//====================================================================
// simulation parameter
//====================================================================
//***** Integration time (at least for interneurons)*/
float dt = 1e-5
setclock 0 {dt}
//*****Data collection time*/
float dt2 = 5e-4
setclock 1 {dt2}
float dt3 = 1e-4 // Clock used for extracellular field object
setclock 2 {dt3}
//float sim_time=0.2 // Total simulation runtime
// Injection currents (From Neymotin / Traub)
//float pyr_inject = 50.0e-12 // Value used in Neymotin paper
float pyr_inject = 200.0e-12 // Value used in Traub91.g
float bc_inject = 0.0 // From Neymotin 2011
float olm_inject = -25.0e-12 // From Neymotin 2011
float msg_inject = 1.885e-11 // From Hajos 2004
// Injection currents (From Hajos / Traub)
float pyr_inject = 200.0e-12 // From Traub 1991
float bc_inject = 1.7592904e-11 // From Hajos 2004
float olm_inject = 0.0 // From Hajos 2004
float msg_inject = 1.885e-11 // From Hajos 2004
//====================================================================
// Dataset paths
//====================================================================
str gp, pp, sp
gp = "./dataset_temp/"
pp = "0_def/"
sp = "t0/"
gp = "./dataset_temp/"
pp = ""
sp = ""
gp = {{dataoutput_path} @ "/"} // Davedit
pp = {{expname_path} @ "/"} // Davedit
sp = {{circtime_path} @ "/"} // Davedit
//============================================================
// network dimensions
//==========================================================
if (small_net)
int pyr_nx = 2 // number of pyramidal cells along x-axis
int pyr_ny = 1 // number of pyramidal cells along y-axis
int olm_nx = 2 // number of feedback interneurons along x-axis
int olm_ny = 1 // number of feedback interneurons along y-axis
int bc_nx = 2 // number of feedforward interneurons along x-axis
int bc_ny = 1 // number of feedforward interneurons along y-axis
int msg_nx = 2 // number of feedforward interneurons along x-axis
int msg_ny = 1 // number of feedforward interneurons along y-axis
if (include_msg_aff_input)
msg_nx = 25
msg_ny = 1
end
else
int pyr_nx = 200 // number of pyramidal cells along x-axis
int pyr_ny = 1 // number of pyramidal cells along y-axis
int olm_nx = 25 // number of feedback interneurons along x-axis
int olm_ny = 1 // number of feedback interneurons along y-axis
int bc_nx = 25 // number of feedforward interneurons along x-axis
int bc_ny = 1 // number of feedforward interneurons along y-axis
int msg_nx = 25 // number of feedforward interneurons along x-axis
int msg_ny = 1 // number of feedforward interneurons along y-axis
end
int n_of_pyr // number of pyramidal cells in array
n_of_pyr = {pyr_nx}*{pyr_ny}
float pyr_dx = 10e-6 // distance between pyramidal cells in x-dimension
float pyr_dy = 10e-6 // distance between pyramidal cells in y-dimension
float pyr_origin_x = 0 // x-coordinate for first element in network
float pyr_origin_y = 0 // y-coordinate for first element in network
int n_of_olm // number of feedback interneurons in array
n_of_olm = {olm_nx}*{olm_ny}
float olm_dx = 20e-6 // distance between olm interneurons in x-dimension
float olm_dy = 40e-6 // distance between olm interneurons in y-dimension
float olm_origin_x = 5e-6 // x-coordinate for first element in network
float olm_origin_y = 5e-6 // y-coordinate for first element in network
int n_of_bc // number of feedforward interneurons in array
n_of_bc = {bc_nx}*{bc_ny}
float bc_dx = 20e-6 // distance between bc interneurons in x-dimension
float bc_dy = 40e-6 // distance between bc interneurons in y-dimension
float bc_origin_x = 5e-6 // x-coordinate for first element in network
float bc_origin_y = 25e-6 // y-coordinate for first element in network
int n_of_msg // number of feedforward interneurons in array
n_of_msg = {msg_nx}*{msg_ny}
float msg_dx = 20e-6 // distance between msg interneurons in x-dimension
float msg_dy = 40e-6 // distance between msg interneurons in y-dimension
float msg_origin_x = 5e-6 // x-coordinate for first element in network
float msg_origin_y = 50e-6 // y-coordinate for first element in network
//Biophysical constants for HN network
float E_AMPA = 0.0
float E_NMDA = 0.0
float E_GABA_A = -0.080
// Frequencies for background synaptic activity
float freq_bkgnd = 1000
float freq_bkgnd_pyr = 1000
float freq_bkgnd_olm = 1000
float freq_bkgnd_nmda = 10
float freq_bkgnd_nmda_pyr = 10
if (noise_off)
float freq_bkgnd = 0
float freq_bkgnd_pyr = 0
float freq_bkgnd_olm = 0
float freq_bkgnd_nmda = 0
float freq_bkgnd_nmda_pyr = 0
end
// Gmaxes for background synaptic activity
float Gmax_pyr_soma_AMPA = 0.05e-9
float Gmax_pyr_dend_AMPA = 0.05e-9
float Gmax_bc_soma_AMPA = 0.02e-9
float Gmax_olm_soma_AMPA = 0.0625e-9
float Gmax_pyr_soma_GABA_A = 0.012e-9
float Gmax_pyr_dend_GABA_A = 0.012e-9
float Gmax_bc_soma_GABA_A = 0.2e-9
float Gmax_olm_soma_GABA_A = 0.2e-9
float Gmax_pyr_dend_NMDA = 6.5e-9
// Gmaxes for CA3 network
float pyr2pyr_AMPA = 0.02e-9
float pyr2bc_AMPA = 0.36e-9
float pyr2olm_AMPA = 0.36e-9
float bc2pyr_GABA_A = 0.72e-9
float bc2bc_GABA_A = 4.5e-9
float olm2pyr_GABA_A = 72e-9
//float msg2bc_GABA_A = 1.6e-9 // From Neymotin 2011
//float msg2olm_GABA_A = 1.6e-9 // From Neymotin 2011
float msg2bc_GABA_A = 0.5e-9 // From Hajos 2004
float msg2olm_GABA_A = 0.5e-9 // From Hajos 2004
float msg2msg_GABA_A = 0.25e-9 // From Hajos 2004
float olm2bc_GABA_A = 0.88e-9 // From Hajos 2004
float olm2msg_GABA_A = 0.5e-9 // From Hajos 2004
float pyr2pyr_NMDA = 0.004e-9
float pyr2bc_NMDA = 1.38e-9
float pyr2olm_NMDA = 0.7e-9
// Synaptic time constants
float AMPA_tau1 = 0.05e-3
float AMPA_tau2 = 5.3e-3
float NMDA_tau1 = 15e-3
float NMDA_tau2 = 150e-3
float GABAA_tau1=0.07e-3 // Neymotin 2011
float GABAA_tau2=9.1e-3 // Neymotin 2011
float GABAA_OLM_tau1 = 0.2e-3 // Neymotin 2011
float GABAA_OLM_tau2 = 20e-3 // Neymotin 2011
float GABAA_MS_tau1 = 20e-3 // Neymotin 2011
float GABAA_MS_tau2 = 40e-3 // Neymotin 2011
float GABAA_MS_tau1 = 0.07e-3 // Davedit (follow same pattern as Hajos, using default GABA const here)
float GABAA_MS_tau2 = 9.1e-3 // Davedit (follow same pattern as Hajos, using default GABA const here)
float Q10_synapse = 1.0
// Destination compartments
str pyr2pyr_compt = "basal_5"
str olm2pyr_compt = "apical_18"
// Connectivity convergences
int pyr2pyr_conv = 25
int pyr2bc_conv = 100
int pyr2olm_conv = 10
int bc2pyr_conv = 50
int bc2bc_conv = 60
int olm2pyr_conv = 20
//int msg2bc_conv = 1 //Neymotin 2011
//int msg2olm_conv = 1 //Neymotin 2011
int msg2bc_conv = 10 //Hajos 2004
int msg2olm_conv = 10 //Hajos 2004
int msg2msg_conv = 10 //Hajos 2004
int olm2bc_conv = 5 //Hajos 2004
int olm2msg_conv = 2 //Hajos 2004
//Traub connectivities
int pyr2pyr_conv = 10
int pyr2bc_conv = 20
int pyr2olm_conv = 10
int bc2pyr_conv = 15
int bc2bc_conv = 25
int olm2pyr_conv = 10
//int msg2bc_conv = 1 //Neymotin 2011
//int msg2olm_conv = 1 //Neymotin 2011
int msg2bc_conv = 5 //Hajos 2004
int msg2olm_conv = 5 //Hajos 2004
int msg2msg_conv = 10 //Hajos 2004
int olm2bc_conv = 5 //Hajos 2004
int olm2msg_conv = 2 //Hajos 2004
if (test_synapses)
pyr2bc_conv = 1
pyr2pyr_conv = 1
pyr2pyr_conv = 1
pyr2bc_conv = 1
pyr2olm_conv = 1
bc2pyr_conv = 1
bc2bc_conv = 1
olm2pyr_conv = 1
msg2bc_conv = 1
msg2olm_conv = 1
msg2msg_conv = 1
end
//==============================================================
// spike generator and randomspike parameters
//==============================================================
float int_refract_HN = 0.001 // sec; refractory-period
float pyr_refract_HN = 0.001 // sec; allows discrimination of single action
float AFF_min_amp = 1 // parameters for randomspike
float AFF_max_amp = 1 // all spikes have unit amplitude
float AFF_rate = 40 // 50 spikes per second; Reinouds suggestion
float AFF_abs_refract = 0.001 // 0.005 consecutive events cannot occur in an
// interval shorter than abs_refract
//=================================================================
// randomization of variables
//=================================================================
float rand_Vinit=-0.010
float rand_VEm=-0.002
//rand_inj=
//=================================================================
// elektrode information
//=================================================================
str e_recsite1 = "/rec_site"
float e_z1_min = -55e-6 // -50e-6; -60e-6; -130e-6 level of lowest recording site for one electrode
float e_z1_max = 96e-6 // 200e-6; 160e-6; 150; 151e-6; 221e-6 since 150 was not used correctly level of highest recording site
float e_dz1 = 12.5e-6 // distance between recording sites of electrode
float e_scale1 = -15 // -50; -10; -15; -30 scale factor used in efield-object
int n_of_e90 = { {{e_z1_max} - {e_z1_min}} / {e_dz1} + 1}
//=================================================================
// conduction velocities and percentage of randomization for delay
//=================================================================
float cond_vel_pyr_ax = 0.5 // m*s^-1; pyramidal cell axons are myelinated
float cond_vel_int_ax = 0.1 // unmyelinated
//float pyr_refract_HN = 0.1 // sec; allows discrimination of single action
float pyr2pyr_NMDA = 0.008e-9
float pyr2bc_NMDA = 0.0034e-9 //davedit
float pyr2olm_NMDA = 0.0034e-9 //davedit
// Tune EPSPs and IPSPs to literature values!
float pyr2pyr_AMPA = 2.6e-9 //Tuned to EPSP value based on Traub - Fast Oscillations (1999). EPSP of 1.0mV @ -65mV
float pyr2bc_AMPA = 0.05e-9 //Tuned to EPSP value based on Traub - Fast Oscillations (1999); Taxidis 2011. EPSP of ~1.5mV @ -65mV
float pyr2olm_AMPA = 0.05e-9 //Tuned to EPSP value based on Traub - Fast Oscillations (1999); Taxidis 2011. EPSP of ~1.4mV @ -65mV
float bc2pyr_GABA_A = 9.2e-9 //Tuned to IPSP value based on Traub - Fast Oscillations (1999). IPSP of ~1.2mV @ -62mV
float olm2pyr_GABA_A = 8.3e-9 //Tuned to IPSP value based on Traub - Fast Oscillations (1999). IPSP of ~1.0mV @ -62mV
float bc2bc_GABA_A = 0.125e-9 //From Hajos et al, 2004; This approximates that used by Taxidis et al (2011). (~0.6mV IPSP)
//
//// Alter afferent input ratio adjustment
////float Gmax_pyr_soma_AMPA = 0.8e-9 //Davedit
////float Gmax_pyr_dend_AMPA = 0.8e-9 //Davedit
//float Gmax_bc_soma_AMPA = 0.00278e-9
//float Gmax_olm_soma_AMPA = 0.00868e-9
//float Gmax_pyr_soma_GABA_A = 0.153e-9
//float Gmax_pyr_dend_GABA_A = 0.153e-9
//float Gmax_bc_soma_GABA_A = 0.00556e-9
//float Gmax_olm_soma_GABA_A = 0.00556e-9
//float Gmax_pyr_dend_NMDA = 6.5e-9
// Adjust afferent input to produce Vm fluctuations at -65mV of approximately 1.5mV standard deviation
float Gmax_olm_soma_AMPA = 0.03e-9
float Gmax_olm_soma_GABA_A = 0.01e-9
float Gmax_bc_soma_AMPA = 0.03e-9
float Gmax_bc_soma_GABA_A = 0.01e-9
float Gmax_pyr_soma_GABA_A = 2.5e-9
float Gmax_pyr_dend_GABA_A = 2.5e-9
// Gmaxes for background synaptic activity
//float Gmax_pyr_soma_AMPA = 0.05e-9
//float Gmax_pyr_dend_AMPA = 0.05e-9
//float Gmax_pyr_soma_GABA_A = 0.012e-9
//float Gmax_pyr_dend_GABA_A = 0.012e-9
// Adjust input currents for new afferent input
//float pyr_inject = 320.0e-12 // From Traub 1991
//float bc_inject = 0.8592904e-11 // From Hajos 2004
//float olm_inject = -0.20e-11 // From Hajos 2004
//float msg_inject = 1.885e-11 // From Hajos 2004
//float msg_inject = 2.00e-11 // From Hajos 2004 // Increased to compensate for olm->msg connectivity
//float bc_inject = 1.3592904e-11 // Increase this again to get back gamma rhythms
float pyr_inject = {pyr_inject0} // From Traub 1991
float bc_inject = 3.8592904e-11 // From Hajos 2004
float olm_inject = 1.0592904e-11 // From Hajos 2004
float msg_inject = 1.885e-11 // From Hajos 2004
float bc_inject = 1.1592904e-11 // From Hajos 2004
float olm_inject = -0.25e-11 // From Neymotin 2010
float msg_inject = 1.885e-11 // From Hajos 2004
float bc_inject = 0.40e-11 // From Hajos 2004
float bc_inject = {bc_inject0} // From Hajos 2004
float olm_inject = {olm_inject0} // From Neymotin 2010
float msg_inject = {msg_inject0} // From Hajos 2004
//
////Tuning Adjustments
//int pyr2pyr_conv = 25
//int pyr2bc_conv = 100
////int pyr2olm_conv = 10
//float bc2pyr_GABA_A = 4.6e-9 //Tuned to IPSP value based on Traub - Fast Oscillations (1999). IPSP of ~1.2mV @ -62mV
////float pyr2pyr_AMPA = 5.2e-9 //Tuned to EPSP value based on Traub - Fast Oscillations (1999). EPSP of 1.0mV @ -65mV
//float Gmax_pyr_soma_AMPA = 0.05e-9 //Neymotin original
//float Gmax_pyr_dend_AMPA = 0.05e-9
//
float bc2pyr_GABA_A = {bc2pyr_GABA_A0} //Tuned to IPSP value based on Traub - Fast Oscillations (1999). IPSP of ~1.2mV @ -62mV
float pyr2pyr_AMPA = {pyr2pyr_AMPA0} //Tuned to EPSP value based on Traub - Fast Oscillations (1999). EPSP of 1.0mV @ -65mV
float Gmax_pyr_soma_AMPA = {Gmax_pyr_bkgnd0} //Neymotin original
float Gmax_pyr_dend_AMPA = {Gmax_pyr_bkgnd0}
if (enable_olm2bc_synapse)
bc_inject = bc_inject + 0.5e-11 // From Hajos 2004
// Should be around this: bc_inject = 1.5592904e-11 // From Hajos 2004
end
if (bc_gammanet)
bc2pyr_conv = 10
bc_inject = 1.0592904e-11
// bc_inject = 1.3592904e-11 // Increase this again to get back gamma rhythms
bc2bc_conv = 20
// Gmax_pyr_soma_GABA_A = 0.0e-9
// Gmax_pyr_dend_GABA_A = 0.0e-9
pyr_inject = 220.0e-12 // From Traub 1991
// pyr2bc_conv = 100 // Set to 100 to reduce bursting, get sporadic behaviour
end
//Disable connections
//float pyr2pyr_AMPA = 0.0
//float pyr2bc_AMPA = 0.0
//float pyr2olm_AMPA = 0.0
//float bc2pyr_GABA_A = 0.0
//float bc2bc_GABA_A = 0.025e-9
//float olm2pyr_GABA_A = 0.0
//float msg2bc_GABA_A = 0.0 // From Hajos 2004
//float msg2olm_GABA_A = 0.0 // From Hajos 2004
//float msg2msg_GABA_A = 0.0 // From Hajos 2004
//float pyr2pyr_NMDA = 0.0
//float pyr2bc_NMDA = 0.0
//float pyr2olm_NMDA = 0.0
if (test_synapses)
float bc_inject = 0.22904e-11
float olm_inject = 0.0
end
//int msg2bc_conv = 20 //Davedit -- increased septal influence (maybe not necessary)
//int msg2olm_conv = 20 //Davedit -- increased septal influence (maybe not necessary)
int msg2bc_div = msg2bc_conv * n_of_bc / n_of_msg
int msg2olm_div = msg2olm_conv * n_of_olm / n_of_msg
//============================================================
// network dimensions
//==========================================================
int AFF_nx = 4 // number of randomspike elements along x-axis
int AFF_ny = 4 // number of randomspike elements along y-axis
int n_of_AFF // number of randomspike elements in array
n_of_AFF = {AFF_nx}*{AFF_ny}
float AFF_dx = 15e-6 // distance between randomspike elements in x-dimension
float AFF_dy = 15e-6 // distance between randomspike elements in y-dimension
float AFF_origin_x_1 = 0 // x-coordinate for first element in network
float AFF_origin_y_1 = 0 // y-coordinate for first element in network
float AFF_origin_x_2 = 0 // x-coordinate for first element in network
float AFF_origin_y_2 = 60e-6 // y-coordinate for first element in network
//===================================================================
// x1,y1,z1, x2,y2,z2 for destination mask of volumeconnect
//==================================================================
float AFF2ca3_x1 = -1 // meter
float AFF2ca3_y1 = -1 // employment of this huge number ensures, that
float AFF2ca3_z1 = -1 // connections are made from each element in the
float AFF2ca3_x2 = 1 // source region to each element in the destination
float AFF2ca3_y2 = 1 // region; AFFerents can have contacts to
float AFF2ca3_z2 = 1 // ca3amidal cells everywhere in the network
float AFF2bc_x1 = -1 // meter
float AFF2bc_y1 = -1 // AFFerents can have contacts to bc interneurons
float AFF2bc_z1 = -1 // everywhere in the network
float AFF2bc_x2 = 1 //
float AFF2bc_y2 = 1 //
float AFF2bc_z2 = 1 //
float ca32ca3_x1 = -1 // meter
float ca32ca3_y1 = -1 // employment of this huge number ensures, that
float ca32ca3_z1 = -1 // connections are made from each element in the
float ca32ca3_x2 = 1 // source region to each element in the destination
float ca32ca3_y2 = 1 // region; ca3amidal cells can have contacts to other
float ca32ca3_z2 = 1 // ca3amidal cell everywhere in the network
float ca32olm_x1 = -1 // ca3amidal cells contact olm interneurons everywhere
float ca32olm_y1 = -1 // in the network
float ca32olm_z1 = -1
float ca32olm_x2 = 1
float ca32olm_y2 = 1
float ca32olm_z2 = 1
float olm2ca3_x1 = 0 // interneurons are only allowed to contact ca3amidal
float olm2ca3_y1 = 0 // cells within a distance of 500microns from the
float olm2ca3_z1 = 0 // respective interneuron; since relative positions
float olm2ca3_x2 = 1000e-6 // and elipsoidal sourcemask are used, 0,0,0 gives
float olm2ca3_y2 = 1000e-6 // the position of the interneuron(center of ellipse)
float olm2ca3_z2 = 1000e-6 // x2,y2,z2 specify lengthes of the axis
float bc2ca3_x1 = 0
float bc2ca3_y1 = 0
float bc2ca3_z1 = 0
float bc2ca3_x2 = 1000e-6
float bc2ca3_y2 = 1000e-6
float bc2ca3_z2 = 1000e-6
//=================================================================
// conduction velocities and percentage of randomization for delay
//=================================================================
float cond_vel_ca3_ax = 0.5 // m*s^-1; ca3amidal cell axons are supposed to be
// myelinated
float cond_vel_olm_ax = 0.2 // unmyelinated
float cond_vel_bc_ax = 0.2 // unmyelinated
float cond_vel_AFF_ax = 0.2 // mossy fibers are unmyelinated (Shepherd)
float rand_delay_ca3_ax = 0.15 // calculated delay +/- upto 15% (connections.g)
float rand_delay_olm_ax = 0.15
float rand_delay_bc_ax = 0.15
float rand_delay_AFF_ax = 0.15
//================================================
// synaptic weights used in volumeweight-function
//===============================================
float from_AFF_weight = 1 // gmax defined by values in cell descriptor files
// AMPA 100.0 in cell descriptor file of bc-interneurons
float from_ca3_weight = 1 // ca3amidal cell on presynaptic site
// AMPA 1.0 in cell descriptor file of olm-interneurons
float from_olm_weight = 1 // olm interneuron on presynaptic site
float from_bc_weight = 1 // bc interneuron on presynaptic site
float rand_from_AFF_weight = 0.15 // calculated weight +/- up to 15%
float rand_from_ca3_weight = 0.15
float rand_from_olm_weight = 0.15
float rand_from_bc_weight = 0.15
float injcurr = 0 // default injection
float bc_hold_cur = -0.03e-9 // Traub II: -0.045 nA current suppreses spontaneo // us firing
float olm_hold_cur = -0.03e-9 // holding currents not employed
float ca3_hold_cur = -0.07e-9
//====================================================================
// hines solver
//====================================================================
int chanmode = 1 // 3
/* chanmodes 0 and 3 allow outgoing messages to non-hsolved elements.
chanmode 3 is fastest.
*/
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