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, et al (2005) A single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles and epileptogenic bursts 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]
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 neuron; Thalamus reticular nucleus cell; Neocortex layer 5-6 pyramidal cell; Neocortex layer 2-3 pyramidal 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;
Implementer(s): Traub, Roger D ;
Search NeuronDB for information about:  Thalamus geniculate nucleus (lateral) principal neuron; Thalamus reticular nucleus cell; Neocortex layer 5-6 pyramidal cell; Neocortex layer 2-3 pyramidal 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
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. (2005)
A single-column thalamocortical network model exhibiting gamma 
oscillations, sleep spindles and epileptogenic bursts.
J Neurophysiol. 93(4):2194-232

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"


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 J Neurophysiol 93(4):2194-232[PubMed]

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Wang Y, Goodfellow M, Taylor PN, Baier G (2014) Dynamic mechanisms of neocortical focal seizure onset PLoS Computational Biology 10(8):e1003787 [Journal] [PubMed]

   A cortical sheet mesoscopic model for investigating focal seizure onset dynamics (Wang et al. 2014) [Model]

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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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