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]
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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;
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 [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
/
traubEtAl2005
data
readme.txt
compile_integration
dexptablebig_setup.f *
dexptablesmall_setup.f *
durand.f *
fnmda.f *
gettime.o
groucho.f
groucho.f.orig
groucho_gapbld.f *
groucho_gapbld_mix.f *
integrate_deepaxax.f
integrate_deepbask.f
integrate_deepLTS.f
integrate_nontuftRS.f
integrate_nRT.f
integrate_spinstell.f
integrate_supaxax.f
integrate_supbask.f
integrate_supLTS.f
integrate_suppyrFRB.f
integrate_suppyrRS.f
integrate_tcr.f
integrate_tuftIB.f
integrate_tuftRS.f
job
makefile
synaptic_compmap_construct.f *
synaptic_map_construct.f *
                            
c Program assumes A, BB1, BB2 defined in calling program
c as follows:
c        A = DEXP(-2.847d0)
c        BB1 = DEXP(-.693d0)
c        BB2 = DEXP(-3.101d0)
        SUBROUTINE FNMDA (VSTOR, OPEN, numcells, numcomps,
     &    MG, L, A, BB1, BB2) 
c Computes "open" for all compartments of cell # L

           integer L, numcells, numcomps, i
       REAL*8 VSTOR(numcomps,numcells), OPEN(numcomps)
       REAL*8 A, BB1, BB2, VM, A1, A2, B1, B2, MG
c modify so that potential is absolute and not relative to
c  "rest"
C  TO DETERMINE VOLTAGE-DEPENDENCE OF NMDA CHANNELS
           DO 1, I = 1, numcomps
           VM = VSTOR(I,L)
           A1 = DEXP(-.016d0*VM - 2.91d0)
           A2 = 1000.d0 * MG * DEXP (-.045d0 * VM - 6.97d0)
           B1 = DEXP(.009d0*VM + 1.22d0)
           B2 = DEXP(.017d0*VM + 0.96d0)
        OPEN(I)     = 1.d0/(1.d0 + (A1+A2)*(A1*BB1 + A2*BB2) /
     X   (A*A1*(B1+BB1) + A*A2*(B2+BB2))  )
C  FROM JAHR & STEVENS, EQ. 4A
C               DO 124, J = 1, 19
C          OPEN(J) = 1./(1.+.667* EXP(-0.07*(VSTOR(J)-60.)) )
C  FROM CHUCK STEVENS
1               CONTINUE
                        END