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 [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 *
                            
            SUBROUTINE synaptic_compmap_construct (thisno,
     &    num_postsynaptic_cells, compmap,
     &    num_presyninputs_perpostsyn_cell, 
     &    num_allowcomp, allow, display)

c Construct a map of compartments at connections of one presynaptic
c cell to type to a postsynaptic cell type.
c compmap (i,j) = compartment number on postsynaptic cell j of its
c  i'th presynaptic input.
c display is an integer flag.  If display = 1, print compmap

        INTEGER thisno,
     &   num_postsynaptic_cells,
     &   num_presyninputs_perpostsyn_cell,
     &   compmap (num_presyninputs_perpostsyn_cell, 
     &                  num_postsynaptic_cells),
     &   num_allowcomp, allow(num_allowcomp)
c num_allowcomp = number of different allowed compartments
c allow = list of allowed compartments
        INTEGER i,j,k,l,m,n,o,p
        INTEGER display

        double precision seed, x(1)

            seed = 377.d0
            map = 0
            k = 1

        do i = 1, num_postsynaptic_cells
        do j = 1, num_presyninputs_perpostsyn_cell
            call durand (seed, k, x)
c This defines a compartment     

           L = int ( x(1) * dble (num_allowcomp) )         
           if (L.eq.0) L = 1
           if (L.gt.num_allowcomp)             
     &           L = num_allowcomp         

           compmap (j,i) = allow(L)

        end do
        end do

c Possibly print out map when done.
       if ((display.eq.1).and.(thisno.eq.0)) then
        write (6,800)                           
800     format(' SYNAPTIC COMPARTMENT MAP ')
        do i = 1, num_postsynaptic_cells
         write (6,50) compmap(1,i), compmap(2,i),
     &        compmap(num_presyninputs_perpostsyn_cell,i)               
50       FORMAT(3i6)
        end do
       endif

                 END