A 1000 cell network model for Lateral Amygdala (Kim et al. 2013)

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Accession:150288
1000 Cell Lateral Amygdala model for investigation of plasticity and memory storage during Pavlovian Conditioning.
Reference:
1 . Kim D, Paré D, Nair SS (2013) Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala. Learn Mem 20:421-30 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell; Synapse; Dendrite;
Brain Region(s)/Organism: Amygdala;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Hodgkin-Huxley neuron;
Channel(s): I Na,t; I L high threshold; I A; I M; I Sodium; I Calcium; I Potassium; I_AHP; Ca pump;
Gap Junctions:
Receptor(s): AMPA; NMDA; Gaba; Dopaminergic Receptor;
Gene(s):
Transmitter(s): Dopamine; Norephinephrine;
Simulation Environment: NEURON;
Model Concept(s): Synaptic Plasticity; Short-term Synaptic Plasticity; Long-term Synaptic Plasticity; Learning; Neuromodulation;
Implementer(s): Kim, Dongbeom [dk258 at mail.missouri.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; AMPA; NMDA; Gaba; Dopaminergic Receptor; I Na,t; I L high threshold; I A; I M; I Sodium; I Calcium; I Potassium; I_AHP; Ca pump; Dopamine; Norephinephrine;
/
KimEtAl2013
README.txt
bg2inter.mod
bg2pyr.mod
ca.mod *
cadyn.mod
cal2.mod *
capool.mod *
function_TMonitor.mod *
h.mod *
im.mod
interD2pyrD_STFD.mod
interD2pyrDDA_STFD.mod
interD2pyrDDANE_STFD.mod
interD2pyrDNE_STFD.mod
interD2pyrV_STFD.mod
interD2pyrVDA_STFD.mod
interV2pyrD_STFD.mod
interV2pyrDDA_STFD.mod
interV2pyrDDANE_STFD.mod
interV2pyrDNE_STFD.mod
interV2pyrV_STFD.mod
interV2pyrVDA_STFD.mod
kadist.mod *
kaprox.mod
kdrca1.mod
kdrca1DA.mod
kdrinter.mod *
leak.mod *
leakDA.mod *
leakinter.mod *
na3.mod
na3DA.mod
nainter.mod *
pyrD2interD_STFD.mod
pyrD2interV_STFD.mod
pyrD2pyrD_STFD.mod
pyrD2pyrDDA_STFD.mod
pyrD2pyrV_STFD.mod
pyrD2pyrVDA_STFD.mod
pyrV2interD_STFD.mod
pyrV2interV_STFD.mod
pyrV2pyrD_STFD.mod
pyrV2pyrDDA_STFD.mod
pyrV2pyrV_STFD.mod
pyrV2pyrVDA_STFD.mod
sahp.mod
sahpNE.mod
shock2interD.mod
shock2interV.mod
shock2pyrD.mod
shock2pyrV.mod
tone2interD.mod
tone2interDNE.mod
tone2interV.mod
tone2interVNE.mod
tone2pyrD.mod
tone2pyrD_LAdv.mod
tone2pyrDNE.mod
tone2pyrDNE_LAdv.mod
tone2pyrV.mod
tone2pyrV_LAdd.mod
tone2pyrVNE.mod
tone2pyrVNE_LAdd.mod
BgGen.hoc
Cell_list.txt
Cell_type.txt
function_ConnectInternal.hoc
function_ConnectTwoCells.hoc
function_NetStimOR.hoc *
function_TimeMonitor.hoc *
function_ToneGen.hoc
function_ToneSignalGen_Ctx.hoc
function_ToneSignalGen_Th.hoc
interneuron_template.hoc
LA_model_main_file.hoc
LAcells_template.hoc
NM.txt
shock2Idd.txt
shock2Idv.txt
shock2LAdd.txt
shock2LAdv.txt
shockcondi.hoc
Syn_Matrix.txt
tone2Idd.txt
tone2Idd2.txt
tone2Idv.txt
tone2Idv2.txt
tone2LAdd.txt
tone2LAdd2.txt
tone2LAdv.txt
tone2LAdv2.txt
                            
//By Pirate Henry 2011 and modified by DK

proc ConnectTwoCells() { local targetid,sourceid,type,initW,delay,threshold localobj target,syn,nc,synlist,nclist
	sourceid = $1
	targetid = $2
	type = $3
//	initW = $4
	delay = $4
//	threshold = $6
	synlist = $o5  //$o7
	nclist = $o6   //$o8
	if (!pc.gid_exists(targetid)) { continue }				// Can't connect to target if it doesn't exist 
		cellid = pc.gid2cell(targetid)
		if ( sourceid <= 395 ) { if (type == 1 || type == 2) {cellid.dend syn = new pyrD2pyrD_STFD(0.9)}
							     if (type == 3 || type == 4) {cellid.dend syn = new pyrD2pyrDDA_STFD(0.9)}
   								 if (type == 5 || type == 6) {cellid.dend syn = new pyrD2pyrV_STFD(0.9)}
							     if (type == 7 || type == 8) {cellid.dend syn = new pyrD2pyrVDA_STFD(0.9)}						 
								 if (type == 9 || type == 10) {
																cellid.dend syn = new pyrD2interD_STFD(0.9)
																}
								 if (type == 11 || type == 12) {
																cellid.dend syn = new pyrD2interV_STFD(0.9)
																}
								 }								 
								 
		if ( sourceid >= 396 && sourceid <=799 ) { if (type == 1 || type == 2) {cellid.dend syn = new pyrV2pyrD_STFD(0.9)}
												   if (type == 3 || type == 4) {cellid.dend syn = new pyrV2pyrDDA_STFD(0.9)}
												   if (type == 5 || type == 6) {cellid.dend syn = new pyrV2pyrV_STFD(0.9)}
												   if (type == 7 || type == 8) {cellid.dend syn = new pyrV2pyrVDA_STFD(0.9)}
												   if (type == 9 || type == 10) {
																				cellid.dend syn = new pyrV2interD_STFD(0.9)
																				}
												   if (type == 11 || type == 12) {
																				cellid.dend syn = new pyrV2interV_STFD(0.9)
																			}
												}	
												   
		if ( sourceid >= 800 && sourceid <=903 ) { if (type == 1) {cellid.soma syn = new interD2pyrD_STFD(0.9)}
												   if (type == 2) {cellid.soma syn = new interD2pyrDNE_STFD(0.9)}	
												   if (type == 3) {cellid.soma syn = new interD2pyrDDA_STFD(0.9)}
												   if (type == 4) {cellid.soma syn = new interD2pyrDDANE_STFD(0.9)}				
												   if (type == 5 || type == 6) {cellid.soma syn = new interD2pyrV_STFD(0.9)}			
												   if (type == 7 || type == 8) {cellid.soma syn = new interD2pyrVDA_STFD(0.9)}}	
												   
		if ( sourceid >= 904 ) { if (type == 1) {cellid.soma syn = new interV2pyrD_STFD(0.9)}
							     if (type == 2) {cellid.soma syn = new interV2pyrDNE_STFD(0.9)}	
								 if (type == 3) {cellid.soma syn = new interV2pyrDDA_STFD(0.9)}
								 if (type == 4) {cellid.soma syn = new interV2pyrDDANE_STFD(0.9)}				
								 if (type == 5 || type == 6) {cellid.soma syn = new interV2pyrV_STFD(0.9)}			
								 if (type == 7 || type == 8) {cellid.soma syn = new interV2pyrVDA_STFD(0.9)}}
						 
		syn.pregid = sourceid
		syn.postgid = targetid
		
		cellid.synlist.append(syn)   // To save synapse data, weight and ca+ concentration
		syn.srcid= sourceid
		syn.destid= targetid
		
		
		nc = pc.gid_connect(sourceid,syn)
		nc.weight = 1
		nc.delay = delay
		nc.threshold = -10
		
														
		//printf("%d %d %d %d %d %d\n" ,syn.postgid,syn.pregid, syn.initW, nc.delay, nc.threshold, type)		
		saveM.printf("%d %d %f %d %d %d\n" ,syn.postgid, syn.pregid, syn.initW, nc.delay, nc.threshold, type)		
		synlist.append(syn)
		nclist.append(nc)
		//{pc.barrier()}	
}

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