ACnet23 primary auditory cortex model (Beeman et al 2019)

 Download zip file 
Help downloading and running models
These scripts were used to model a patch of layer 2/3 primary auditory cortex, making use of the the improvements to PGENESIS by Crone, et al. (2019). This single layer model contains a 48 x 48 grid of pyramidal cells (PCs) and a 24 x 24 grid of basket cells (BCs). The reduced PC models have 17 compartments with dimensions and passive properties that were fit to human cortical PC reconstructions. This parallel version of the simulation was used by Beeman, et al. (2019) to understand the effects of inhibition of PCs by BCs on auditory evoked potentials.
1 . Beeman D, Yu A, Crone J (2019) Studying evoked potentials in large cortical networks with PGENESIS 2.4 BMC Neuroscience 20 Suppl 1:P46
2 . Crone JC, Vindiola MM, Yu AB, Boothe DL, Beeman D, Oie KS, Franaszczuk PJ (2019) Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator Frontiers in Neuroinformatics 13:69
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Auditory cortex;
Cell Type(s): Neocortex L2/3 pyramidal GLU cell; Neocortex fast spiking (FS) interneuron;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: PGENESIS; GENESIS;
Model Concept(s):
Implementer(s): Beeman, Dave;
Search NeuronDB for information about:  Neocortex L2/3 pyramidal GLU cell; GabaA; AMPA; Gaba; Glutamate;
// MBG-protodefs.g - Definition of prototype elements for MGBv relay cell

/* NOTE: This assumes that a previously included protodefs file
   has created /library with the elements below:

include compartments

create spikegen spike
setfield spike  thresh 0.00  abs_refract 1.0e-3  output_amp 1


// functions to create modified Traub and Miles tabchannels
include MGBchans.g

/* MGBchans.g assigns values to the global variables EREST_ACT, ENA, EK, and
   SOMA_A.  The first three will be superceded by any values defined below.
   The value of SOMA_A is not relevant, as the cell reader calculates the
   compartment area.


   EREST_ACT = -0.063
   ENA       =  0.050
   EK        = -0.090
// Use default values

/* file for synaptic channels */
include synchans // from Neurokit/prototypes

/* synchans.g defines:
   EGlu = 0.045
   EGABA = -0.082

EGlu = 0.0
EGABA = -0.08

// Make a "library element" to hold the prototypes which will be used
// by the cell reader to add compartments and channels to the cell.

if (!{exists /library})     // But, only if it doesn't already exist
    create neutral /library

// We don't want the library to try to calculate anything, so we disable it
disable /library

// To ensure that all subsequent elements are made in the library
pushe /library

/* Functions in MGBchans.g are used to create prototype channels
   Na_traub_mod and K_traub_mod   

// Make a prototype excitatory channel, "Ex_channel" - from synchans.g
make_Ex_channel     /* synchan with Ek = 0.0, tau1 = tau2 = 3 msec */

// Make a prototype inhibitory channel, "Inh_channel"
make_Inh_channel     /* synchan with Ek = -0.08, tau1 = tau2 = 20 msec */

pope // Return to the original place in the element tree