Current Dipole in Laminar Neocortex (Lee et al. 2013)

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Accession:151685
Laminar neocortical model in NEURON/Python, adapted from Jones et al 2009. https://bitbucket.org/jonescompneurolab/corticaldipole
Reference:
1 . Lee S, Jones SR (2013) Distinguishing mechanisms of gamma frequency oscillations in human current source signals using a computational model of a laminar neocortical network. Front Hum Neurosci 7:869 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s):
Channel(s): I Na,t; I K; I M; I Calcium; I h; I T low threshold; I K,Ca;
Gap Junctions:
Receptor(s): GabaA; GabaB; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON (web link to model); Python (web link to model); NEURON; Python;
Model Concept(s): Magnetoencephalography; Temporal Pattern Generation; Activity Patterns; Gamma oscillations; Oscillations; Current Dipole; Touch;
Implementer(s): Lee, Shane [shane_lee at brown.edu];
Search NeuronDB for information about:  GabaA; GabaB; AMPA; NMDA; I Na,t; I T low threshold; I K; I M; I h; I K,Ca; I Calcium;
# expected run time < 10 s with 4 cores
# numbers of cells making up the pyramidal grids
N_pyr_x: 5
N_pyr_y: 5

# maximal conductances for all synapses
# max conductances TO L2Pyrs
gbar_L2Pyr_L2Pyr_ampa: 5e-4
gbar_L2Pyr_L2Pyr_nmda: 5e-4
gbar_L2Basket_L2Pyr_gabaa: 5e-2
gbar_L2Basket_L2Pyr_gabab: 5e-2

# max conductances TO L2Baskets
gbar_L2Pyr_L2Basket: 5e-2
gbar_L2Basket_L2Basket: 0.
# gbar_L2Basket_L2Basket: 2e-2

# max conductances TO L5Pyrs
gbar_L5Pyr_L5Pyr_ampa: 5e-4
gbar_L5Pyr_L5Pyr_nmda: 5e-4
gbar_L2Pyr_L5Pyr: 2.5e-4
gbar_L2Basket_L5Pyr: 1e-3
gbar_L5Basket_L5Pyr_gabaa: 2.5e-2
gbar_L5Basket_L5Pyr_gabab: 1e-2

# max conductances TO L5Baskets
gbar_L5Basket_L5Basket: 2e-2
gbar_L5Pyr_L5Basket: 4e-3
gbar_L2Pyr_L5Basket: 0.

# Ongoing proximal alpha rhythm
distribution_prox: normal
t0_input_prox: 50.
tstop_input_prox: 200.
f_input_prox: 10.
f_stdev_prox: 20.
events_per_cycle_prox: 2

# Ongoing distal alpha rhythm
distribution_dist: normal
t0_input_dist: 50.
tstop_input_dist: 250.
f_input_dist: 0.
f_stdev_dist: 20.
events_per_cycle_dist: 2

# thalamic input amplitudes and delays
input_prox_A_weight_L2Pyr_ampa: 4e-5
input_prox_A_weight_L2Pyr_nmda: 0.
input_prox_A_weight_L5Pyr_ampa: 4e-5
input_prox_A_weight_L5Pyr_nmda: 0.
input_prox_A_weight_inh_ampa: 8e-5
input_prox_A_weight_inh_nmda: 0.
input_prox_A_delay_L2: 0.1
input_prox_A_delay_L5: 1.0

# current values, not sure where these distal values come from, need to check
input_dist_A_weight_L2Pyr_ampa: 4e-5
input_dist_A_weight_L2Pyr_nmda: 0.
input_dist_A_weight_L5Pyr_ampa: 4e-5
input_dist_A_weight_L5Pyr_nmda: 0.
input_dist_A_weight_inh_ampa: 8e-5
input_dist_A_weight_inh_nmda: 0.
input_dist_A_delay_L2: 5.0
input_dist_A_delay_L5: 5.0

# evprox (early) input
t_evprox_early: 5000.
sigma_t_evprox_early: 2.5
gbar_evprox_early_L2Pyr: 1e-3
gbar_evprox_early_L2Basket: 2e-3
gbar_evprox_early_L5Pyr: 5e-4
gbar_evprox_early_L5Basket: 1e-3

# evdist input
dt_evprox0_evdist: -1
t_evdist: 10000.
sigma_t_evdist: 6.
gbar_evdist_L2Pyr: 2e-3
gbar_evdist_L2Basket: 1e-3
gbar_evdist_L5Pyr: 2e-3
# gbar_evdist_L5Pyr: 1e-3

# evprox (late) input
dt_evprox0_evprox1: -1
t_evprox_late: 15000.
sigma_t_evprox_late: 7.
gbar_evprox_late_L2Pyr: 5.3e-3
gbar_evprox_late_L2Basket: 5.3e-3
gbar_evprox_late_L5Pyr: 2.7e-3
gbar_evprox_late_L5Basket: 2.7e-3

# amplitudes of individual gaussian random inputs to L2Pyr and L5Pyr
# L2 Basket params
L2Basket_Gauss_A_weight: 0.
L2Basket_Gauss_mu: 2000.
L2Basket_Gauss_sigma: 3.6
L2Basket_Pois_A_weight: 0.
L2Basket_Pois_lamtha: 0.

# L2 Pyr params
L2Pyr_Gauss_A_weight: 0.
L2Pyr_Gauss_mu: 2000.
L2Pyr_Gauss_sigma: 3.6
L2Pyr_Pois_A_weight: 0.
L2Pyr_Pois_lamtha: 0.

# L5 Pyr params
L5Pyr_Gauss_A_weight: 0.
L5Pyr_Gauss_mu: 2000.
L5Pyr_Gauss_sigma: 4.8
L5Pyr_Pois_A_weight: 0.
L5Pyr_Pois_lamtha: 0.

# L5 Basket params
L5Basket_Gauss_A_weight: 0.
L5Basket_Gauss_mu: 2000.
L5Basket_Gauss_sigma: 2.
L5Basket_Pois_A_weight: 0.
L5Basket_Pois_lamtha: 0.

# Tonic input to L2 Pyramidal cells
Itonic_A_L2Pyr_soma: 0.
Itonic_t0_L2Pyr_soma: 50.
Itonic_T_L2Pyr_soma: -1

# Tonic input to L5 Pyramidal cells
Itonic_A_L5Pyr_soma: 0.
Itonic_t0_L5Pyr_soma: 50.
Itonic_T_L5Pyr_soma: -1

# Numerics
tstop: 250.
dt: 0.025

# Poisson input
T_pois: 1000.