IzhikevichNrn Class Reference

#include <IzhikevichNrn.h>

Collaboration diagram for IzhikevichNrn:

Public Member Functions
double	getA () const
bool	getAccommodating () const
double	getAlpha () const
double	getB () const
double	getBeta () const
double	getC () const
double	getD () const
double	getGamma () const
double	getIm () const
double	getInitU () const
double	getInitVm () const
double	getInject () const
double	getRmByTau () const
double	getU () const
double	getU0 () const
double	getVm () const
double	getVmax () const
void	handleChannel (double Gk, double Ek)
	IzhikevichNrn ()
void	process (const Eref &eref, ProcPtr proc)
void	reinit (const Eref &eref, ProcPtr proc)
void	setA (double value)
void	setAccommodating (bool value)
void	setAlpha (double value)
void	setB (double value)
void	setBeta (double value)
void	setC (double value)
void	setD (double value)
void	setGamma (double value)
void	setInitU (double value)
void	setInitVm (double value)
void	setInject (double value)
void	setRmByTau (double value)
void	setU0 (double value)
void	setVm (double value)
void	setVmax (double value)
	~IzhikevichNrn ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Private Attributes
double	a_
bool	accommodating_
double	alpha_
double	b_
double	beta_
double	c_
double	d_
double	gamma_
double	Im_
double	initU_
double	initVm_
double	inject_
double	RmByTau_
double	savedVm_
double	sum_inject_
double	u0_
double	u_
double	Vm_
double	Vmax_

Detailed Description

Definition at line 35 of file IzhikevichNrn.h.

Constructor & Destructor Documentation

IzhikevichNrn::IzhikevichNrn

(

)

Definition at line 273 of file IzhikevichNrn.cpp.

                            :
        alpha_(40000.0), // 0.04 physiological unit
        beta_(5000.0), // 5 physiological unit
        gamma_(140.0), // 140 physiological unit
        RmByTau_(1e6), // Assuming Izhikevich was using nA as unit of
        // current, 1e6 Ohm will be the scaling term for SI
        a_(20.0),
        b_(200.0),
        c_(-0.065), // -65 mV
        d_(2.0), // assuming u is in mV/ms
        Vm_(-0.065),
        u_(-13.0),
        Vmax_(0.03), // 30 mV
        initVm_(-0.065),// -65 mV
        initU_(-13.0),
        sum_inject_(0.0),
        Im_(0.0),
        savedVm_(-0.065),
        accommodating_(false),
        u0_(-0.065),
        inject_(0.0)
{
    ;
}

IzhikevichNrn::~IzhikevichNrn

(

)

Definition at line 298 of file IzhikevichNrn.cpp.

{
    ;
}

Member Function Documentation

double IzhikevichNrn::getA

(

)

const

Definition at line 307 of file IzhikevichNrn.cpp.

References a_.

Referenced by initCinfo().

{
    return a_;
}

Here is the caller graph for this function:

bool IzhikevichNrn::getAccommodating

(

)

const

Definition at line 444 of file IzhikevichNrn.cpp.

References accommodating_.

Referenced by initCinfo().

{
    return accommodating_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getAlpha

(

)

const

Definition at line 379 of file IzhikevichNrn.cpp.

References alpha_.

Referenced by initCinfo().

{
    return alpha_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getB

(

)

const

Definition at line 317 of file IzhikevichNrn.cpp.

References b_.

Referenced by initCinfo().

{
    return b_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getBeta

(

)

const

Definition at line 389 of file IzhikevichNrn.cpp.

References beta_.

Referenced by initCinfo().

{
    return beta_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getC

(

)

const

Definition at line 326 of file IzhikevichNrn.cpp.

References c_.

Referenced by initCinfo().

{
    return c_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getD

(

)

const

Definition at line 336 of file IzhikevichNrn.cpp.

References d_.

Referenced by initCinfo().

{
    return d_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getGamma

(

)

const

Definition at line 399 of file IzhikevichNrn.cpp.

References gamma_.

Referenced by initCinfo().

{
    return gamma_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getIm

(

)

const

Definition at line 414 of file IzhikevichNrn.cpp.

References Im_.

Referenced by initCinfo().

{
    return Im_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getInitU

(

)

const

Definition at line 434 of file IzhikevichNrn.cpp.

References initU_.

Referenced by initCinfo().

{
    return initU_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getInitVm

(

)

const

Definition at line 424 of file IzhikevichNrn.cpp.

References initVm_.

Referenced by initCinfo().

{
    return initVm_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getInject

(

)

const

Definition at line 409 of file IzhikevichNrn.cpp.

References inject_.

Referenced by initCinfo().

{
    return inject_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getRmByTau

(

)

const

Definition at line 346 of file IzhikevichNrn.cpp.

References RmByTau_.

Referenced by initCinfo().

{
    return RmByTau_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getU

(

)

const

Definition at line 354 of file IzhikevichNrn.cpp.

References u_.

Referenced by initCinfo().

{
    return u_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getU0

(

)

const

Definition at line 454 of file IzhikevichNrn.cpp.

References u0_.

Referenced by initCinfo().

{
    return u0_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getVm

(

)

const

Definition at line 359 of file IzhikevichNrn.cpp.

References savedVm_.

Referenced by initCinfo().

{
    return savedVm_;
}

Here is the caller graph for this function:

double IzhikevichNrn::getVmax

(

)

const

Definition at line 369 of file IzhikevichNrn.cpp.

References Vmax_.

Referenced by initCinfo().

{
    return Vmax_;
}

Here is the caller graph for this function:

void IzhikevichNrn::handleChannel	(	double	Gk,
		double	Ek
	)

Definition at line 459 of file IzhikevichNrn.cpp.

References sum_inject_, and Vm_.

Referenced by initCinfo().

{
    sum_inject_ += Gk * (Ek - Vm_);
}

Here is the caller graph for this function:

const Cinfo * IzhikevichNrn::initCinfo ( )

static

Definition at line 49 of file IzhikevichNrn.cpp.

References getA(), getAccommodating(), getAlpha(), getB(), getBeta(), getC(), getD(), getGamma(), getIm(), getInitU(), getInitVm(), getInject(), getRmByTau(), getU(), getU0(), getVm(), getVmax(), handleChannel(), Neutral::initCinfo(), IzhikevichNrnCinfo, process(), reinit(), setA(), setAccommodating(), setAlpha(), setB(), setBeta(), setC(), setD(), setGamma(), setInitU(), setInitVm(), setInject(), setRmByTau(), setU0(), setVm(), setVmax(), spikeOut(), and VmOut().

{

    static DestFinfo process(
            "process",
            "Handles process call",
            new ProcOpFunc< IzhikevichNrn >( &IzhikevichNrn::process));
    static DestFinfo reinit(
            "reinit",
            "Handles reinit call",
            new ProcOpFunc<IzhikevichNrn>( &IzhikevichNrn::reinit));

    static Finfo * processShared[] = {
        &process,
        &reinit
    };

    static SharedFinfo proc(
            "proc",
            "Shared message to receive Process message from scheduler",
            processShared, sizeof( processShared ) / sizeof( Finfo* ) );

    // Field definitions

    static ValueFinfo<IzhikevichNrn, double> Vmax(
            "Vmax",
            "Maximum membrane potential. Membrane potential is reset to c whenever"
            " it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage,"
            " rather than THRSHOLD voltage. The threshold depends on the previous"
            " history.",
            &IzhikevichNrn::setVmax,
            &IzhikevichNrn::getVmax);
    static ValueFinfo<IzhikevichNrn, double> c(
            "c",
            "Reset potential. Membrane potential is reset to c whenever it reaches"
            " Vmax.",
            &IzhikevichNrn::setC,
            &IzhikevichNrn::getC);
    static ValueFinfo<IzhikevichNrn, double> d(
            "d",
            "Parameter d in Izhikevich model. Unit is V/s.",
            &IzhikevichNrn::setD,
            &IzhikevichNrn::getD);
    static ValueFinfo<IzhikevichNrn, double> a(
            "a",
            "Parameter a in Izhikevich model. Unit is s^{-1}",
            &IzhikevichNrn::setA,
            &IzhikevichNrn::getA);
    static ValueFinfo<IzhikevichNrn, double> b(
            "b",
            "Parameter b in Izhikevich model. Unit is s^{-1}",
            &IzhikevichNrn::setB,
            &IzhikevichNrn::getB);
    static ValueFinfo<IzhikevichNrn, double> Vm(
            "Vm",
            "Membrane potential, equivalent to v in Izhikevich equation.",
            &IzhikevichNrn::setVm,
            &IzhikevichNrn::getVm);
    static ReadOnlyValueFinfo<IzhikevichNrn, double> u(
            "u",
            "Parameter u in Izhikevich equation. Unit is V/s",
            &IzhikevichNrn::getU);
    static ReadOnlyValueFinfo<IzhikevichNrn, double> Im(
            "Im",
            "Total current going through the membrane. Unit is A.",
            &IzhikevichNrn::getIm);
    static ValueFinfo<IzhikevichNrn, double> initVm(
            "initVm",
            "Initial membrane potential. Unit is V.",
            &IzhikevichNrn::setInitVm,
            &IzhikevichNrn::getInitVm);
    static ValueFinfo<IzhikevichNrn, double> inject(
            "inject",
            "External current injection into the neuron",
            &IzhikevichNrn::setInject,
            &IzhikevichNrn::getInject);
    static ValueFinfo<IzhikevichNrn, double> initU(
            "initU",
            "Initial value of u.",
            &IzhikevichNrn::setInitU,
            &IzhikevichNrn::getInitU);

    static ValueFinfo<IzhikevichNrn, double> alpha(
            "alpha",
            "Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in "
            "physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}",
            &IzhikevichNrn::setAlpha,
            &IzhikevichNrn::getAlpha);

    static ValueFinfo<IzhikevichNrn, double> beta(
            "beta",
            "Coefficient of v in Izhikevich model. Defaults to 5 in physiological"
            " unit, 5000.0 for SI units. Unit is s^{-1}",
            &IzhikevichNrn::setBeta,
            &IzhikevichNrn::getBeta);
    static ValueFinfo<IzhikevichNrn, double> gamma(
            "gamma",
            "Constant term in Izhikevich model. Defaults to 140 in both"
            " physiological and SI units. unit is V/s.",
            &IzhikevichNrn::setGamma,
            &IzhikevichNrn::getGamma);
    static ValueFinfo<IzhikevichNrn, double> RmByTau(
            "RmByTau",
            "Hidden coefficient of input current term (I) in Izhikevich model. Defaults to 1e9 Ohm/s.",
            &IzhikevichNrn::setRmByTau,
            &IzhikevichNrn::getRmByTau);

    static ValueFinfo<IzhikevichNrn, bool> accommodating(
            "accommodating",
            "True if this neuron is an accommodating one. The equation for recovery"
            " variable u is special in this case.",
            &IzhikevichNrn::setAccommodating,
            &IzhikevichNrn::getAccommodating);

    static ValueFinfo<IzhikevichNrn, double> u0(
            "u0",
            "This is used for accommodating neurons where recovery variables u is"
            " computed as: u += tau*a*(b*(Vm-u0))",
            &IzhikevichNrn::setU0,
            &IzhikevichNrn::getU0);

    // MsgDest definition
    static DestFinfo injectMsg(
            "injectMsg",
            "Injection current into the neuron.",
            new OpFunc1<IzhikevichNrn, double>( &IzhikevichNrn::setInject));

    static DestFinfo cDest(
            "cDest",
            "Destination message to modify parameter c at runtime.",
            new OpFunc1<IzhikevichNrn, double>(&IzhikevichNrn::setC));

    static DestFinfo dDest(
            "dDest",
            "Destination message to modify parameter d at runtime.",
            new OpFunc1<IzhikevichNrn, double>(&IzhikevichNrn::setD));

    static DestFinfo aDest(
            "aDest",
            "Destination message modify parameter a at runtime.",
            new OpFunc1<IzhikevichNrn, double>(&IzhikevichNrn::setA));

    static DestFinfo bDest(
            "bDest",
            "Destination message to modify parameter b at runtime",
            new OpFunc1<IzhikevichNrn, double>(&IzhikevichNrn::setB));


    static DestFinfo handleChannel("handleChannel",
                                   "Handles conductance and reversal potential arguments from Channel",
                                   new OpFunc2<IzhikevichNrn, double, double >(&IzhikevichNrn::handleChannel));

    static Finfo * channelShared[] = {
        &handleChannel,
        VmOut()
    };

    static SharedFinfo channel("channel",
            "This is a shared message from a IzhikevichNrn to channels."
            "The first entry is a MsgDest for the info coming from "
            "the channel. It expects Gk and Ek from the channel "
            "as args. The second entry is a MsgSrc sending Vm ",
                               channelShared, sizeof( channelShared ) / sizeof( Finfo* )
    );
    static Finfo* IzhikevichNrnFinfos[] = {
        &proc,
        &Vmax,
        &c,
        &d,
        &a,
        &b,
        &u,
        &Vm,
        &Im,
        &inject,
        &RmByTau,
        &accommodating,
        &u0,
        &initVm,
        &initU,
        &alpha,
        &beta,
        &gamma,
        &injectMsg,
        &cDest,
        &dDest,
        &bDest,
        &aDest,
        VmOut(),
        spikeOut(),
        &channel,
    };

    static string doc[] = {
        "Name", "IzhikevichNrn",
        "Author", "Subhasis Ray",
        "Description", "Izhikevich model of spiking neuron "
        "(Izhikevich,EM. 2003. Simple model of spiking neurons. Neural"
        " Networks, IEEE Transactions on 14(6). pp 1569-1572).\n"
        " This class obeys the equations (in physiological units):\n"
        "  dVm/dt = 0.04 * Vm^2 + 5 * Vm + 140 - u + inject\n"
        "  du/dt = a * (b * Vm - u)\n"
        " if Vm >= Vmax then Vm = c and u = u + d\n"
        " Vmax = 30 mV in the paper."
    };
    static Dinfo< IzhikevichNrn > dinfo;
    static Cinfo IzhikevichNrnCinfo(
        "IzhikevichNrn",
        Neutral::initCinfo(),
        IzhikevichNrnFinfos,
        sizeof( IzhikevichNrnFinfos ) / sizeof( Finfo* ),
        &dinfo,
        doc,
        sizeof(doc)/sizeof(string));

    return &IzhikevichNrnCinfo;
}

Here is the call graph for this function:

void IzhikevichNrn::process	(	const Eref &	eref,
		ProcPtr	proc
	)

Definition at line 464 of file IzhikevichNrn.cpp.

References a_, accommodating_, alpha_, b_, beta_, c_, ProcInfo::currTime, d_, ProcInfo::dt, gamma_, Im_, inject_, RmByTau_, savedVm_, spikeOut(), sum_inject_, u0_, u_, Vm_, Vmax_, and VmOut().

Referenced by initCinfo().

{
    Vm_ += proc->dt * ((alpha_ * Vm_ + beta_) * Vm_
                       + gamma_ - u_ + RmByTau_ * sum_inject_);
    if (accommodating_){
        u_ += proc->dt * a_ * b_ * (Vm_ - u0_);
    } else {
        u_ += proc->dt * a_ * (b_ * Vm_ - u_);
    }
    Im_ = sum_inject_;
    sum_inject_ = inject_;
    // This check is to ensure that checking Vm field will always
    // return Vmax when Vm actually crosses Vmax.
    if (Vm_ >= Vmax_){
        Vm_ = c_;
        u_ += d_;
        savedVm_ = Vmax_;
        VmOut()->send(eref, Vmax_);
        spikeOut()->send(eref, proc->currTime);
    } else {
        savedVm_ = Vm_;
        VmOut()->send(eref, Vm_);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void IzhikevichNrn::reinit	(	const Eref &	eref,
		ProcPtr	proc
	)

Definition at line 489 of file IzhikevichNrn.cpp.

References Im_, initU_, initVm_, savedVm_, sum_inject_, u_, Vm_, and VmOut().

Referenced by initCinfo().

{
    sum_inject_ = 0.0;
    Vm_ = initVm_;
    u_ = initU_;
    Im_ = 0.0;
    savedVm_ = Vm_;
    VmOut()->send(eref, Vm_);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void IzhikevichNrn::setA

(

double

value

)

Definition at line 302 of file IzhikevichNrn.cpp.

References a_, and value.

Referenced by initCinfo().

{
    a_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setAccommodating

(

bool

value

)

Definition at line 439 of file IzhikevichNrn.cpp.

References accommodating_, and value.

Referenced by initCinfo().

{
    accommodating_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setAlpha

(

double

value

)

Definition at line 374 of file IzhikevichNrn.cpp.

References alpha_, and value.

Referenced by initCinfo().

{
    alpha_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setB

(

double

value

)

Definition at line 312 of file IzhikevichNrn.cpp.

References b_, and value.

Referenced by initCinfo().

{
    b_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setBeta

(

double

value

)

Definition at line 384 of file IzhikevichNrn.cpp.

References beta_, and value.

Referenced by initCinfo().

{
    beta_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setC

(

double

value

)

Definition at line 321 of file IzhikevichNrn.cpp.

References c_, and value.

Referenced by initCinfo().

{
    c_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setD

(

double

value

)

Definition at line 331 of file IzhikevichNrn.cpp.

References d_, and value.

Referenced by initCinfo().

{
    d_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setGamma

(

double

value

)

Definition at line 394 of file IzhikevichNrn.cpp.

References gamma_, and value.

Referenced by initCinfo().

{
    gamma_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setInitU

(

double

value

)

Definition at line 429 of file IzhikevichNrn.cpp.

References initU_, and value.

Referenced by initCinfo().

{
    initU_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setInitVm

(

double

value

)

Definition at line 419 of file IzhikevichNrn.cpp.

References initVm_, and value.

Referenced by initCinfo().

{
    initVm_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setInject

(

double

value

)

Definition at line 404 of file IzhikevichNrn.cpp.

References inject_, and value.

Referenced by initCinfo().

{
    inject_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setRmByTau

(

double

value

)

Definition at line 341 of file IzhikevichNrn.cpp.

References RmByTau_, and value.

Referenced by initCinfo().

{
    RmByTau_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setU0

(

double

value

)

Definition at line 449 of file IzhikevichNrn.cpp.

References u0_, and value.

Referenced by initCinfo().

{
    u0_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setVm

(

double

value

)

Definition at line 350 of file IzhikevichNrn.cpp.

References value, and Vm_.

Referenced by initCinfo().

{
    Vm_ = value;
}

Here is the caller graph for this function:

void IzhikevichNrn::setVmax

(

double

value

)

Definition at line 364 of file IzhikevichNrn.cpp.

References value, and Vmax_.

Referenced by initCinfo().

{
    Vmax_ = value;
}

Here is the caller graph for this function:

Member Data Documentation

double IzhikevichNrn::a_

private

Definition at line 101 of file IzhikevichNrn.h.

Referenced by getA(), process(), and setA().

bool IzhikevichNrn::accommodating_

private

Definition at line 113 of file IzhikevichNrn.h.

Referenced by getAccommodating(), process(), and setAccommodating().

double IzhikevichNrn::alpha_

private

Definition at line 97 of file IzhikevichNrn.h.

Referenced by getAlpha(), process(), and setAlpha().

double IzhikevichNrn::b_

private

Definition at line 102 of file IzhikevichNrn.h.

Referenced by getB(), process(), and setB().

double IzhikevichNrn::beta_

private

Definition at line 98 of file IzhikevichNrn.h.

Referenced by getBeta(), process(), and setBeta().

double IzhikevichNrn::c_

private

Definition at line 103 of file IzhikevichNrn.h.

Referenced by getC(), process(), and setC().

double IzhikevichNrn::d_

private

Definition at line 104 of file IzhikevichNrn.h.

Referenced by getD(), process(), and setD().

double IzhikevichNrn::gamma_

private

Definition at line 99 of file IzhikevichNrn.h.

Referenced by getGamma(), process(), and setGamma().

double IzhikevichNrn::Im_

private

Definition at line 111 of file IzhikevichNrn.h.

Referenced by getIm(), process(), and reinit().

double IzhikevichNrn::initU_

private

Definition at line 109 of file IzhikevichNrn.h.

Referenced by getInitU(), reinit(), and setInitU().

double IzhikevichNrn::initVm_

private

Definition at line 108 of file IzhikevichNrn.h.

Referenced by getInitVm(), reinit(), and setInitVm().

double IzhikevichNrn::inject_

private

Definition at line 115 of file IzhikevichNrn.h.

Referenced by getInject(), process(), and setInject().

double IzhikevichNrn::RmByTau_

private

Definition at line 100 of file IzhikevichNrn.h.

Referenced by getRmByTau(), process(), and setRmByTau().

double IzhikevichNrn::savedVm_

private

Definition at line 112 of file IzhikevichNrn.h.

Referenced by getVm(), process(), and reinit().

double IzhikevichNrn::sum_inject_

private

Definition at line 110 of file IzhikevichNrn.h.

Referenced by handleChannel(), process(), and reinit().

double IzhikevichNrn::u0_

private

Definition at line 114 of file IzhikevichNrn.h.

Referenced by getU0(), process(), and setU0().

double IzhikevichNrn::u_

private

Definition at line 106 of file IzhikevichNrn.h.

Referenced by getU(), process(), and reinit().

double IzhikevichNrn::Vm_

private

Definition at line 105 of file IzhikevichNrn.h.

Referenced by handleChannel(), process(), reinit(), and setVm().

double IzhikevichNrn::Vmax_

private

Definition at line 107 of file IzhikevichNrn.h.

Referenced by getVmax(), process(), and setVmax().

---

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

• moose-core/biophysics/IzhikevichNrn.h
• moose-core/biophysics/IzhikevichNrn.cpp