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

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

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, et al (2005) A single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles and epileptogenic bursts: Appendix B. J Neurophysiol 93(4):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:	Network;
Brain Region(s)/Organism:	Neocortex; Thalamus;
Cell Type(s):	Thalamic relay neuron; Thalamic reticular neuron; Neocortical pyramidal neuron: deep; Neocortical pyramidal neuron: superficial; Neocortical Fast Spiking (FS) interneuron; Neocortical Regular Spiking (RS) neuron; Neocortical Low Threshold Spiking (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;
Implementer(s):	Traub, Roger D ;

Search NeuronDB for information about: Thalamic relay neuron; Thalamic reticular neuron; Neocortical pyramidal neuron: deep; Neocortical pyramidal neuron: superficial; 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;

Model files

Help downloading and running models

dexptablesmall_setup.f

integrate_nontuftRS.f

integrate_nRT.f

integrate_spinstell.f

integrate_supaxax.f

integrate_supbask.f

integrate_supLTS.f

integrate_suppyrFRB.f

synaptic_compmap_construct.f

synaptic_map_construct.f

Readme for the model code associated with the paper

Traub RD, Contreras D, Cunningham MO, Murray H, Lebeau FE, Roopun A, 
Bibbig A, Wilent WB, Higley M, Whittington MA.
A single-column thalamocortical network model exhibiting gamma 
oscillations, sleep spindles and epileptogenic bursts.
J Neurophysiol. 2004 Nov 3; [Epub ahead of print]

These model files were supplied by Roger Traub with minor fixes
by Tom Morse and Michael Hines. 7/14/06

Note: in the file, job, the cd /home/traub/groucho will need to be
replaced with cd /home/yourdirectory/groucho which is where you issue
the qsub command.  Also you may need an extra path like:

# for LAM/Intel MPI version
export PATH=$PATH:.:/usr/local/lam/bin

supplied in your .bashrc file.  Here are some guidelines supplied
by Roger Traub on building and running the model:

1st compile all the integration subroutines, with compile_integration,
which uses ifc.

Then type "make", which compiles the main program (with mpifwhatever) 
and links everything to give an executable. Then "qsub job", which 
ships the lot to the master node of the Linux cluster; that in turn 
loads the stuff onto 14 cpu's.

groucho.f = main program
compile_integration = does what it says, compiles integration subroutines
makefile creates an executable for "job"
job = what gets submitted, with command "qsub job"

ModelDB Home SenseLab Home Help
Questions, comments, problems? Email the ModelDB Administrator
How to cite ModelDB
This site is Copyright 2012 Shepherd Lab, Yale University