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 ;
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
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nrntraub
cells
dat
hoc
mod
net
README
balanal.hoc *
balcomp.hoc *
cell_templates.hoc *
clear.hoc *
finit.hoc *
fortmap.hoc *
gidcell.hoc *
gidcell.ses *
init.hoc
manage_setup.hoc
mosinit.hoc *
onecell.hoc *
onecell.ses *
prcellstate.hoc *
printcon.hoc *
savestatetest.sh
spkplt.hoc *
vclampg.hoc *
vcompclamp.hoc *
vcompsim.hoc *
                            
objref type_vinit, vgaba, typename[14]
type_vinit = new Vector(14)
vgaba = new Vector(14)

//cell type id according to the mpirank in the fortran program
//cell.type() returns this value. Note that the table order is below is the
//same as the base order in groucho.hoc
for i=0, 13 {
	j = fscan()
	typename[j] = new String() getstr(typename[j].s, 1)
	type_vinit.x[j] = fscan()  vgaba.x[j] = fscan()
}

suppyrRS_template.hoc:  rank = 0  suppyrRS    -70 -81
suppyrFRB_template.hoc: rank = 1  suppyrFRB   -70 -81
supbask_template.hoc:   rank = 2  supbask     -65 -75
supaxax_template.hoc:   rank = 3  supaxax     -65 -75
supLTS_template.hoc:    rank = 4  supLTS      -65 -75
spinstell_template.hoc: rank = 5  spinstell   -65 -75
tuftIB_template.hoc:    rank = 6  tuftIB      -70 -75
tuftRS_template.hoc:    rank = 7  tuftRS      -70 -75
nontuftRS_template.hoc: rank = 8  nontuftRS   -70 -75
deepbask_template.hoc:  rank = 9  deepbask    -65 -75
deepaxax_template.hoc:  rank = 10 deepaxax    -65 -75
deepLTS_template.hoc:   rank = 11 deepLTS     -65 -75
TCR_template.hoc:       rank = 12 TCR         -70 -81
nRT_template.hoc:       rank = 13 nRT         -75 -75

//note that the TCR rank value is used explicitly in initialization since the
//states are initialized at a different voltage value than the membrane potential.

TCRtype = 12

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