Effects of neural morphology on global and focal NMDA-spikes (Poleg-Polsky 2015)

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Accession:185123
This entry contains the NEURON files required to recreate figures 4-8 of the paper "Effects of Neural Morphology and Input Distribution on Synaptic Processing by Global and Focal NMDA-spikes" by Alon Poleg-Polsky
Reference:
1 . Poleg-Polsky A (2015) Effects of Neural Morphology and Input Distribution on Synaptic Processing by Global and Focal NMDA-Spikes. PLoS One 10:e0140254 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex layer 4 neuron;
Channel(s): I N; I K; I K,leak;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Dendritic Action Potentials; Ion Channel Kinetics; Active Dendrites; Detailed Neuronal Models; Synaptic Integration; Synaptic-input statistic; Dendritic Bistability;
Implementer(s): Polsky, Alon [alonpol at tx.technion.ac.il];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; AMPA; NMDA; I N; I K; I K,leak;
	load_file("nrngui.hoc")							
	//load_file("layerV1.hoc")	//The morphology to use			
	load_file("layer23_4.hoc")	//The morphology to use			
	startseed=1		
	runnum=0
	insertHH=01
	//****EXCITATORY CELLS

	numINPUTperCELL=300	//number of presynaptic cells (inputs) to first generation
	numINHIBINPUTperCELL=000
	objref cell
	//***INPUTS	
	baselineISI=1e100		//frequesncy of basal firing (ms)
	patternISI=10	//frequency of pattern firing (ms)
	patternNUM=1		//number of pattern APs
	patternSTART=10	//10 when pattern starts
	patternEND=10//100
	patternINHIBISI=100	//frequency of pattern firing (ms)
	patternINHIBNUM=1		//number of pattern APs
	patternINHIBSTART=100	//when pattern starts
	patternINHIBEND=1100
	//***ANALYSIS
	spikethresh=-35	//min threshold for the NMDA spike
	spikeminlen=30	//min duration of NDMA spike
	placeterminal=1//puts synapses only on the terminal dends and their parents
	numbetween=0//autoset by user selection of specific dendrites
	
	//****SYNAPTIC CONDUCTACES
	gnmdamax=00.7
	if (runnum>1){gnmdamax=0}

	gampamax=0.3//.5
	ggabamax=00.5
	decayampa_glutamate=1
	decaynmda_glutamate=1
	n_glutamate=0.2
	tau_ampa_glutamate=1
	decaytime_gaba=6
	//***ACTIVE	
	na_s=0.5//1//2//.5
	k_s=0.05//05//.2//15//0.01
	km_s=0//0.03
	na_d=0
	k_d=0.01////.01
	km_d=0//1
	gpas=010000
	//****OTHER OBJECTS and VARIABLES
	objref rLOC,temp,temp2,rLOCINHIB,rTIME,rINHIBTIME,rISI,rINHIBISI//,rLATERAL,rFEEDF,rTIME,rINPUT,
	objref ginputs,gVmain,shape,gSPIKE,nil,pc
	pc = new ParallelContext()		

	showdends=0//1
	showsoma=1

	randomseed=startseed
	syncorr=01
	


	//****PROCEDURES
	tstop = 60//1500//200
	dt = 0.1	
	v_init = -60
	steps_per_ms = 10				

	load_file("functions.hoc")	
	

	initrandom(0)

	makecells(0)
	active()
		
	objref gVmain
	gVmain=new Graph(0)
	gVmain.view(0,-60,tstop,60,950,280,500,230) 
	if(showdends){
		forall {//dends	
			gVmain.addvar("v(0.5)",1,1)
		}
	}
	gVmain.addexpr("cell.soma.v(0.5)",2,1)
	graphList[0].append(gVmain)

	load_file("net.ses")
	init_plots_panels()
		

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