A single column thalamocortical network model (Traub et al 2005)

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Accession:45539
To better understand population phenomena in thalamocortical neuronal ensembles, we have constructed a preliminary network model with 3,560 multicompartment neurons (containing soma, branching dendrites, and a portion of axon). Types of neurons included superficial pyramids (with regular spiking [RS] and fast rhythmic bursting [FRB] firing behaviors); RS spiny stellates; fast spiking (FS) interneurons, with basket-type and axoaxonic types of connectivity, and located in superficial and deep cortical layers; low threshold spiking (LTS) interneurons, that contacted principal cell dendrites; deep pyramids, that could have RS or intrinsic bursting (IB) firing behaviors, and endowed either with non-tufted apical dendrites or with long tufted apical dendrites; thalamocortical relay (TCR) cells; and nucleus reticularis (nRT) cells. To the extent possible, both electrophysiology and synaptic connectivity were based on published data, although many arbitrary choices were necessary.
References:
1 . Traub RD, Contreras D, Cunningham MO, Murray H, LeBeau FE, Roopun A, Bibbig A, Wilent WB, Higley MJ, Whittington MA (2005) Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. J Neurophysiol 93:2194-232 [PubMed]
2 . Traub RD, Contreras D, Whittington MA (2005) Combined experimental/simulation studies of cellular and network mechanisms of epileptogenesis in vitro and in vivo. J Clin Neurophysiol 22:330-42 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex; Thalamus;
Cell Type(s): Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions: Gap junctions;
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; FORTRAN;
Model Concept(s): Activity Patterns; Bursting; Temporal Pattern Generation; Oscillations; Simplified Models; Epilepsy; Sleep; Spindles;
Implementer(s): Traub, Roger D [rtraub at us.ibm.com];
Search NeuronDB for information about:  Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Files displayed below are from the implementation
/
nrntraub
hoc
balcomp.hoc *
defvar.hoc *
lbcreate.hoc *
mscreate.hoc *
parlib.hoc
parlib2.hoc *
traubcon.hoc *
traubcon_net.hoc *
                            
{load_file("stdlib.hoc")}
proc default_var() {localobj s, pc
	s = new String()
	if (name_declared($s1) == 0) {
		if (argtype(2) == 2) {
			sprint(s.s, "~strdef %s", $s1)
			execute(s.s)
			sprint(s.s, "%s = \"%s\"", $s1, $s2)
		}else{
			hoc_ac_ = $2
			sprint(s.s, "%s = hoc_ac_", $s1)
		}
		execute(s.s)
	}
	pc = new ParallelContext()
	if (pc.id == 0) {
		sprint(s.s, "print \"%s  \", %s", $s1, $s1)
		execute(s.s)
	}
}


// BlueGene has an occasional system error with respect to
// incessantly changing directories with load_file
// following should work as long as nothing loaded twice
// and only used for files relative to the project
strdef curdir
curdir = "./"
proc localloadfile() {localobj dir, f, sf, oldcd, path
//	load_file($s1)
//	return

	oldcd = new String()
	oldcd.s = curdir

	sf = new StringFunctions()
	dir = new String()
	path = new String()
	f = new String()
	i = sf.head($s1, "/[^/]*$", dir.s)
	f.s = $s1
	if (i == -1) {
		dir.s = ""
	}else{
		sprint(dir.s, "%s/", dir.s)
		sf.right(f.s, i+1)
	}
	sprint(curdir, "%s%s", curdir, dir.s)
	sprint(path.s, "%s%s", curdir, f.s)
//printf("loading %s\n", path.s)
	xopen(path.s)
	curdir = oldcd.s
}

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