Hodgkin-Huxley neurons with Traub & Miles algorithm. More...

#include <neuronModels.h>

Inheritance diagram for NeuronModels::TraubMiles:

Public Types
typedef Snippet::ValueBase< 7 >	ParamValues

typedef Models::VarInitContainerBase< 4 >	VarValues

typedef Models::VarInitContainerBase< 0 >	PreVarValues

typedef Models::VarInitContainerBase< 0 >	PostVarValues

Public Types inherited from Models::Base
typedef std::vector< Var >	VarVec

typedef std::vector< VarRef >	VarRefVec

typedef std::vector< EGPRef >	EGPRefVec

Public Types inherited from Snippet::Base
typedef std::vector< std::string >	StringVec

typedef std::vector< EGP >	EGPVec

typedef std::vector< ParamVal >	ParamValVec

typedef std::vector< DerivedParam >	DerivedParamVec

Public Member Functions
virtual std::string	getSimCode () const override
	Gets the code that defines the execution of one timestep of integration of the neuron model. More...

virtual std::string	getThresholdConditionCode () const override
	Gets code which defines the condition for a true spike in the described neuron model. More...

virtual StringVec	getParamNames () const override
	Gets names of of (independent) model parameters. More...

virtual VarVec	getVars () const override
	Gets names and types (as strings) of model variables. More...

Public Member Functions inherited from NeuronModels::Base
virtual std::string	getResetCode () const
	Gets code that defines the reset action taken after a spike occurred. This can be empty. More...

virtual std::string	getSupportCode () const
	Gets support code to be made available within the neuron kernel/funcion. More...

virtual Models::Base::ParamValVec	getAdditionalInputVars () const

virtual bool	isAutoRefractoryRequired () const
	Does this model require auto-refractory logic? More...

boost::uuids::detail::sha1::digest_type	getHashDigest () const
	Update hash from model. More...

void	validate () const
	Validate names of parameters etc. More...

Public Member Functions inherited from Models::Base
size_t	getVarIndex (const std::string &varName) const
	Find the index of a named variable. More...

Public Member Functions inherited from Snippet::Base
virtual	~Base ()

virtual DerivedParamVec	getDerivedParams () const

virtual EGPVec	getExtraGlobalParams () const

size_t	getExtraGlobalParamIndex (const std::string &paramName) const
	Find the index of a named extra global parameter. More...

Static Public Member Functions
static const NeuronModels::TraubMiles *	getInstance ()

Additional Inherited Members
Protected Member Functions inherited from Models::Base
void	updateHash (boost::uuids::detail::sha1 &hash) const

void	validate () const
	Validate names of parameters etc. More...

Protected Member Functions inherited from Snippet::Base
void	updateHash (boost::uuids::detail::sha1 &hash) const

void	validate () const
	Validate names of parameters etc. More...

Static Protected Member Functions inherited from Snippet::Base
template<typename T >
static size_t	getNamedVecIndex (const std::string &name, const std::vector< T > &vec)

Detailed Description

Hodgkin-Huxley neurons with Traub & Miles algorithm.

This conductance based model has been taken from [9] and can be described by the equations:

$\begin{eqnarray*} C \frac{d V}{dt} &=& -I_{{\rm Na}} -I_K-I_{{\rm leak}}-I_M-I_{i,DC}-I_{i,{\rm syn}}-I_i, \\ I_{{\rm Na}}(t) &=& g_{{\rm Na}} m_i(t)^3 h_i(t)(V_i(t)-E_{{\rm Na}}) \\ I_{{\rm K}}(t) &=& g_{{\rm K}} n_i(t)^4(V_i(t)-E_{{\rm K}}) \\ \frac{dy(t)}{dt} &=& \alpha_y (V(t))(1-y(t))-\beta_y(V(t)) y(t), \end{eqnarray*}$

where $y_i= m, h, n$ , and

$\begin{eqnarray*} \alpha_n&=& 0.032(-50-V)/\big(\exp((-50-V)/5)-1\big) \\ \beta_n &=& 0.5\exp((-55-V)/40) \\ \alpha_m &=& 0.32(-52-V)/\big(\exp((-52-V)/4)-1\big) \\ \beta_m &=& 0.28(25+V)/\big(\exp((25+V)/5)-1\big) \\ \alpha_h &=& 0.128\exp((-48-V)/18) \\ \beta_h &=& 4/\big(\exp((-25-V)/5)+1\big). \end{eqnarray*}$

and typical parameters are $C=0.143$ nF, $g_{{\rm leak}}= 0.02672$ $\mu$ S, $E_{{\rm leak}}= -63.563$ mV, $g_{{\rm Na}}=7.15$ $\mu$ S, $E_{{\rm Na}}= 50$ mV, $g_{{\rm {\rm K}}}=1.43$ $\mu$ S, $E_{{\rm K}}= -95$ mV.

It has 4 variables:

V - membrane potential E
m - probability for Na channel activation m
h - probability for not Na channel blocking h
n - probability for K channel activation n

and 7 parameters:

gNa - Na conductance in 1/(mOhms * cm^2)
ENa - Na equi potential in mV
gK - K conductance in 1/(mOhms * cm^2)
EK - K equi potential in mV
gl - Leak conductance in 1/(mOhms * cm^2)
El - Leak equi potential in mV
C - Membrane capacity density in muF/cm^2

Note: Internally, the ordinary differential equations defining the model are integrated with a linear Euler algorithm and GeNN integrates 25 internal time steps for each neuron for each network time step. I.e., if the network is simulated at DT= 0.1 ms, then the neurons are integrated with a linear Euler algorithm with lDT= 0.004 ms. This variant uses IF statements to check for a value at which a singularity would be hit. If so, value calculated by L'Hospital rule is used.

Member Typedef Documentation

◆ ParamValues

typedef Snippet::ValueBase< 7 > NeuronModels::TraubMiles::ParamValues

◆ PostVarValues

typedef Models::VarInitContainerBase<0> NeuronModels::TraubMiles::PostVarValues

◆ PreVarValues

typedef Models::VarInitContainerBase<0> NeuronModels::TraubMiles::PreVarValues

◆ VarValues

typedef Models::VarInitContainerBase< 4 > NeuronModels::TraubMiles::VarValues

Member Function Documentation

◆ getInstance()

static const NeuronModels::TraubMiles* NeuronModels::TraubMiles::getInstance ( )

inlinestatic

◆ getParamNames()

virtual StringVec NeuronModels::TraubMiles::getParamNames ( ) const

inlineoverridevirtual

Gets names of of (independent) model parameters.

Reimplemented from Snippet::Base.

Reimplemented in NeuronModels::TraubMilesNStep.

◆ getSimCode()

virtual std::string NeuronModels::TraubMiles::getSimCode ( ) const

inlineoverridevirtual

Gets the code that defines the execution of one timestep of integration of the neuron model.

The code will refer to for the value of the variable with name "NN". It needs to refer to the predefined variable "ISYN", i.e. contain , if it is to receive input.

Reimplemented from NeuronModels::Base.

Reimplemented in NeuronModels::TraubMilesNStep, NeuronModels::TraubMilesAlt, and NeuronModels::TraubMilesFast.

◆ getThresholdConditionCode()

virtual std::string NeuronModels::TraubMiles::getThresholdConditionCode ( ) const

inlineoverridevirtual

Gets code which defines the condition for a true spike in the described neuron model.

This evaluates to a bool (e.g. "V > 20").

Reimplemented from NeuronModels::Base.

◆ getVars()

virtual VarVec NeuronModels::TraubMiles::getVars ( ) const

inlineoverridevirtual

Gets names and types (as strings) of model variables.

Reimplemented from Models::Base.

The documentation for this class was generated from the following file:

neuronModels.h

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ParamValues

◆ PostVarValues

◆ PreVarValues

◆ VarValues

Member Function Documentation

◆ getInstance()

◆ getParamNames()

◆ getSimCode()

◆ getThresholdConditionCode()

◆ getVars()