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Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation (Luque et al 2019)

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Accession:256140
"Cerebellar Purkinje cells mediate accurate eye movement coordination. However, it remains unclear how oculomotor adaptation depends on the interplay between the characteristic Purkinje cell response patterns, namely tonic, bursting, and spike pauses. Here, a spiking cerebellar model assesses the role of Purkinje cell firing patterns in vestibular ocular reflex (VOR) adaptation. The model captures the cerebellar microcircuit properties and it incorporates spike-based synaptic plasticity at multiple cerebellar sites. ..."
Reference:
1 . Luque NR, Naveros F, Carrillo RR, Ros E, Arleo A (2019) Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation. PLoS Comput Biol 15:e1006298 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Realistic Network;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum Purkinje GABA cell; Cerebellum interneuron granule GLU cell; Vestibular neuron; Abstract integrate-and-fire leaky neuron;
Channel(s): I K; I Na,t; I L high threshold; I M;
Gap Junctions:
Receptor(s): AMPA; Gaba;
Gene(s):
Transmitter(s):
Simulation Environment: EDLUT; NEURON; MATLAB;
Model Concept(s): Activity Patterns; Sleep; Long-term Synaptic Plasticity; Vestibular;
Implementer(s): Luque, Niceto R. [nluque at ugr.es];
Search NeuronDB for information about:  Cerebellum Purkinje GABA cell; Cerebellum interneuron granule GLU cell; AMPA; Gaba; I Na,t; I L high threshold; I K; I M;
/
LuqueEtAl2019
EDLUT
Articulo purkinje
CASE_A
src
neuron_model
BufferedState.cpp *
EgidioGranuleCell_TimeDriven.cpp *
EgidioGranuleCell_TimeDriven_GPU.cu *
EventDrivenNeuronModel.cpp *
LIFTimeDrivenModel_1_2.cpp *
LIFTimeDrivenModel_1_2_GPU.cu *
LIFTimeDrivenModel_1_4.cpp *
LIFTimeDrivenModel_1_4_GPU.cu *
NeuronModel.cpp *
NeuronModelTable.cpp *
NeuronState.cpp *
SRMState.cpp *
SRMTableBasedModel.cpp *
SRMTimeDrivenModel.cpp *
TableBasedModel.cpp *
TableBasedModelHF.cpp *
TimeDrivenNeuronModel.cpp *
TimeDrivenNeuronModel_GPU.cu *
TimeDrivenPurkinjeCell.cpp *
Vanderpol.cpp *
VectorBufferedState.cpp *
VectorNeuronState.cpp *
VectorNeuronState_GPU.cpp *
VectorSRMState.cpp *
                            
/***************************************************************************
 *                           BufferedState.cpp                             *
 *                           -------------------                           *
 * copyright            : (C) 2010 by Jesus Garrido                        *
 * email                : jgarrido@atc.ugr.es                              *
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU General Public License as published by  *
 *   the Free Software Foundation; either version 3 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/

#include "../../include/neuron_model/BufferedState.h"

BufferedState::BufferedState(unsigned int NumVariables, unsigned int NumBuffers):
	NeuronState(NumVariables), FirstElement(0), LastElement(0), BufferAmplitude(0), NumberOfElements(0), NumberOfBuffers(NumBuffers) {
	FirstElement = (ActivityNode **) new ActivityNode * [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->FirstElement[i] = 0;
	}
		
	LastElement = (ActivityNode **) new ActivityNode * [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->LastElement[i] = 0;
	}
		
	BufferAmplitude = (float *) new float [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->BufferAmplitude[i] = 0;
	}
		
	NumberOfElements = (unsigned int *) new unsigned int [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->NumberOfElements[i] = 0;
	}
		
}

BufferedState::BufferedState(const BufferedState & OldState): NeuronState(OldState), FirstElement(0), LastElement(0),
		BufferAmplitude(0), NumberOfElements(0), NumberOfBuffers(OldState.NumberOfBuffers) {

	FirstElement = (ActivityNode **) new ActivityNode * [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->FirstElement[i] = 0;
	}
		
	LastElement = (ActivityNode **) new ActivityNode * [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->LastElement[i] = 0;
	}
		
	BufferAmplitude = (float *) new float [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->BufferAmplitude[i] = 0;
	}
		
	NumberOfElements = (unsigned int *) new unsigned int [NumberOfBuffers];

	for (unsigned int i=0; i<NumberOfBuffers; ++i){
		this->NumberOfElements[i] = 0;
	}
		

	for (unsigned int i=0; i<this->NumberOfBuffers; ++i){
		this->BufferAmplitude[i] = OldState.BufferAmplitude[i];

		ActivityNode * Iterator = OldState.FirstElement[i];

		while (Iterator!=0){
			ActivityNode * NewElement = (ActivityNode *) new ActivityNode;

			NewElement->Spike = Iterator->Spike;
			NewElement->NextNode = 0;

			if (this->FirstElement[i]==0){
				// This is the first element of the list
				this->FirstElement[i] = NewElement;
				this->LastElement[i] = NewElement;
			} else {
				// Add the element after the last element
				this->LastElement[i]->NextNode = NewElement;
				this->LastElement[i] = NewElement;
			}

			this->NumberOfElements[i] ++;

			Iterator = Iterator->NextNode;
		}
	}
}

void BufferedState::SetBufferAmplitude(unsigned int NumBuffer, float BufferAmpl){
	this->BufferAmplitude[NumBuffer] = BufferAmpl;
}

BufferedState::~BufferedState() {
	// TODO Auto-generated destructor stub
	for (unsigned int i=0; i<this->NumberOfBuffers; ++i){
		ActivityNode * Iterator = this->FirstElement[i];

		while (Iterator!=0){
			ActivityNode * NextElement = Iterator->NextNode;

			delete Iterator;

			Iterator = NextElement;
		}

	}

	delete [] this->NumberOfElements;
	this->NumberOfElements = 0;
	delete [] this->BufferAmplitude;
	this->BufferAmplitude = 0;
	delete [] this->FirstElement;
	this->FirstElement = 0;
	delete [] this->LastElement;
	this->LastElement = 0;
}

void BufferedState::AddActivity(Interconnection * InputConnection){
	ActivityNode * NewElement = (ActivityNode *) new ActivityNode;

	unsigned int NumBuffer = (unsigned int) InputConnection->GetType();

	NewElement->Spike.first = 0;
	NewElement->Spike.second = InputConnection;
	NewElement->NextNode = 0;

	if (this->FirstElement[NumBuffer]==0){
		// This is the first element of the list
		this->FirstElement[NumBuffer] = NewElement;
		this->LastElement[NumBuffer] = NewElement;
	} else {
		// Add the element after the last element
		this->LastElement[NumBuffer]->NextNode = NewElement;
		this->LastElement[NumBuffer] = NewElement;
	}

	this->NumberOfElements[NumBuffer] ++;
}

void BufferedState::CheckActivity(){
	for (unsigned int i=0; i<this->NumberOfBuffers; ++i){
		// If the first element is older than we accept, remove it.
		ActivityNode * Iterator = this->FirstElement[i];
		while (Iterator!=0 && Iterator->Spike.first>this->BufferAmplitude[i]){
			ActivityNode * Next = Iterator->NextNode;
			delete Iterator;
			this->FirstElement[i] = Next;
			if (Next==0){
				// Empty buffer
				this->LastElement[i] = 0;
			}
			Iterator = Next;
			this->NumberOfElements[i] --;
		}
	}
}

void BufferedState::AddElapsedTime(float ElapsedTime){
	NeuronState::AddElapsedTime(ElapsedTime);

	for (unsigned int i=0; i<this->NumberOfBuffers; ++i){
		ActivityNode * Iterator = this->FirstElement[i];
		while (Iterator!=0){
			Iterator->Spike.first += ElapsedTime;
			Iterator = Iterator->NextNode;
		}
	}

	this->CheckActivity();
}

unsigned int BufferedState::GetNumberOfSpikes(unsigned int NumBuffer){
	return this->NumberOfElements[NumBuffer];
}

double BufferedState::GetSpikeTimeAt(unsigned int Position, unsigned int NumBuffer){
	ActivityNode * Iterator = this->FirstElement[NumBuffer];
	for (unsigned int i = 0; i<Position && Iterator!=0; ++i, Iterator=Iterator->NextNode){
	}
	return (Iterator==0)?-1:Iterator->Spike.first;
}

Interconnection * BufferedState::GetInterconnectionAt(unsigned int Position, unsigned int NumBuffer){
	ActivityNode * Iterator = this->FirstElement[NumBuffer];
	for (unsigned int i = 0; i<Position && Iterator!=0; ++i, Iterator=Iterator->NextNode){
	}
	return (Iterator==0)?0:Iterator->Spike.second;
}

BufferedState::Iterator BufferedState::Begin(unsigned int NumBuffer){
	return Iterator(this->FirstElement[NumBuffer]);
}

BufferedState::Iterator BufferedState::End(){
	return Iterator();
}

BufferedState::Iterator::Iterator():element(0){}

BufferedState::Iterator::Iterator(const BufferedState::Iterator & ItAux){
	this->element = ItAux.element;
}

BufferedState::Iterator::Iterator(ActivityNode * ElemAux){
	this->element=ElemAux;
}

BufferedState::Iterator & BufferedState::Iterator::operator++(){
	this->element = this->element->NextNode;

	return *this;
}

bool BufferedState::Iterator::operator==(BufferedState::Iterator Aux){
	return this->element==Aux.element;
}

bool BufferedState::Iterator::operator!=(BufferedState::Iterator Aux){
	return this->element!=Aux.element;
}

double BufferedState::Iterator::GetSpikeTime(){
	return this->element->Spike.first;
}

Interconnection * BufferedState::Iterator::GetConnection(){
	return this->element->Spike.second;
}

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