (mS_per_cm2)');
LEGEND_STATES(:,2) = strpad('V_D in component dendritic_compartment (mV)');
LEGEND_CONSTANTS(:,6) = strpad('C_m in component model_parameters (uF_per_cm2)');
LEGEND_CONSTANTS(:,7) = strpad('p in component model_parameters (dimensionless)');
LEGEND_STATES(:,3) = strpad('n in component gating_variables (dimensionless)');
LEGEND_STATES(:,4) = strpad('h in component gating_variables (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('m_infinity in component gating_variables (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('V_L in component dendritic_compartment (mV)');
LEGEND_CONSTANTS(:,9) = strpad('V_NMDA in component dendritic_compartment (mV)');
LEGEND_ALGEBRAIC(:,2) = strpad('I_L in component dendritic_compartment (uA_per_cm2)');
LEGEND_ALGEBRAIC(:,13) = strpad('I_D in component dendritic_compartment (uA_per_cm2)');
LEGEND_ALGEBRAIC(:,10) = strpad('I_pump in component dendritic_compartment (uA_per_cm2)');
LEGEND_ALGEBRAIC(:,11) = strpad('I_NMDA in component dendritic_compartment (uA_per_cm2)');
LEGEND_ALGEBRAIC(:,12) = strpad('I_Na_NMDA in component dendritic_compartment (uA_per_cm2)');
LEGEND_CONSTANTS(:,10) = strpad('R_pump in component dendritic_compartment (uA_per_cm2)');
LEGEND_CONSTANTS(:,11) = strpad('alpha in component dendritic_compartment (mMcm2_per_uAs)');
LEGEND_CONSTANTS(:,12) = strpad('g_NMDA in component dendritic_compartment (mS_per_cm2)');
LEGEND_CONSTANTS(:,13) = strpad('g_Na_NMDA in component dendritic_compartment (mS_per_cm2)');
LEGEND_CONSTANTS(:,14) = strpad('g_L in component dendritic_compartment (mS_per_cm2)');
LEGEND_STATES(:,5) = strpad('Na in component dendritic_compartment (mM)');
LEGEND_CONSTANTS(:,15) = strpad('Na_eq in component dendritic_compartment (mM)');
LEGEND_CONSTANTS(:,16) = strpad('K_p in component dendritic_compartment (mM)');
LEGEND_CONSTANTS(:,17) = strpad('Mg_o in component dendritic_compartment (mM)');
LEGEND_CONSTANTS(:,18) = strpad('K_Mg in component dendritic_compartment (mM)');
LEGEND_CONSTANTS(:,19) = strpad('q in component dendritic_compartment (mV)');
LEGEND_ALGEBRAIC(:,6) = strpad('phi_Na in component dendritic_compartment (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('phi_Na_eq in component dendritic_compartment (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('n_infinity in component gating_variables (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('h_infinity in component gating_variables (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('tau_h in component gating_variables (second)');
LEGEND_ALGEBRAIC(:,8) = strpad('tau_n in component gating_variables (second)');
LEGEND_RATES(:,1) = strpad('d/dt V_s in component soma_compartment (mV)');
LEGEND_RATES(:,2) = strpad('d/dt V_D in component dendritic_compartment (mV)');
LEGEND_RATES(:,5) = strpad('d/dt Na in component dendritic_compartment (mM)');
LEGEND_RATES(:,4) = strpad('d/dt h in component gating_variables (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt n in component gating_variables (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) = -64;
CONSTANTS(:,1) = 55;
CONSTANTS(:,2) = -85;
CONSTANTS(:,3) = 3.2;
CONSTANTS(:,4) = 3.2;
CONSTANTS(:,5) = 0.0;
STATES(:,2) = -25.0;
CONSTANTS(:,6) = 1;
CONSTANTS(:,7) = 0.5;
STATES(:,3) = 0.002;
STATES(:,4) = 1;
CONSTANTS(:,8) = -50;
CONSTANTS(:,9) = 0;
CONSTANTS(:,10) = 18.0;
CONSTANTS(:,11) = 0.5;
CONSTANTS(:,12) = 1.25;
CONSTANTS(:,13) = 1.0;
CONSTANTS(:,14) = 0.18;
STATES(:,5) = 5.09;
CONSTANTS(:,15) = 8;
CONSTANTS(:,16) = 15;
CONSTANTS(:,17) = 1.4;
CONSTANTS(:,18) = 10.0;
CONSTANTS(:,19) = 12.5;
CONSTANTS(:,20) = power(CONSTANTS(:,15), 3.00000)./(power(CONSTANTS(:,15), 3.00000)+power(CONSTANTS(:,16), 3.00000));
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(:,4) = 1.00000./(1.00000+exp((STATES(:,1)+30.0000)./8.30000));
ALGEBRAIC(:,7) = 0.400000.*(1.00000+2.00000./(1.00000+exp((STATES(:,1)+25.0000)./5.00000)));
RATES(:,4) = (ALGEBRAIC(:,4) - STATES(:,4))./ALGEBRAIC(:,7);
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp( - (STATES(:,1)+31.0000)./5.30000));
ALGEBRAIC(:,8) = (0.800000+1.60000./(1.00000+exp( 0.100000.*(STATES(:,1)+25.0000))))./(1.00000+exp( - 0.100000.*(STATES(:,1)+70.0000)));
RATES(:,3) = (ALGEBRAIC(:,3) - STATES(:,3))./ALGEBRAIC(:,8);
ALGEBRAIC(:,5) = 1.00000./(1.00000+exp( - (STATES(:,1)+35.0000)./6.20000));
ALGEBRAIC(:,9) = CONSTANTS(:,4).*STATES(:,4).*(STATES(:,1) - CONSTANTS(:,1)).*power(ALGEBRAIC(:,5), 3.00000);
ALGEBRAIC(:,1) = CONSTANTS(:,3).*(STATES(:,1) - CONSTANTS(:,2)).*power(STATES(:,3), 2.00000);
RATES(:,1) = - ( 1000.00.*(ALGEBRAIC(:,1)+ALGEBRAIC(:,9)+ (CONSTANTS(:,5)./CONSTANTS(:,7)).*(STATES(:,1) - STATES(:,2))))./CONSTANTS(:,6);
ALGEBRAIC(:,2) = CONSTANTS(:,14).*(STATES(:,2) - CONSTANTS(:,8));
ALGEBRAIC(:,6) = power(STATES(:,5), 3.00000)./(power(STATES(:,5), 3.00000)+power(CONSTANTS(:,16), 3.00000));
ALGEBRAIC(:,10) = CONSTANTS(:,10).*(ALGEBRAIC(:,6) - CONSTANTS(:,20));
ALGEBRAIC(:,11) = (CONSTANTS(:,12)./(1.00000+ (CONSTANTS(:,17)./CONSTANTS(:,18)).*exp( - (STATES(:,2)./CONSTANTS(:,19))))).*(STATES(:,2) - CONSTANTS(:,9));
RATES(:,2) = - ( 1000.00.*(ALGEBRAIC(:,11)+ALGEBRAIC(:,10)+ALGEBRAIC(:,2)+ (CONSTANTS(:,5)./(1.00000 - CONSTANTS(:,7))).*(STATES(:,2) - STATES(:,1))))./CONSTANTS(:,6);
ALGEBRAIC(:,12) = (CONSTANTS(:,13)./(1.00000+ (CONSTANTS(:,17)./CONSTANTS(:,18)).*exp( - (STATES(:,2)./CONSTANTS(:,19))))).*(STATES(:,2) - CONSTANTS(:,1));
RATES(:,5) = CONSTANTS(:,11).*( - ALGEBRAIC(:,12) - 3.00000.*ALGEBRAIC(:,10));
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(:,4) = 1.00000./(1.00000+exp((STATES(:,1)+30.0000)./8.30000));
ALGEBRAIC(:,7) = 0.400000.*(1.00000+2.00000./(1.00000+exp((STATES(:,1)+25.0000)./5.00000)));
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp( - (STATES(:,1)+31.0000)./5.30000));
ALGEBRAIC(:,8) = (0.800000+1.60000./(1.00000+exp( 0.100000.*(STATES(:,1)+25.0000))))./(1.00000+exp( - 0.100000.*(STATES(:,1)+70.0000)));
ALGEBRAIC(:,5) = 1.00000./(1.00000+exp( - (STATES(:,1)+35.0000)./6.20000));
ALGEBRAIC(:,9) = CONSTANTS(:,4).*STATES(:,4).*(STATES(:,1) - CONSTANTS(:,1)).*power(ALGEBRAIC(:,5), 3.00000);
ALGEBRAIC(:,1) = CONSTANTS(:,3).*(STATES(:,1) - CONSTANTS(:,2)).*power(STATES(:,3), 2.00000);
ALGEBRAIC(:,2) = CONSTANTS(:,14).*(STATES(:,2) - CONSTANTS(:,8));
ALGEBRAIC(:,6) = power(STATES(:,5), 3.00000)./(power(STATES(:,5), 3.00000)+power(CONSTANTS(:,16), 3.00000));
ALGEBRAIC(:,10) = CONSTANTS(:,10).*(ALGEBRAIC(:,6) - CONSTANTS(:,20));
ALGEBRAIC(:,11) = (CONSTANTS(:,12)./(1.00000+ (CONSTANTS(:,17)./CONSTANTS(:,18)).*exp( - (STATES(:,2)./CONSTANTS(:,19))))).*(STATES(:,2) - CONSTANTS(:,9));
ALGEBRAIC(:,12) = (CONSTANTS(:,13)./(1.00000+ (CONSTANTS(:,17)./CONSTANTS(:,18)).*exp( - (STATES(:,2)./CONSTANTS(:,19))))).*(STATES(:,2) - CONSTANTS(:,1));
ALGEBRAIC(:,13) = ALGEBRAIC(:,11)+ALGEBRAIC(:,10)+ALGEBRAIC(:,2);
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