//genesis genesis2.2 script
/**************************************************************************
* This file defines important simulation parameters for GnRH cell model *
* with synapses. Everything uses SI units. *
***************************************************************************/
echo loading constants file, Crank Nicholson method.
/* variables controlling hsolve integration */
float dt = 1.0e-5
int tab_xdivs = 149; int tab_xfills = 2999
/* This line sets up the size of the tabchannels */
/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
float tab_xmin = -0.10; float tab_xmax = 0.05; float Ca_tab_max = 0.300
/* make filename for input of compartments to save Vm */
str outputcompsfname = "ksg0423a_outputcomps.txt"
/* Make filename for storing a snapshot of the cell for RESTORE */
str snapshotname = "ksg0423a_snapshot.save"
/*Make filenames for output of Membrane Voltage and Synaptic Conductances*/
str data_fname = "./output/Vm_traces.asc"
str gsyn_AMPA_fname = "./output/gsyn_AMPA_traces.asc"
str gsyn_GABA_fname = "./output/gsyn_GABA_traces.asc"
str current_data_fname = "./output/Current_traces.asc"
/*Set up the name for the cell, which will be the hsolve element */
str cellpath = "/gnrh"
/*Set up the name for the Morphology file to be read in, defining the cell */
str dotp = "ksg0423a.p"
//str dotp = "variable.p"
//str dotp = "single_comp.p"
/******************** Cell Specific Parameters for KSG0425a **************************/
//float CM = 0.008179 //0.01 // Result of G.A. for Ksg0425a passive short-cip model
//float RMs = 1.754 // Result of G.A. for Ksg0425a passive short-cip model
//float RMd = {RMs} // keep RM's the same for now
//float RA = 2.362 // Result of G.A. for Ksg0425a passive short-cip model
/***** preset constants *****/
//float ELEAK = -0.0477 //-0.0513// -0.070 // Ek value used for the leak conductance
//float EREST_ACT = -0.05524 //{ELEAK} // -0.056 //-0.0513 //-0.070 // Vm value used for the //RESET
/************************************************************************************
** End of cell-specific parameters for KSG0425a: Uncomment for work on this cell
************************************************************************************/
/****************************** Cell Specific Parameters for KSG0423a ***********/
/***** cable parameters *****/
float CM = 0.0084075 //0.01 // Result of G.A. for Ksg0423a passive short-cip model
float RMs = 3.06381 // Result of G.A. for Ksg0423a passive short-cip model
float RMd = {RMs} // keep RM's the same for now
float RA = 0.966306 // Result of G.A. for Ksg0423a passive short-cip model
/***** preset constants *****/
float ELEAK =-0.070 //-0.0675 //-0.04985 gives RMP = -50 mV RMP
///Resting Membrane Potential(a,b) = -50 mV for ELEAK =-0.06976
//-0.036 from cip response tuning with 20 mV shifted Na and Kdr activations (-38.6 mV RMP)
//-0.048 //-0.048 from model tuning
// -0.05 //-0.0513
// -0.070 // Ek value used for the leak conductance
float EREST_ACT = - 0.050 //-0.05549 // {ELEAK} // -0.059 //-0.070 // Vm value used for the RESET
/************************************************************************************
** End of cell-specific parameters for KSG0423a: Uncomment for work on this cell
************************************************************************************/
float soma_NaF_scale =41 //50 //36 //40 //25 //120
//Resting Membrane Potential(a) = -50 mV for soma_NaF_scale =25
//Resting Membrane Potential(b) = -50 mV for soma_NaF_scale =37
//float soma_NaF_scale = 8
float soma_Kdr_scale =7.7//7.54//7.44 //7.0// 5.78 //4
//Resting Membrane Potential(a) = -50 mV for soma_Kdr_scale =7.14
//Resting Membrane Potential(b) = -50 mV for soma_Kdr_scale =7.40
//float soma_Kdr_scale = 45
float axon_NaF_scale = 7 //2
//float axon_NaF_scale = 25
float axon_Kdr_scale = 50 //50
//float axon_Kdr_scale = 125
float soma_CaL_scale =2.53 // 2.51// 2.69//2.497 //2.88 //2.467 //2.44 // 2.4
float axon_CaL_scale = 2.7
//Resting Membrane Potential(a) = -50 mV for CaL_scale =2.469
//Resting Membrane Potential(b) = -50 mV for CaL_scale =2.48
/* Conductance Scaling Values for Ksg0423a with GnRH synapses
(May not be good for Ksg0425a)*/
float cond_scale_s =1
float cond_scale_a = 1
//float cond_scale_s = 1
//float cond_scale_a = 0.41
/* Conductance Scaling Values for Ksg0425a with GnRH synapses */
//float cond_scale_s = 0.1
//float cond_scale_a = 1.0
float GNa = 28.87 // 28.87
float GKdr = 17.32 // 17.32
float GCaL = 0.9384 // 0.9384
/***** Active Channels ******/
// only used for proto channels
float ECa = 0.1
float GCa = 1, GK = 1, Gh = 1 //GNa = 1
float ENa = 0.060
float GNaFs = {soma_NaF_scale}*{GNa}*{cond_scale_s} //433.1 //48043.0 //75000.0
float GNaFd = 0 //48043.0 //27740.0 //75000.0
float GNaFa = {axon_NaF_scale}*{GNa}*{cond_scale_a} //48043.0 //75000.0
float EK = -0.085
float GKdrs = {soma_Kdr_scale}*{GKdr}*{cond_scale_s} //144.36 //6000.0
float GKdrd = 0
float GKdra = {axon_Kdr_scale}*{GKdr}*{cond_scale_a}
float GCaLs = {GCaL}*{soma_CaL_scale}
float GCaLa = {GCaL}*{soma_CaL_scale}
str syn_compt = "soma" //The compartment with an AMPA synapse
str syn_compt_GABA = "soma" // The compartment with a GABA synapse
float run_time = 0.5 // number of seconds to run simulation
//Synaptic conductances
/**********************************************************************
** The parameters for these synapses were copied from J. Edgerton
** and J. Hanson's GP scripts, specifically "GP1_defaults.g"
** AMPA Synapse parameters revised to reflect data from K. Suter (04)
**********************************************************************/
/***** synapses: *****/
float Adelay = 0.02 //0.05 // Delay before spike train begins (Sec.)
float Awidth = 2 //0.2 // Duration of Spike Train (Sec.)
// msec
float Afreq = 0.1 // Frequency of stimulation (Hz)
float Ainterval = 1/{Afreq} //0.02 // Interval between spikes (Sec.)
// Excitatory inputs
float num_AMPA_syns = 0 //5 // Numnber of synapses
float syn_strength_AMPA = 3 //2.5 //Magnitude of unitary conductance
float G_AMPA_gnrh = 0.50e-9 // 0.5e-9 // base conductance for gnrh AMPA synapse //(0.25e-9 for GP)
float G_AMPA ={syn_strength_AMPA}*{G_AMPA_gnrh}
float tauRise_AMPA = 0.0005
float tauFall_AMPA = 0.0012
float AMPA_freq = 5 // AMPA-mediated excitation is always 1 Hz unless title indicates other
float G_NMDA = {{G_AMPA}*.05} //not used yet!
float tauRise_NMDA = 0.01
float tauFall_NMDA = 0.03
// Inhibitory inputs
float num_GABA_syns = 0
float syn_strength_GABA = 1
float G_GABA_gnrh = 0.5e-9
float GABA_freq = 5
float G_GABA = {syn_strength_GABA}*{G_GABA_gnrh}
float tauRise_GABA = 0.000764
float tauFall_GABA = 0.01210
// Reversal potentials
float E_AMPA = 0
float E_NMDA = 0
float E_GABA = -0.0365