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 *
                            
This is the readme for the model associated with the paper:

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

This code was contributed by R Traub.

The source code is standard fortran with special instructions for the
mpi parallel environment.  Included are 2 pdf files with illustrative
output, an example of the main program (alphayY67.f), a number of
fortran subroutines and one in C, and the “makefile” which does
compilation and linking.

I have run the code on an IBM power chip residing in IBM’s Cognitive
Computing Cluster, at a time when the AIX operating system was in use
(that is IBM’s version of Linux).  The machine model is given in the
ms text, but is probably not relevant.  The CCC has since switched to
Linux.  The code should also run under Linux, but I have not tried it;
however, I have converted similar programs from AIX to Linux without
difficulty; the routines simply need to be compiled with the Fortran
compiler in use on the operating system, and an appropriate makefile
used.  The details of the makefile are going to be system-dependent.

The code does not run on data.  Each run is autonomous, with
parameters chosen by the programmer.  I also do not expect that the
code will run on a desktop, given the need for mpi.