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

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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.
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]
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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;
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
durand.hoc *
groucho_gapbld.hoc *
groucho_gapbld_mix.hoc *
network_specification_interface.hoc *
serial_or_par_wrapper.hoc *
synaptic_compmap_construct.hoc *
synaptic_map_construct.hoc *
// groucho_gapbld_mix.hoc
****************************this is one big comment ************************
! 15 Nov. 2003, variation of groucho_gapbld.f to allow for gj
! between 2 cell populations, eg suppyrRS and suppyrFRB, or
! tuftRS and tuftIB.  Structure of gjtable as before, with col. 1
! giving cell of 1st type and col. 3 giving coupled cell of 2nd type.

      SUBROUTINE GROUCHO_gapbld_mix (thisno, numcells1, numcells2,
     & numgj, gjtable, allowedcomps, num_allowedcomps, display)
c       Construct a gap-junction network for groucho.f
$1 thisno double
$2 numcells1 = number of cells in 1st population.
$3 numcells2 = number of cells in 2nd population.
$4 numgj = total number of gj to be formed between these populations.
// this is the output: gjtable = table of gj's: each row is a gj.  
   Entries are: cell A, compartment on cell A; cell B, compartment on cell B
$o5 allowedcomps = a list of compartments where gj allowed to form
$6 num_allowedcomps = number of compartments in a cell on which a gj 
$7 display
c    might form.
c display is an integer flag.  If display = 1, print gjtable

        INTEGER thisno, numcells1, numcells2, numgj, gjtable(numgj,4),
     &    num_allowedcomps, allowedcomps(num_allowedcomps)
        INTEGER i,j,k,l,m,n,o,p, ictr /0/
c ictr keeps track of how many gj have been "built"
        INTEGER display

        double precision seed, x1(1), x2(1), y(2)
****************************this is one big comment ************************
objref gjtable,x1, x2, y1
obfunc groucho_gapbld_mix() { // see note above for arguments:
	thisno  = $1
	numcells1 = $2
	numcells2 = $3
	numgj = $4
	allowedcomps = $o5
	num_allowedcomps = $6
	display = $7
//	print "Arrived at groucho_gapbld_mix with display = ",display

	seed = new Vector()
	objref gjtable
	gjtable = new Matrix(numgj+1, 4+1) // FORTRAN-like indicies start at 1

	ictr = 0

// 2
	while (ictr < numgj) {
		k = 1
	    not_unique = 1
	    while (not_unique) {
		x1 = durand (seed, k, x1) // durand returns vec c-style indicies
		x2 = durand (seed, k, x2)
// c This defines a candidate cell pair
                k = 2
		y = durand (seed, k, y)
// c This defines a candidate pair of compartments

		i = int ( x1.x[0] * numcells1 ) + 1
		j = int ( x2.x[0] * numcells2 ) + 1

// c Is the ORDERED cell pair (i,j) in the list so far?
// superfluous but true           if (ictr.eq.0) goto 1

		not_unique = 0
		for eL = 1, ictr {
		  if ((gjtable.x(eL,1) == i) && (gjtable.x(eL,3) == j)) {not_unique = 1}
		if (one_tenth_ncell) {
			not_unique = 0
	    } // loop replaces  if (p.eq.1) goto 2

// c Proceed with construction
// 1
	    ictr = ictr + 1
	    m = int ( y.x[0] * num_allowedcomps ) + 1
	    n = int ( y.x[1] * num_allowedcomps ) + 1

	    gjtable.x[ictr][1] = i
	    gjtable.x[ictr][3] = j
	    gjtable.x[ictr][2] = allowedcomps.x[m]
	    gjtable.x[ictr][4] = allowedcomps.x[n]

	} // loop replacing if (ictr.lt.numgj) goto 2

// c Possibly print out gjtable when done.
//	print "at end of groucho_gapbld_mix display = ",display,", thisno = ",thisno
	if ((display == 1) && (thisno == 0)) {
		print " MIX GJTABLE"
		for i = 1, numgj {
	          printf("%6d, %6d %6d %6d \n",gjtable.x(i,1), gjtable.x(i,2), \
                                       gjtable.x(i,3), gjtable.x(i,4))
//	print "successfully printed or not"
	return gjtable