Auditory cortex layer IV network model (Beeman 2013)

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Accession:150678
"... The primary objective of this modeling study was to determine the effects of axonal conduction velocity (often neglected, but significant), as well as synaptic time constants, on the ability of such a network to create and propagate cortical waves. ... The model is also being used to study the interaction between single and two-tone input and normal background activity, and the effects of synaptic depression from thalamic inputs. The simulation scripts have the additional purpose of serving as tutorial examples for the construction of cortical networks with GENESIS. The present model has fostered the development of the G-3 Python network analysis and visualization tools used in this study... It is my hope that this short tutorial and the example simulation scripts can provide a head start for a graduate student or postdoc who is beginning a cortical modeling project. "
Reference:
1 . Beeman D (2013) A modeling study of cortical waves in primary auditory cortex BMC Neuroscience 14(Supl 1):P23
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 V1 pyramidal corticothalamic L6 cell; Neocortex V1 interneuron basket PV cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Tutorial/Teaching;
Implementer(s): Beeman, Dave;
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 interneuron basket PV cell;
  
// genesis

/* FILE INFORMATION
     GENESIS implementation by D. Beeman of the channel models described in
     Alain Destexhe and Denis Par, Impact of network activity on the
     integrative properties of neocortical pyramidal neurons in vivo.
     Journal of Neurophysiology 81: 1531-1547, 1999

   Some adjustments were made to represent the model in

     Destexhe A, Rudolph M, Fellous JM and Sejnowski TJ.
     Fluctuating synaptic conductances recreate in-vivo-like activity in
     neocortical neurons. Neuroscience 107: 13-24, 2001.

   Based on the NEURON demonstration 'FLUCT' by Alain Destexhe.
   http://cns.iaf.cnrs-gif.fr
*/

// passive membrane parameters
float   CM
float   RA
float   RM

// channel equilibrium potentials (V)
float   EREST_ACT = -0.063  // value for vtraub in Destexhe et al. (2001)
// float   EREST_ACT = -0.058 // value for vtraub in Destexhe and Par (1999)
float   ENA       =  0.050
float   EK        = -0.090

/* These channels use the setupalpha function to create tabchannel tables
   to represent alpha and beta values in the form (A+B*V)/(C+exp((V+D)/F))
   The first 6 arguments are the coefficients for alpha, and the last 6
   are for beta
*/

//========================================================================
//                Tabchannel Hippocampal fast Na channel
// Based on Traub, R. D. and Miles, R.  Neuronal Networks of the hippocampus
// Cambridge University Press (1991)
//========================================================================

function make_Na_traub_mod
    str chanpath = "Na_traub_mod"
    if ({argc} == 1)
       chanpath = {argv 1}
    end
    if (({exists {chanpath}}))
                return
    end

    create tabchannel {chanpath}
    setfield ^  \
        Ek      {ENA}   \               //      V
        Ik      0       \               //      A
        Gk      0       \               //      S
        Xpower  3       \
        Ypower  1       \
        Zpower  0

    setupalpha {chanpath} X  \
        {320e3  * (0.013 + EREST_ACT)}                 \
        -320e3 -1.0 {-1.0   * (0.013 + EREST_ACT)}     \
        -0.004                                          \
        {-280e3 * (0.040 + EREST_ACT)}                 \
        280e3                                           \
        -1.0                                            \
        {-1.0   * (0.040 + EREST_ACT)}                 \
        5.0e-3
    // Traub and Miles Na inactivation was shifted by Destexhe and Par
    // but this version uses no offset
    // float offset = -0.010 
    float offset = 0.0 
    setupalpha {chanpath} Y  \
        128.0                           \
        0.0                             \
        0.0                             \
        {-1.0 * (0.017 + EREST_ACT + offset)}    \
        0.018                           \
        4.0e3                           \
        0.0                             \
        1.0                             \
        {-1.0 * (0.040 + EREST_ACT + offset)}    \
        -5.0e-3
end

//========================================================================
//                Tabchannel K(DR) Hippocampal cell channel
// Based on Traub, R. D. and Miles, R.  Neuronal Networks of the hippocampus
// Cambridge University Press (1991)
//========================================================================
function make_K_traub_mod
    str chanpath = "K_traub_mod"
    if ({argc} == 1)
       chanpath = {argv 1}
    end
    if (({exists {chanpath}}))
                return
    end

    create tabchannel {chanpath}
    setfield ^  \
        Ek      {EK}    \               //      V
        Ik      0       \               //      A
        Gk      0       \               //      S
        Xpower  4       \
        Ypower  0       \
        Zpower  0

    setupalpha {chanpath} X  \
        {32e3 * (0.015 + EREST_ACT)}    \
        -32e3                           \
        -1.0                            \
        {-1.0 * (0.015 + EREST_ACT) }   \
        -0.005                          \
        500                             \
        0.0                             \
        0.0                             \
        {-1.0 * (0.010 + EREST_ACT) }   \
        0.04
end

//========================================================================
//                Synaptically activated channels
//========================================================================

float EAMPA = 0.0
float EGABA = -0.080

function make_AMPA_bask
    str chanpath = "AMPA_bask"
    if ({argc} == 1)
       chanpath = {argv 1}
    end
    if ({exists {chanpath}})
       return
    end
    float tau1 = 0.003
    float tau2 = 0.003
    create  synchan      {chanpath}
    setfield        ^       \
        Ek                      {EAMPA} \
        tau1            {tau1} \        // sec
        tau2            {tau2} \        // sec
        gmax            0 // Siemens
end

function make_GABA_bask
    str chanpath = "GABA_bask"
    if ({argc} == 1)
       chanpath = {argv 1}
    end
    if ({exists {chanpath}})
       return
    end
    float tau1 = 0.003
    float tau2 = 0.008
    create  synchan      {chanpath}
    setfield        ^       \
        Ek                      {EGABA} \
        tau1            {tau1} \        // sec
        tau2            {tau2} \        // sec
        gmax            0 // Siemens
end

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