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.
Reference:
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]
Citations  Citation Browser
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
/
nrntraub
mod
alphasyndiffeq.mod *
alphasynkin.mod *
alphasynkint.mod *
ampa.mod *
ar.mod *
cad.mod *
cal.mod *
cat.mod *
cat_a.mod *
gabaa.mod *
iclamp_const.mod *
k2.mod *
ka.mod *
ka_ib.mod *
kahp.mod *
kahp_deeppyr.mod *
kahp_slower.mod *
kc.mod *
kc_fast.mod *
kdr.mod *
kdr_fs.mod *
km.mod *
naf.mod *
naf_tcr.mod *
naf2.mod *
nap.mod *
napf.mod *
napf_spinstell.mod *
napf_tcr.mod *
par_ggap.mod *
pulsesyn.mod *
rampsyn.mod *
rand.mod *
ri.mod *
traub_nmda.mod *
                            
COMMENT
Four helpful hints:

1) before calling scale_connection_coef, one must call some NEURON
function (such as ri(x)) that forces calculation of all the connection
coefficients for all the sections.

2) if any diam or L is changed, then one must re-call the
scale_connection_coef procedure again for all compartments AFTER
re-forcing the normal calculation of them via a call to, e.g. ri(x).

3) note that ri(0.5) gives the resistance in mega ohms between 0.5
location and the 0 end and ri(1) gives the resistance in mega ohms
between the 0.5 location and the 1 end.

4) Call with a section access'ed.  Call below with (1,factor) to
change the axial resistance of (a parent's) x=0.5 to x=1 part and call
with (0.5, factor) to change the axial resistance for (a child's) x=0
to x=0.5 part.  Note: factor = current_ri_value/desired__ri_value.

ENDCOMMENT

NEURON { SUFFIX nothing }

VERBATIM
const char* secname();
ENDVERBATIM

PROCEDURE scale_connection_coef(x, factor) {
VERBATIM {
	Section* sec;
	Node* nd;
#if defined(t)
	_NrnThread* _nt = nrn_threads;
#endif
	sec = chk_access();
	if (_lx <= 0. || _lx > 1.) {
		hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
	}
	/*printf("scale_connection_coefs %s(%g) %d\n", secname(sec), _lx, sec->nnode);*/
	/* assumes 0 end of child connected to parent */
	if (_lx == 1.) {
		nd = sec->pnode[sec->nnode-1];
	}else{
		nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
	}
	/*printf("%g %g\n", NODEA(nd), NODEB(nd));*/
#if defined(t)
	_nt = nd->_nt;
#endif
	NODEA(nd) *= _lfactor;
	NODEB(nd) *= _lfactor;
}
ENDVERBATIM
}