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

 Download zip file   Auto-launch 
Help downloading and running models
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
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 *
                            
thread_per_piece_ = 0
proc thread_per_piece() {local n  localobj sl
//printf("%d nthread=%d\n", pc.id, gidvec.size)
	sl = new SectionList()
	sl.allroots()
	n = 0 forsec sl { n += 1 }
	if (n <= 10) {
		pc.nthread(n, 0)
	}else{
		thread_per_piece_ = 1
	}
}

proc balanalfile() {local i, j, cxtotal, cx, ct, tid, gid \
    localobj lb, cxpiece, srl, f, cell
	i = pc.allreduce(thread_per_piece_, 1)
	if (i > 0 && pc.id == 0) {
		printf("%d hosts with too many pieces for 1 piece per thread\n", i)
	}
	lb = new LoadBalance()
	cxtotal = lb.cpu_complexity()
	cxpiece = lb.pieces_cx(srl)

	f = new File()
	if (pc.id == 0) {
		f.wopen($s1)
		f.printf("%d\n", pc.nhost)
		f.close()
	}
	for j=0, pc.nhost-1 {
		if (pc.id == j) {
			f.aopen($s1)
			f.printf("%d\n", cxpiece.size)
			for i=0, cxpiece.size - 1 {
				srl.object(i).sec tid = pc.sec_in_thread
				if (tid != i) {
execerror("bad gidvec to thread relation", "")
				}
				cx = cxpiece.x[i]
				ct = pc.thread_ctime(tid)
				f.printf(" %d %g %g\n", i, cx, ct)
			}
			f.close()
		}
		pc.barrier
	}
}