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 *
                            
      FUNCTION ran1(idum)
      INTEGER idum,IA,IM,IQ,IR,NTAB,NDIV
      DOUBLE PRECISION ran1,AM,EPS,RNMX
      PARAMETER (IA=16807,IM=2147483647,AM=1.d0/IM,IQ=127773,IR=2836,
     *NTAB=32,NDIV=1+(IM-1)/NTAB,EPS=3.d-16,RNMX=1.d0-EPS)
      INTEGER j,k,iv(NTAB),iy
      SAVE iv,iy
      DATA iv /NTAB*0/, iy /0/
      if (idum.le.0.or.iy.eq.0) then
        idum=max(-idum,1)
        do 11 j=NTAB+8,1,-1
          k=idum/IQ
          idum=IA*(idum-k*IQ)-IR*k
          if (idum.lt.0) idum=idum+IM
          if (j.le.NTAB) iv(j)=idum
11      continue
        iy=iv(1)
      endif
      k=idum/IQ
      idum=IA*(idum-k*IQ)-IR*k
      if (idum.lt.0) idum=idum+IM
      j=1+iy/NDIV
      iy=iv(j)
      iv(j)=idum
      ran1=min(AM*iy,RNMX)
      return
      END

      subroutine durand(seed, npts, x)
      implicit none
      integer npts, i, idum
      real*8  seed, ran1,  x(npts)
      if (seed .lt. 0.0d0  .or. seed .gt. 2147483648.0) then
         write(6,*) 'seed must be a positive integer < 2.1474*10**9'
         seed = 135791113.0
      end if
      idum = -int(seed)
      do i = 1, npts
           x(i) = ran1(idum)
      end do
      seed = dble(idum)
      end