Alpha rhythm in vitro visual cortex (Traub et al 2020)

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Accession:263703
The paper describes an experimental model of the alpha rhythm generated by layer 4 pyramidal neurons in a visual cortex slice. The simulation model is derived from that of Traub et al. (2005) J Neurophysiol, developed for thalamocortical oscillations.
Reference:
1 . Traub RD, Hawkins K, Adams NE, Hall SP, Simon A, Whittington MA (2020) Layer 4 pyramidal neuron dendritic bursting underlies a post-stimulus visual cortical alpha rhythm Nature Communications Biology, in press
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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: Thalamus; Neocortex;
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 layer 4 pyramidal cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron; Neocortex spiny stellate cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: FORTRAN;
Model Concept(s): Brain Rhythms; Dendritic Action Potentials;
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; I Na,p; I Na,t; I L high threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
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alpha_rhythm_code_RT
readme.txt
alphaY33.pdf
alphaY67.f
alphaY67.pdf
dexptablebig_setup.f *
dexptablesmall_setup.f *
durand.f *
fnmda.f *
gettime.c *
groucho_gapbld.f *
groucho_gapbld_mix.f *
integrate_deepaxaxx.f *
integrate_deepbaskx.f *
integrate_deepLTSx.f *
integrate_deepng.f *
integrate_nontuftRSXXB.f
integrate_nrtxB.f *
integrate_spinstelldiegoxB.f *
integrate_supaxaxx.f *
integrate_supbaskx.f *
integrate_supLTSX.f *
integrate_supng.f *
integrate_suppyrFRBxPB.f *
integrate_suppyrRSXPB.f
integrate_tcrxB.f *
integrate_tuftIBVx3B.f
integrate_tuftRSXXB.f *
makefile
otis.f *
otis_table_setup.f *
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