ACnet23 primary auditory cortex model (Beeman et al 2019)

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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
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;
Section 18.7.3 of the BoG (Utility Functions for Synapses) describes and
gives a listing for the synapse_info function.

Usage:   synapse_info path_to_synchan
Example: synapse_info /network/cell[5]/apical1/Ex_channel

This is used to return a list of synaptic connections to the channel, their
sources, weights, and delays.  It uses some of the built-in GENESIS commands:

getsyncount [presynaptic-element] [postsynaptic-element]
getsynindex <presynptic-element> <postpostsynaptic-element> [-number n]
getsynsrc <postsynaptic-element> <index>
getsyndest  <presynptic-element> <n> [-index] //n is the no of spike message


function synapse_info(path)
   str path,src
   int i
   float weight,delay, x0, y0, z0, x, y, z, rp, rv
   floatformat %.3g
   echo "For synchan path: " {path}
   for(i=0;i<{getsyncount {path}};i=i+1)
       src={getsynsrc {path} {i}}
       weight={getfield {path} synapse[{i}].weight}
       delay={getfield {path} synapse[{i}].delay }
       echo synapse[{i}] : rc = {src} weight ={weight} delay ={delay}
       x0 = {getfield {src} x}
       y0 = {getfield {src} y}
       z0 = {getfield {src} z}
       x =  {getfield {path} x}
       y =  {getfield {path} y}
       z =  {getfield {path} z}
       rp = {sqrt {(x0-x)*(x0-x) + (y0-y)*(y0-y)}}
       rv = {sqrt {(x0-x)*(x0-x) + (y0-y)*(y0-y) + (z0-z)*(z0-z)}}
       echo "radial distance = "{rv} " planar distance = "{rp}

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