#include <GraupnerBrunel2012CaPlasticitySynHandler.h>

Inheritance diagram for GraupnerBrunel2012CaPlasticitySynHandler:

Collaboration diagram for GraupnerBrunel2012CaPlasticitySynHandler:

Public Member Functions
void	addPostSpike (const Eref &e, double time)

void	addSpike (unsigned int index, double time, double weight)

unsigned int	addSynapse ()
	Adds a new synapse, returns its index. More...

void	dropSynapse (unsigned int droppedSynNumber)

bool	getBistable () const

double	getCa () const

double	getCaInit () const

double	getCaPost () const

double	getCaPre () const

double	getDelayD () const

double	getGammaD () const

double	getGammaP () const

double	getNoiseSD () const

bool	getNoisy () const

double	getTauCa () const

double	getTauSyn () const

double	getThetaD () const

double	getThetaP () const

double	getTopSpike (unsigned int index) const

double	getWeightMax () const

double	getWeightMin () const

double	getWeightScale () const

	GraupnerBrunel2012CaPlasticitySynHandler ()

GraupnerBrunel2012CaPlasticitySynHandler &	operator= (const GraupnerBrunel2012CaPlasticitySynHandler &other)

void	reinitSeed ()

void	setBistable (bool v)

void	setCa (double v)

void	setCaInit (double v)

void	setCaPost (double v)

void	setCaPre (double v)

void	setDelayD (double v)

void	setGammaD (double v)

void	setGammaP (double v)

void	setNoiseSD (double v)

void	setNoisy (bool v)

void	setTauCa (double v)

void	setTauSyn (double v)

void	setThetaD (double v)

void	setThetaP (double v)

void	setWeightMax (double v)

void	setWeightMin (double v)

void	setWeightScale (double v)

weightFactors	updateCaWeightFactors (double currTime)

void	updateWeight (Synapse synPtr, weightFactors wFacPtr)

unsigned int	vGetNumSynapses () const

Synapse *	vGetSynapse (unsigned int i)

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

void	vSetNumSynapses (unsigned int num)

	~GraupnerBrunel2012CaPlasticitySynHandler ()

Public Member Functions inherited from SynHandlerBase
unsigned int	getNumSynapses () const

Synapse *	getSynapse (unsigned int i)

void	process (const Eref &e, ProcPtr p)

bool	rangeWarning (const string &field, double value)

void	reinit (const Eref &e, ProcPtr p)

void	setNumSynapses (unsigned int num)

	SynHandlerBase ()

virtual	~SynHandlerBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from SynHandlerBase
static SrcFinfo1< double > *	activationOut ()

static const Cinfo *	initCinfo ()

Private Attributes
bool	bistable_

double	Ca_

double	CaInit_

double	CaPost_

double	CaPre_

double	delayD_

priority_queue< PreSynEvent, vector< PreSynEvent > , CompareSynEvent >	delayDPreEvents_

moose::MOOSE_NORMAL_DISTRIBUTION < double >	dist_

priority_queue< PreSynEvent, vector< PreSynEvent > , CompareSynEvent >	events_

double	gammaD_

double	gammaP_

double	lastCaUpdateTime_

double	noiseSD_

bool	noisy_

priority_queue< PostSynEvent, vector< PostSynEvent > , ComparePostSynEvent >	postEvents_

moose::MOOSE_RANDOM_DEVICE	rd_

moose::MOOSE_RNG_DEFAULT_ENGINE	rng_

unsigned long	seed_

vector< Synapse >	synapses_

double	tauCa_

double	tauSyn_

double	thetaD_

double	thetaP_

double	weightMax_

double	weightMin_

double	weightScale_

Detailed Description

This handles simple synapses without plasticity. It uses a priority queue to manage them. This gets inefficient for large numbers of synapses but is pretty robust.

Definition at line 43 of file GraupnerBrunel2012CaPlasticitySynHandler.h.

Constructor & Destructor Documentation

GraupnerBrunel2012CaPlasticitySynHandler::GraupnerBrunel2012CaPlasticitySynHandler ( )

Definition at line 235 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References bistable_, Ca_, CaInit_, CaPost_, CaPre_, delayD_, dist_, gammaD_, gammaP_, noiseSD_, noisy_, reinitSeed(), seed_, tauCa_, tauSyn_, thetaD_, thetaP_, weightMax_, weightMin_, and weightScale_.

 {
     Ca_          = 0.0;
     CaInit_      = 0.0;
     tauCa_       = 1.0;
     tauSyn_      = 1.0;
     CaPre_       = 0.0;
     CaPost_      = 0.0;
     thetaD_      = 0.0;
     thetaP_      = 0.0;
     gammaD_      = 0.0;
     gammaP_      = 0.0;
     delayD_      = 0.0;
     weightMin_   = 0.0;
     weightMax_   = 0.0;
     weightScale_ = 1.0;
     noisy_       = false;
     noiseSD_     = 0.0;
     bistable_    = true;
     seed_        = 0;
     dist_ = moose::MOOSE_NORMAL_DISTRIBUTION<double>{0, 1};
     reinitSeed();
 
     // std::cout << " Mean " << dist_.mean() << " std " << dist_.stddev() << std::endl;
 }

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GraupnerBrunel2012CaPlasticitySynHandler::~GraupnerBrunel2012CaPlasticitySynHandler ( )

Definition at line 261 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

262 {

263 }

Member Function Documentation

void GraupnerBrunel2012CaPlasticitySynHandler::addPostSpike	(	const Eref &	e,
		double	time
	)

Definition at line 338 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References postEvents_.

Referenced by initCinfo().

 {
     postEvents_.push( PostSynEvent( time ) );
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::addSpike	(	unsigned int	index,
		double	time,
		double	weight
	)

virtual

Record arrival of a new spike event. The 'time' is time for eventual arrival of the spike, and is typically well in the future. The index specifies which synapse the spike came to.

Implements SynHandlerBase.

Definition at line 321 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References delayD_, delayDPreEvents_, events_, and synapses_.

 {
     assert( index < synapses_.size() );
     events_.push( PreSynEvent( index, time, weight ) );
     delayDPreEvents_.push( PreSynEvent( index, time+delayD_, weight ) );
 }

unsigned int GraupnerBrunel2012CaPlasticitySynHandler::addSynapse ( )

virtual

Adds a new synapse, returns its index.

Implements SynHandlerBase.

Definition at line 603 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References synapses_.

 {
     unsigned int newSynIndex = synapses_.size();
     synapses_.resize( newSynIndex + 1 );
     synapses_[newSynIndex].setHandler( this );
     return newSynIndex;
 }

void GraupnerBrunel2012CaPlasticitySynHandler::dropSynapse ( unsigned int droppedSynNumber )

virtual

Drops an existing synapse, triggered by deleteMsg of an input to the child synapse. This is a little messy because we can't change the indices of the other synapses. The Handler has to figure out how to handle the 'holes' in its array of synapses.

Implements SynHandlerBase.

Definition at line 612 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References synapses_.

 {
     assert( msgLookup < synapses_.size() );
     synapses_[msgLookup].setWeight( -1.0 );
 }

bool GraupnerBrunel2012CaPlasticitySynHandler::getBistable ( ) const

Definition at line 755 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References bistable_.

Referenced by initCinfo().

 {
     return bistable_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getCa ( ) const

Definition at line 623 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References Ca_.

Referenced by initCinfo().

 {
     return Ca_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getCaInit ( ) const

Definition at line 633 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References CaInit_.

Referenced by initCinfo().

 {
     return CaInit_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getCaPost ( ) const

Definition at line 653 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References CaPost_.

Referenced by initCinfo().

 {
     return CaPost_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getCaPre ( ) const

Definition at line 643 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References CaPre_.

Referenced by initCinfo().

 {
     return CaPre_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getDelayD ( ) const

Definition at line 703 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References delayD_.

Referenced by initCinfo().

 {
     return delayD_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getGammaD ( ) const

Definition at line 683 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References gammaD_.

Referenced by initCinfo().

 {
     return gammaD_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getGammaP ( ) const

Definition at line 693 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References gammaP_.

Referenced by initCinfo().

 {
     return gammaP_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getNoiseSD ( ) const

Definition at line 745 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References noiseSD_.

Referenced by initCinfo().

 {
     return noiseSD_;
 }

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bool GraupnerBrunel2012CaPlasticitySynHandler::getNoisy ( ) const

Definition at line 735 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References noisy_.

Referenced by initCinfo().

 {
     return noisy_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getTauCa ( ) const

Definition at line 714 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References tauCa_.

Referenced by initCinfo().

 {
     return tauCa_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getTauSyn ( ) const

Definition at line 725 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References tauSyn_.

Referenced by initCinfo().

 {
     return tauSyn_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getThetaD ( ) const

Definition at line 673 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References thetaD_.

Referenced by initCinfo().

 {
     return thetaD_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getThetaP ( ) const

Definition at line 663 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References thetaP_.

Referenced by initCinfo().

 {
     return thetaP_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getTopSpike ( unsigned int index ) const

virtual

Implements SynHandlerBase.

Definition at line 329 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References events_.

 {
     if ( events_.empty() )
         return 0.0;
     return events_.top().time;
 }

double GraupnerBrunel2012CaPlasticitySynHandler::getWeightMax ( ) const

Definition at line 765 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightMax_.

Referenced by initCinfo().

 {
     return weightMax_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getWeightMin ( ) const

Definition at line 775 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightMin_.

Referenced by initCinfo().

 {
     return weightMin_;
 }

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double GraupnerBrunel2012CaPlasticitySynHandler::getWeightScale ( ) const

Definition at line 785 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightScale_.

Referenced by initCinfo().

 {
     return weightScale_;
 }

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const Cinfo * GraupnerBrunel2012CaPlasticitySynHandler::initCinfo ( )

static

Definition at line 18 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References addPostSpike(), getBistable(), getCa(), getCaInit(), getCaPost(), getCaPre(), getDelayD(), getGammaD(), getGammaP(), getNoiseSD(), getNoisy(), SynHandlerBase::getNumSynapses(), SynHandlerBase::getSynapse(), getTauCa(), getTauSyn(), getThetaD(), getThetaP(), getWeightMax(), getWeightMin(), getWeightScale(), Synapse::initCinfo(), SynHandlerBase::initCinfo(), setBistable(), setCa(), setCaInit(), setCaPost(), setCaPre(), setDelayD(), setGammaD(), setGammaP(), setNoiseSD(), setNoisy(), SynHandlerBase::setNumSynapses(), setTauCa(), setTauSyn(), setThetaD(), setThetaP(), setWeightMax(), setWeightMin(), setWeightScale(), and synHandlerCinfo.

 {
     static string doc[] =
     {
         "Name", "GraupnerBrunel2012CaPlasticitySynHandler",
         "Author", "Aditya Gilra",
         "Description",
         "The GraupnerBrunel2012CaPlasticitySynHandler handles synapses"
         "with Ca-based plasticity as per Higgins et al. 2014 and Graupner and Brunel 2012."
         "Note 1:"
         "   Here, Ca ('chemical Ca') is updated only at each pre-spike, pre-spike+delayD and post-spike!"
         "   So it is inaccurate to use it for say Ca-dependent K channels in the electrical compartment,"
         "   for which you use are advised to use the CaPool i.e. 'electrical Ca'."
         "Note 2:"
         "   Ca here is post-synaptic 'chemical Ca' common for all synapses in this SynHandler,"
         "   so weights of all pre-synapses connected to this SynHandler get updated"
         "   at each pre-spike, pre-spike+delayD and post-spike!"
         "   So if all pre-synaptic weights start out the same, they remain the same!!"
         "   If you want to consider each pre-synapse independently,"
         "   have independent SynHandlers for each synapse."
         "   If these SynHandlers are in the same electrical compartment,"
         "   you're essentially assuming these are on different spines,"
         "   with their own 'chemical Ca' which won't match the"
         "   'electrical Ca' of the compartment (=dendrite)."
         "   If you put each SynHandler with a single synapse"
         "   in its own electrical compartment (=spine),"
         "   only then can you have an 'electrical Ca'"
         "   corresponding to the 'chemical Ca'."
         "Three priority queues are used to manage pre, post, and pre+delayD spikes."
     };
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > Ca(
         "Ca",
         "Ca is a post-synaptic decaying variable as a proxy for Ca concentration"
         "and receives an impulse whenever a pre- or post- spike occurs."
         "Caution: Ca is updated via an event-based rule, so it is only updated and valid"
         "when a pre- or post- spike has occured, or at time delayD after a pre-spike."
         "Do not use it to control a Ca dependent current, etc."
         "See notes in the class Description: all pre-synapses get updated via the same post-synaptic Ca.",
         &GraupnerBrunel2012CaPlasticitySynHandler::setCa,
         &GraupnerBrunel2012CaPlasticitySynHandler::getCa
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > CaInit(
         "CaInit",
         "CaInit is the initial value for Ca",
         &GraupnerBrunel2012CaPlasticitySynHandler::setCaInit,
         &GraupnerBrunel2012CaPlasticitySynHandler::getCaInit
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > tauCa(
         "tauCa",
         "tauCa is the time constant for decay of Ca",
         &GraupnerBrunel2012CaPlasticitySynHandler::setTauCa,
         &GraupnerBrunel2012CaPlasticitySynHandler::getTauCa
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > tauSyn(
         "tauSyn",
         "tauSyn is the time constant for synaptic weight evolution equation",
         &GraupnerBrunel2012CaPlasticitySynHandler::setTauSyn,
         &GraupnerBrunel2012CaPlasticitySynHandler::getTauSyn
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > CaPre(
         "CaPre",
         "CaPre is added to Ca on every pre-spike",
         &GraupnerBrunel2012CaPlasticitySynHandler::setCaPre,
         &GraupnerBrunel2012CaPlasticitySynHandler::getCaPre
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > CaPost(
         "CaPost",
         "CaPost is added to Ca on every post-spike",
         &GraupnerBrunel2012CaPlasticitySynHandler::setCaPost,
         &GraupnerBrunel2012CaPlasticitySynHandler::getCaPost
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > delayD(
         "delayD",
         "Time delay D after pre-spike, when Ca is increased by Capre."
         " delayD represents NMDA rise time.",
         &GraupnerBrunel2012CaPlasticitySynHandler::setDelayD,
         &GraupnerBrunel2012CaPlasticitySynHandler::getDelayD
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > gammaP(
         "gammaP",
         "gammaP is the potentiation factor for synaptic weight increase if Ca>thetaP",
         &GraupnerBrunel2012CaPlasticitySynHandler::setGammaP,
         &GraupnerBrunel2012CaPlasticitySynHandler::getGammaP
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > gammaD(
         "gammaD",
         "gammaD is the depression factor for synaptic weight decrease if Ca>thetaD",
         &GraupnerBrunel2012CaPlasticitySynHandler::setGammaD,
         &GraupnerBrunel2012CaPlasticitySynHandler::getGammaD
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > thetaP(
         "thetaP",
         "Potentiation threshold for Ca"
         "User must ensure thetaP>thetaD, else simulation results will be wrong.",
         &GraupnerBrunel2012CaPlasticitySynHandler::setThetaP,
         &GraupnerBrunel2012CaPlasticitySynHandler::getThetaP
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > thetaD(
         "thetaD",
         "Depression threshold for Ca"
         "User must ensure thetaP>thetaD, else simulation results will be wrong.",
         &GraupnerBrunel2012CaPlasticitySynHandler::setThetaD,
         &GraupnerBrunel2012CaPlasticitySynHandler::getThetaD
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, bool > bistable(
         "bistable",
         "If true, the synapse is bistable as in GraupnerBrunel2012 paper."
         "The effect of potential on the weight update is usually ignorable"
         " if Ca is above thetaP and thetaD most of the time.",
         &GraupnerBrunel2012CaPlasticitySynHandler::setBistable,
         &GraupnerBrunel2012CaPlasticitySynHandler::getBistable
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, bool > noisy(
         "noisy",
         "If true, turn noise on as per noiseSD",
         &GraupnerBrunel2012CaPlasticitySynHandler::setNoisy,
         &GraupnerBrunel2012CaPlasticitySynHandler::getNoisy
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > noiseSD(
         "noiseSD",
         "Standard deviation of noise added to Ca",
         &GraupnerBrunel2012CaPlasticitySynHandler::setNoiseSD,
         &GraupnerBrunel2012CaPlasticitySynHandler::getNoiseSD
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > weightMax(
         "weightMax",
         "An upper bound on the weight",
         &GraupnerBrunel2012CaPlasticitySynHandler::setWeightMax,
         &GraupnerBrunel2012CaPlasticitySynHandler::getWeightMax
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > weightMin(
         "weightMin",
         "A lower bound on the weight",
         &GraupnerBrunel2012CaPlasticitySynHandler::setWeightMin,
         &GraupnerBrunel2012CaPlasticitySynHandler::getWeightMin
     );
 
     static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > weightScale(
         "weightScale",
         "Scale all pre-synaptic weights by weightScale before adding to activation (default 1.0)"
         "In the terminology of the paper Higgins et al 2012, weight is synaptic efficacy,"
         "while weightScale*weight is what finally is added to activation variable.",
         &GraupnerBrunel2012CaPlasticitySynHandler::setWeightScale,
         &GraupnerBrunel2012CaPlasticitySynHandler::getWeightScale
     );
 
     static DestFinfo addPostSpike(
         "addPostSpike",
         "Handles arriving spike messages from post-synaptic neuron, inserts into postEvent queue.",
         new EpFunc1< GraupnerBrunel2012CaPlasticitySynHandler, \
         double >( &GraupnerBrunel2012CaPlasticitySynHandler::addPostSpike ) );
 
     static FieldElementFinfo< SynHandlerBase, Synapse > synFinfo(
         "synapse",
         "Sets up field Elements for synapse",
         Synapse::initCinfo(),
         &SynHandlerBase::getSynapse,
         &SynHandlerBase::setNumSynapses,
         &SynHandlerBase::getNumSynapses
     );
 
     static Finfo* GraupnerBrunel2012CaPlasticitySynHandlerFinfos[] =
     {
         &synFinfo,     // FieldElement
         &addPostSpike, // DestFinfo
         &Ca,           // Field
         &CaInit,       // Field
         &tauCa,        // Field
         &tauSyn,       // Field
         &CaPre,        // Field
         &CaPost,       // Field
         &delayD,       // Field
         &thetaP,       // Field
         &thetaD,       // Field
         &gammaP,       // Field
         &gammaD,       // Field
         &weightMax,    // Field
         &weightMin,    // Field
         &weightScale,  // Field
         &noisy,        // Field
         &noiseSD,      // Field
         &bistable      // Field
     };
 
     static Dinfo< GraupnerBrunel2012CaPlasticitySynHandler > dinfo;
     static Cinfo synHandlerCinfo (
         "GraupnerBrunel2012CaPlasticitySynHandler",
         SynHandlerBase::initCinfo(),
         GraupnerBrunel2012CaPlasticitySynHandlerFinfos,
         sizeof( GraupnerBrunel2012CaPlasticitySynHandlerFinfos ) / sizeof ( Finfo* ),
         &dinfo,
         doc,
         sizeof( doc ) / sizeof( string )
     );
 
     return &synHandlerCinfo;
 }

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GraupnerBrunel2012CaPlasticitySynHandler & GraupnerBrunel2012CaPlasticitySynHandler::operator= ( const GraupnerBrunel2012CaPlasticitySynHandler & other )

Definition at line 278 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References delayDPreEvents_, events_, postEvents_, and synapses_.

 {
     synapses_ = ssh.synapses_;
     for ( vector< Synapse >::iterator
             i = synapses_.begin(); i != synapses_.end(); ++i )
         i->setHandler( this );
 
     // For no apparent reason, priority queues don't have a clear operation.
     while( !events_.empty() )
         events_.pop();
     while( !delayDPreEvents_.empty() )
         events_.pop();
     while( !postEvents_.empty() )
         postEvents_.pop();
 
     return *this;
 }

void GraupnerBrunel2012CaPlasticitySynHandler::reinitSeed ( void )

Definition at line 265 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References moose::getGlobalSeed(), MOOSE_DEBUG, rd_, rng_, and seed_.

Referenced by GraupnerBrunel2012CaPlasticitySynHandler().

 {
     if( 0 == seed_ )
         seed_ = moose::getGlobalSeed();
 
     if( 0 == seed_ )
         seed_ = rd_();
 
     MOOSE_DEBUG( "Seed is set to " << seed_ );
     rng_.seed( seed_ );
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setBistable ( bool v )

Definition at line 750 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References bistable_.

Referenced by initCinfo().

 {
     bistable_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setCa ( double v )

Definition at line 618 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References Ca_.

Referenced by initCinfo().

 {
     Ca_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setCaInit ( double v )

Definition at line 628 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References CaInit_.

Referenced by initCinfo().

 {
     CaInit_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setCaPost ( double v )

Definition at line 648 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References CaPost_.

Referenced by initCinfo().

 {
     CaPost_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setCaPre ( double v )

Definition at line 638 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References CaPre_.

Referenced by initCinfo().

 {
     CaPre_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setDelayD ( double v )

Definition at line 698 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References delayD_.

Referenced by initCinfo().

 {
     delayD_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setGammaD ( double v )

Definition at line 678 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References gammaD_.

Referenced by initCinfo().

 {
     gammaD_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setGammaP ( double v )

Definition at line 688 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References gammaP_.

Referenced by initCinfo().

 {
     gammaP_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setNoiseSD ( double v )

Definition at line 740 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References noiseSD_.

Referenced by initCinfo().

 {
     noiseSD_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setNoisy ( bool v )

Definition at line 730 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References noisy_.

Referenced by initCinfo().

 {
     noisy_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setTauCa ( double v )

Definition at line 708 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References SynHandlerBase::rangeWarning(), and tauCa_.

Referenced by initCinfo().

 {
     if ( rangeWarning( "tauCa", v ) ) return;
     tauCa_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setTauSyn ( double v )

Definition at line 719 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References SynHandlerBase::rangeWarning(), and tauSyn_.

Referenced by initCinfo().

 {
     if ( rangeWarning( "tauSyn", v ) ) return;
     tauSyn_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setThetaD ( double v )

Definition at line 668 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References thetaD_.

Referenced by initCinfo().

 {
     thetaD_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setThetaP ( double v )

Definition at line 658 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References thetaP_.

Referenced by initCinfo().

 {
     thetaP_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setWeightMax ( double v )

Definition at line 760 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightMax_.

Referenced by initCinfo().

 {
     weightMax_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setWeightMin ( double v )

Definition at line 770 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightMin_.

Referenced by initCinfo().

 {
     weightMin_ = v;
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::setWeightScale ( double v )

Definition at line 780 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightScale_.

Referenced by initCinfo().

 {
     weightScale_ = v;
 }

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weightFactors GraupnerBrunel2012CaPlasticitySynHandler::updateCaWeightFactors ( double currTime )

Definition at line 343 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightFactors::A, weightFactors::B, weightFactors::C, Ca_, weightFactors::D, dist_, weightFactors::E, gammaD_, gammaP_, lastCaUpdateTime_, moose::log(), noiseSD_, noisy_, rng_, weightFactors::t0, tauCa_, tauSyn_, weightFactors::tD, thetaD_, thetaP_, and weightFactors::tP.

Referenced by vProcess().

 {
     double CaOld = Ca_;
     double deltaT = currTime-lastCaUpdateTime_;
     // Update Ca, but CaPre and CaPost are added in vProcess()
     Ca_ *= exp(-deltaT/tauCa_);
     lastCaUpdateTime_ = currTime;
     weightFactors wUp; // by default all are set to 0.0
 
     // calculate/approximate time spent above potentiation and depression thresholds
     // see pg 13 of Higgins et al | October 2014 | Volume 10 | Issue 10 | e1003834 | PLOS Comp Biol
     // starting from bottom condition, going upwards in the algorithm given in above paper
     if (CaOld <= thetaD_)
     {
     }
     else if (CaOld <= thetaP_)
     {
         //cout << "tD<Caold<tP" << "\n";
         if (Ca_ <= thetaD_)
         {
             wUp.tD = tauCa_*log(CaOld/thetaD_);
             //cout << "Ca<tD" << "\n";
         }
         else
         {
             wUp.tD = deltaT;
             //cout << "Ca>tD" << "\n";
         }
     }
     else
     {
         //cout << "Caold>tP" << "\n";
         if (Ca_ <= thetaD_)
         {
             wUp.tP = tauCa_*log(CaOld/thetaP_);
             wUp.tD = tauCa_*log(thetaP_/thetaD_);
             //cout << "Ca<tD" << "\n";
             //cout << "Caold = " << CaOld << "thetaP = " << thetaP_ << "\n";
         }
         else if (Ca_ <= thetaP_)
         {
             wUp.tP = tauCa_*log(CaOld/thetaP_);
             wUp.tD = deltaT - wUp.tP;
             //cout << "Ca<tP" << "\n";
         }
         else
         {
             wUp.tP = deltaT;
             //cout << "Ca>tP" << "\n";
         }
     }
     wUp.t0 = deltaT - wUp.tP - wUp.tD;
 
     // Depending on tP and tD, I return A,B,C factors for weight update
     // (see page 13 of Higgins et al 2014).
     // A,B,C,D,E are used to compute the weight change for one or multiple synapses
     // A is weight independent, B,D are weight dependent and C,E are accumulated noise
     if (wUp.tP > 0)
     {
         double gPgD = gammaP_+gammaD_;
         wUp.A = gammaP_/gPgD*(1.0-exp(-wUp.tP*gPgD/tauSyn_));
         wUp.B = exp(-wUp.tP*gPgD/tauSyn_);
         if (noisy_)
         {
             wUp.C = noiseSD_ * dist_(rng_) *
                     sqrt( ( 1.0-exp(-2*gPgD*wUp.tP/tauSyn_) ) / gPgD );
             // cout << " A = " << wUp.A << " B = " << wUp.B << " C = " << wUp.C << "\n";
         }
         else
         {
             wUp.C = 0.0;
         }
     }
 
     if (wUp.tD > 0)
     {
         wUp.D = exp(-wUp.tD*gammaD_/tauSyn_);
         if (noisy_)
         {
             wUp.E = noiseSD_ * dist_( rng_ ) *
                     sqrt( ( 1.0-exp(-2*gammaD_*wUp.tD/tauSyn_) ) / 2.0/gammaD_ );
             //cout << "D = " << wUp.D << " E = " << wUp.E << "\n";
         }
         else
         {
             wUp.E = 0.0;
         }
     }
 
     //cout << currTime  << " tD = " << wUp.tD << " tP = " << wUp.tP << "\n";
     // tP, tD, A, B, C, D, E of wUp
     // are set to 0.0 by default in struct constructor
     return wUp;     // return by value, i.e. copies the struct, so wUp going out of scope doesn't matter
     // malloc and returning pointer is more expensive for small structs
     // see: http://stackoverflow.com/questions/9590827/is-it-safe-to-return-a-struct-in-c-c
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::updateWeight	(	Synapse *	synPtr,
		weightFactors *	wFacPtr
	)

Definition at line 440 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References weightFactors::A, weightFactors::B, bistable_, weightFactors::C, weightFactors::D, weightFactors::E, Synapse::getWeight(), Synapse::setWeight(), weightFactors::t0, tauSyn_, weightFactors::tD, weightFactors::tP, weightMax_, and weightMin_.

Referenced by vProcess().

 {
     double newWeight = synPtr->getWeight();
     //cout << " oldweight = " << newWeight << "\n";
     if (wFacPtr->tP > 0.0)
     {
         newWeight = wFacPtr->A + wFacPtr->B*newWeight + wFacPtr->C;
         //cout << " midweight = " << newWeight << "\n";
     }
     if (wFacPtr->tD > 0.0)
     {
         newWeight = wFacPtr->D*newWeight + wFacPtr->E; // update the weight again
         //cout << " newweight = " << newWeight << "\n";
     }
 
     // potential is usually ignorable when t0 is small,
     // i.e. Ca is mostly above thetaD or thetaP
     //cout << "before bistable newWeight = " << newWeight << "\n";
     if (bistable_)
     {
         double chi0 = pow((newWeight-0.5),2.0) / (newWeight*(newWeight-1));
         double weightDeviation = 0.5*sqrt( 1.0 + 1.0/(chi0*exp(wFacPtr->t0/2.0/tauSyn_)-1.0) );
         if (newWeight<0.5)
         {
             newWeight = 0.5 - weightDeviation;
         }
         else
         {
             newWeight = 0.5 + weightDeviation;
         }
     }
     //cout << "after bistable newWeight = " << newWeight << "\n";
 
     // clip weight within [weightMin,weightMax]
     newWeight = std::max(weightMin_, std::min(newWeight, weightMax_));
     //cout << " clipweight = " << newWeight << "\n";
     //cout << " A = " << wFacPtr->A << " B = " << wFacPtr->B << " C = " << wFacPtr->C
     //    << " D = " << wFacPtr->D << " E = " << wFacPtr->E << " newW = "<< newWeight << "\n";
     synPtr->setWeight( newWeight );
 }

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unsigned int GraupnerBrunel2012CaPlasticitySynHandler::vGetNumSynapses ( ) const

virtual

Implements SynHandlerBase.

Definition at line 306 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References synapses_.

 {
     return synapses_.size();
 }

Synapse * GraupnerBrunel2012CaPlasticitySynHandler::vGetSynapse ( unsigned int i )

virtual

Implements SynHandlerBase.

Definition at line 311 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References dummy, and synapses_.

 {
     static Synapse dummy;
     if ( i < synapses_.size() )
         return &synapses_[i];
     cout << "Warning: GraupnerBrunel2012CaPlasticitySynHandler::getSynapse: index: " << i <<
          " is out of range: " << synapses_.size() << endl;
     return &dummy;
 }

void GraupnerBrunel2012CaPlasticitySynHandler::vProcess	(	const Eref &	e,
		ProcPtr	p
	)

virtual

Implements SynHandlerBase.

Definition at line 481 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References SynHandlerBase::activationOut(), Ca_, CaPost_, CaPre_, ProcInfo::currTime, delayDPreEvents_, ProcInfo::dt, events_, Synapse::getWeight(), postEvents_, synapses_, PreSynEvent::synIndex, updateCaWeightFactors(), updateWeight(), and weightScale_.

 {
     double activation = 0.0;
     double currTime = p->currTime;
     bool CaFactorsUpdated = false; // Ca-decay and weight Factors updation is done only once
     // if any pre-spike, pre-spike+delayD or post-spike occurs
     // Ca is bumped by CaPre and CaPost on
     // pre-spike+delayD and post-spike respectively
     // At the end, if any event above occurred,
     // change all pre-synaptic weights based on Ca
     weightFactors wFacs;
 
     // process pre-synaptic spike events for activation, Ca and weight update
     while( !events_.empty() && events_.top().time <= currTime )
     {
         PreSynEvent currEvent = events_.top();
 
         unsigned int synIndex = currEvent.synIndex;
         // Warning, coder! 'STDPSynapse currSyn = synapses_[synIndex];' is wrong,
         // it creates a new, shallow-copied object.
         // We want only to point to the same object.
         Synapse* currSynPtr = &synapses_[synIndex];
 
         // activate the synapse for every pre-spike
         // If the synapse has a delay, the weight could be updated during the delay!
         // currEvent.weight is the weight before the delay!
         // Might be better to use currSynPtr->getWeight()
         //      or even the latest updated weight below?!
         // Using currSynPtr->getWeight().
         // Still, weight update is event driven and not continuous
         //      so using currSynPtr->getWeight() takes care of
         //      weight updates due to events/spikes during the delay
         //      but doesn't take care of continuous weight evolution during the delay.
         // The weight update is done
         //          after sending the current weight to activation
         // Maybe I should use the updated weight to send to activation?!
 
         // See: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#synchan
         // Send out weight / dt for every spike
         //      Since it is an impulse active only for one dt,
         //      need to send it divided by dt.
         // Can connect activation to SynChan (double exp)
         //      or to LIF as an impulse to voltage.
         //activation += currEvent.weight * weightScale_ / p->dt;
         activation += currSynPtr->getWeight() * weightScale_ / p->dt;
 
         // update only once for this time-step if an event occurs
         if (!CaFactorsUpdated)
         {
             // update Ca and weightFactors
             wFacs = updateCaWeightFactors( currTime );
             CaFactorsUpdated = true;
         }
 
         events_.pop();
     }
     if ( activation != 0.0 )
         SynHandlerBase::activationOut()->send( e, activation );
 
     // process delayed pre-synaptic spike events for Ca and weight update
     // delayD after pre-spike accounts for NMDA rise time
     while( !delayDPreEvents_.empty() && delayDPreEvents_.top().time <= currTime )
     {
         // Update Ca, and add CaPre
         // update only once for this time-step if an event occurs
         if (!CaFactorsUpdated)
         {
             // update Ca and weightFactors
             wFacs = updateCaWeightFactors( currTime );
             CaFactorsUpdated = true;
         }
         Ca_ += CaPre_;
 
         delayDPreEvents_.pop();
     }
 
     // process post-synaptic spike events for Ca and weight update
     while( !postEvents_.empty() && postEvents_.top().time <= currTime )
     {
         // update Ca, then add CaPost
         // update only once for this time-step if an event occurs
         if (!CaFactorsUpdated)
         {
             // update Ca and weightFactors
             wFacs = updateCaWeightFactors( currTime );
             CaFactorsUpdated = true;
         }
         Ca_ += CaPost_;
 
         postEvents_.pop();
     }
 
     // If any event has happened, update all pre-synaptic weights
     // If you want individual Ca for each pre-synapse
     // create individual SynHandlers for each
     if (CaFactorsUpdated)
     {
         // Change weight of all synapses
         for (unsigned int i=0; i<synapses_.size(); i++)
         {
             // Warning, coder! 'Synapse currSyn = synapses_[i];' is wrong,
             // it creates a new, shallow-copied object.
             // We want only to point to the same object.
             Synapse* currSynPtrHere = &synapses_[i];
             updateWeight(currSynPtrHere,&wFacs);
         }
     }
 
 }

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void GraupnerBrunel2012CaPlasticitySynHandler::vReinit	(	const Eref &	e,
		ProcPtr	p
	)

virtual

Implements SynHandlerBase.

Definition at line 591 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References Ca_, CaInit_, delayDPreEvents_, events_, and postEvents_.

 {
     // For no apparent reason, priority queues don't have a clear operation.
     while( !events_.empty() )
         events_.pop();
     while( !delayDPreEvents_.empty() )
         events_.pop();
     while( !postEvents_.empty() )
         postEvents_.pop();
     Ca_ = CaInit_;
 }

void GraupnerBrunel2012CaPlasticitySynHandler::vSetNumSynapses ( unsigned int num )

virtual

Implements SynHandlerBase.

Definition at line 298 of file GraupnerBrunel2012CaPlasticitySynHandler.cpp.

References synapses_.

 {
     unsigned int prevSize = synapses_.size();
     synapses_.resize( v );
     for ( unsigned int i = prevSize; i < v; ++i )
         synapses_[i].setHandler( this );
 }