Layer 5 Pyramidal Neuron (Shai et al., 2015)

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Accession:180373
This work contains a NEURON model for a layer 5 pyramidal neuron (based on Hay et al., 2011) with distributed groups of synapses across the basal and tuft dendrites. The results of that simulation are used to fit a phenomenological model, which is also included in this file.
Reference:
1 . Shai AS, Anastassiou CA, Larkum ME, Koch C (2015) Physiology of layer 5 pyramidal neurons in mouse primary visual cortex: coincidence detection through bursting. PLoS Comput Biol 11:e1004090 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Dendritic Action Potentials; Active Dendrites;
Implementer(s):
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Glutamate;
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ShaiEtAl2015
simulationcode
Ca_HVA.mod *
Ca_LVAst.mod *
CaDynamics_E2.mod *
epsp.mod *
glutamate.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
NaTs2_t.mod *
SK_E2.mod *
SKv3_1.mod *
AccessoryFunctions.hoc
DefineSections.hoc
distSynsCluster.hoc
distSynsCluster2.hoc
distSynsUniform.hoc
distSynsUniform2.hoc
distSynsUniformAlpha.hoc
Fig3A.hoc
neuron203.os
O_vd_C.dat
O_vs_C.dat
Run.hoc
varycolor.m
                            
proc Compute_Zin() { localobj z

   z = new Impedance()      
   L5PC.soma { z.loc(0.5) } 
   z.compute(0)                         
                       
   Zin = 0
   L5PC.soma { Zin = z.input(0.5) } 
   print "Input impedance: ", Zin
}

proc Compute_ZinDend() { localobj z

   z = new Impedance()      
   L5PC.apic[36] { z.loc(0.9) } 
   z.compute(0)                         
                       
   Zin = 0
   L5PC.apic[36] { Zin = z.input(0.9) } 
   print "Dend Input impedance: ", Zin
}


proc Compute_Sag() { localobj istim, vvec, tvec
	
	istim = new IClamp(0.5)
	istim.del = 500
	istim.dur = 1000
	istim.amp = -.3
	
	vvec = new Vector()
	vvec.record(&L5PC.soma.v)
	
	tvec = new Vector()
	tvec.record(&t)

	tstop = 1000
	init()
	run()
	
	trest = tvec.indwhere(">",499)

	vrest = vvec.x[trest-1]
	vmin = vvec.min()
	vss = vvec.x[vvec.size()-1]

	sag = (vmin-vss)/(vss-vrest)*100
	print "Sag: ", sag
	print "Vrest: ", vrest
}



proc Compute_SagDend() { localobj istim, vvec, tvec
	L5PC.apic[36]{
	istim = new IClamp(0.9)
	istim.del = 500
	istim.dur = 1000
	istim.amp = -.3
	}
	
	vvec = new Vector()
	vvec.record(&L5PC.apic[36].v(0.9))
	
	tvec = new Vector()
	tvec.record(&t)

	tstop = 1000
	init()
	run()
	
	trest = tvec.indwhere(">",499)

	vrest = vvec.x[trest-1]
	vmin = vvec.min()
	vss = vvec.x[vvec.size()-1]

	sag = (vmin-vss)/(vss-vrest)*100
	print "SagDend: ", sag
	print "VrestDend: ", vrest
}

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