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]
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;
""" params_default.py - master dictionary of modifiable params
    Copyright (C) 2013 Shane Lee and Stephanie Jones

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
"""

# returns default params
def get_params_default():
    """ Note that nearly all start times are set BEYOND tstop for this file
        Most values here are set to whatever default value inactivates them,
        such as 0 for conductance
    """
    p = {
        # simulation end time (ms)
        'tstop': 250.,

        # numbers of cells making up the pyramidal grids
        'N_pyr_x': 1,
        'N_pyr_y': 1,

        # 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.,

        # maximal conductances for all synapses
        # max conductances TO L2Pyrs
        'gbar_L2Pyr_L2Pyr_ampa': 0.,
        'gbar_L2Pyr_L2Pyr_nmda': 0.,
        'gbar_L2Basket_L2Pyr_gabaa': 0.,
        'gbar_L2Basket_L2Pyr_gabab': 0.,

        # max conductances TO L2Baskets
        'gbar_L2Pyr_L2Basket': 0.,
        'gbar_L2Basket_L2Basket': 0.,

        # max conductances TO L5Pyr
        'gbar_L5Pyr_L5Pyr_ampa': 0.,
        'gbar_L5Pyr_L5Pyr_nmda': 0.,
        'gbar_L2Pyr_L5Pyr': 0.,
        'gbar_L2Basket_L5Pyr': 0.,
        'gbar_L5Basket_L5Pyr_gabaa': 0.,
        'gbar_L5Basket_L5Pyr_gabab': 0.,

        # max conductances TO L5Baskets
        'gbar_L5Basket_L5Basket': 0.,
        'gbar_L5Pyr_L5Basket': 0.,
        'gbar_L2Pyr_L5Basket': 0.,

        # Ongoing proximal alpha rhythm
        'distribution_prox': 'normal',
        't0_input_prox': 1000.,
        'tstop_input_prox': 250.,
        'f_input_prox': 10.,
        'f_stdev_prox': 20.,
        'events_per_cycle_prox': 2,

        # Ongoing distal alpha rhythm
        'distribution_dist': 'normal',
        't0_input_dist': 1000.,
        'tstop_input_dist': 250.,
        'f_input_dist': 10.,
        'f_stdev_dist': 20.,
        'events_per_cycle_dist': 2,

        # thalamic input amplitudes abd delays
        'input_prox_A_weight_L2Pyr_ampa': 0.,
        'input_prox_A_weight_L2Pyr_nmda': 0.,
        'input_prox_A_weight_L5Pyr_ampa': 0.,
        'input_prox_A_weight_L5Pyr_nmda': 0.,
        'input_prox_A_weight_inh_ampa': 0.,
        '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': 0.,
        'input_dist_A_weight_L2Pyr_nmda': 0.,
        'input_dist_A_weight_L5Pyr_ampa': 0.,
        'input_dist_A_weight_L5Pyr_nmda': 0.,
        'input_dist_A_weight_inh_ampa': 0.,
        'input_dist_A_weight_inh_nmda': 0.,
        'input_dist_A_delay_L2': 5.,
        'input_dist_A_delay_L5': 5.,

        # evprox (early) feed strength
        'gbar_evprox_early_L2Pyr': 0.,
        'gbar_evprox_early_L5Pyr': 0.,
        'gbar_evprox_early_L2Basket': 0.,
        'gbar_evprox_early_L5Basket': 0.,

        # evprox (late) feed strength
        'gbar_evprox_late_L2Pyr': 0.,
        'gbar_evprox_late_L5Pyr': 0.,
        'gbar_evprox_late_L2Basket': 0.,
        'gbar_evprox_late_L5Basket': 0.,

        # evdist feed strengths
        'gbar_evdist_L2Pyr': 0.,
        'gbar_evdist_L5Pyr': 0.,
        'gbar_evdist_L2Basket': 0.,

        # times and stdevs for evoked responses
        't_evprox_early': 2000.,
        'sigma_t_evprox_early': 2.5,

        'dt_evprox0_evdist': -1,
        't_evdist': 2000.,
        'sigma_t_evdist': 6.,

        'dt_evprox0_evprox1': -1,
        't_evprox_late': 2000.,
        'sigma_t_evprox_late': 7.,

        # IClamp params for L2Pyr
        'Itonic_A_L2Pyr_soma': 0.,
        'Itonic_t0_L2Pyr_soma': 0.,
        'Itonic_T_L2Pyr_soma': -1.,

        # IClamp param for L2Basket
        'Itonic_A_L2Basket': 0.,
        'Itonic_t0_L2Basket': 0.,
        'Itonic_T_L2Basket': -1.,

        # IClamp params for L5Pyr
        'Itonic_A_L5Pyr_soma': 0.,
        'Itonic_t0_L5Pyr_soma': 0.,
        'Itonic_T_L5Pyr_soma': -1.,

        # IClamp param for L5Basket
        'Itonic_A_L5Basket': 0.,
        'Itonic_t0_L5Basket': 0.,
        'Itonic_T_L5Basket': -1.,

        # default end time for pois inputs
        't0_pois': 0.,
        'T_pois': -1,
        'dt': 0.025,
    }

    # grab cell-specific params and update p accordingly
    p_L2Pyr = get_L2Pyr_params_default()
    p_L5Pyr = get_L5Pyr_params_default()
    p.update(p_L2Pyr)
    p.update(p_L5Pyr)

    return p

# returns default params for L2 pyramidal cell
def get_L2Pyr_params_default():
    return {
        # Soma
        'L2Pyr_soma_L': 22.1,
        'L2Pyr_soma_diam': 23.4,
        'L2Pyr_soma_cm': 0.6195,
        'L2Pyr_soma_Ra': 200.,

        # Dendrites
        'L2Pyr_dend_cm': 0.6195,
        'L2Pyr_dend_Ra': 200.,

        'L2Pyr_apicaltrunk_L': 59.5,
        'L2Pyr_apicaltrunk_diam': 4.25,

        'L2Pyr_apical1_L': 306.,
        'L2Pyr_apical1_diam': 4.08,

        'L2Pyr_apicaltuft_L': 238.,
        'L2Pyr_apicaltuft_diam': 3.4,

        'L2Pyr_apicaloblique_L': 340.,
        'L2Pyr_apicaloblique_diam': 3.91,

        'L2Pyr_basal1_L': 85.,
        'L2Pyr_basal1_diam': 4.25,

        'L2Pyr_basal2_L': 255.,
        'L2Pyr_basal2_diam': 2.72,

        'L2Pyr_basal3_L': 255.,
        'L2Pyr_basal3_diam': 2.72,

        # Synapses
        'L2Pyr_ampa_e': 0.,
        'L2Pyr_ampa_tau1': 0.5,
        'L2Pyr_ampa_tau2': 5.,

        'L2Pyr_nmda_e': 0.,
        'L2Pyr_nmda_tau1': 1.,
        'L2Pyr_nmda_tau2': 20.,

        'L2Pyr_gabaa_e': -80.,
        'L2Pyr_gabaa_tau1': 0.5,
        'L2Pyr_gabaa_tau2': 5.,

        'L2Pyr_gabab_e': -80.,
        'L2Pyr_gabab_tau1': 1.,
        'L2Pyr_gabab_tau2': 20.,

        # Biophysics soma
        'L2Pyr_soma_gkbar_hh': 0.01,
        'L2Pyr_soma_gnabar_hh': 0.18,
        'L2Pyr_soma_el_hh': -65.,
        'L2Pyr_soma_gl_hh': 4.26e-5,
        'L2Pyr_soma_gbar_km': 250.,

        # Biophysics dends
        'L2Pyr_dend_gkbar_hh': 0.01,
        'L2Pyr_dend_gnabar_hh': 0.15,
        'L2Pyr_dend_el_hh': -65.,
        'L2Pyr_dend_gl_hh': 4.26e-5,
        'L2Pyr_dend_gbar_km': 250.,
    }

# returns default params for L5 pyramidal cell
def get_L5Pyr_params_default():
    return {
        # Soma
        'L5Pyr_soma_L': 39.,
        'L5Pyr_soma_diam': 28.9,
        'L5Pyr_soma_cm': 0.85,
        'L5Pyr_soma_Ra': 200.,

        # Dendrites
        'L5Pyr_dend_cm': 0.85,
        'L5Pyr_dend_Ra': 200.,

        'L5Pyr_apicaltrunk_L': 102.,
        'L5Pyr_apicaltrunk_diam': 10.2,

        'L5Pyr_apical1_L': 680.,
        'L5Pyr_apical1_diam': 7.48,

        'L5Pyr_apical2_L': 680.,
        'L5Pyr_apical2_diam': 4.93,

        'L5Pyr_apicaltuft_L': 425.,
        'L5Pyr_apicaltuft_diam': 3.4,

        'L5Pyr_apicaloblique_L': 255.,
        'L5Pyr_apicaloblique_diam': 5.1,

        'L5Pyr_basal1_L': 85.,
        'L5Pyr_basal1_diam': 6.8,

        'L5Pyr_basal2_L': 255.,
        'L5Pyr_basal2_diam': 8.5,

        'L5Pyr_basal3_L': 255.,
        'L5Pyr_basal3_diam': 8.5,

        # Synapses
        'L5Pyr_ampa_e': 0.,
        'L5Pyr_ampa_tau1': 0.5,
        'L5Pyr_ampa_tau2': 5.,

        'L5Pyr_nmda_e': 0.,
        'L5Pyr_nmda_tau1': 1.,
        'L5Pyr_nmda_tau2': 20.,

        'L5Pyr_gabaa_e': -80.,
        'L5Pyr_gabaa_tau1': 0.5,
        'L5Pyr_gabaa_tau2': 5.,

        'L5Pyr_gabab_e': -80.,
        'L5Pyr_gabab_tau1': 1.,
        'L5Pyr_gabab_tau2': 20.,

        # Biophysics soma
        'L5Pyr_soma_gkbar_hh': 0.01,
        'L5Pyr_soma_gnabar_hh': 0.16,
        'L5Pyr_soma_el_hh': -65.,
        'L5Pyr_soma_gl_hh': 4.26e-5,
        'L5Pyr_soma_gbar_ca': 60.,
        'L5Pyr_soma_taur_cad': 20.,
        'L5Pyr_soma_gbar_kca': 2e-4,
        'L5Pyr_soma_gbar_km': 200.,
        'L5Pyr_soma_gbar_cat': 2e-4,
        'L5Pyr_soma_gbar_ar': 1e-6,

        # Biophysics dends
        'L5Pyr_dend_gkbar_hh': 0.01,
        'L5Pyr_dend_gnabar_hh': 0.14,
        'L5Pyr_dend_el_hh': -71.,
        'L5Pyr_dend_gl_hh': 4.26e-5,
        'L5Pyr_dend_gbar_ca': 60.,
        'L5Pyr_dend_taur_cad': 20.,
        'L5Pyr_dend_gbar_kca': 2e-4,
        'L5Pyr_dend_gbar_km': 200.,
        'L5Pyr_dend_gbar_cat': 2e-4,
        'L5Pyr_dend_gbar_ar': 1e-6,
    }

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