This document describes how to interactively run the model that was used in the paper

Chiayu Q. Chiu*, Thomas M. Morse*, Karima AitOuares, Lauren C. Panzera, Paras A. Patel, Francesca Nani, Frederic Knoflach, Maria-Clemencia Hernandez, Monika Jadi, Michael J. Higley (2026) SST interneurons facilitate dendritic calcium signaling via tonic activation of alpha5-GABA receptors Neuron

If instead you would like to regenerate the figures in the paper please consult the readme.html

After installing NEURON, compile the mod files in this archives root folder with

nrnivmodl mod_files

## To run interactively

python3 -i tonic_GABAAR_distal.py

The default tonic GABAA receptors are distributed at a constant density throughout the dendrites however we also explored distal and upward ramp distributions (hence the name distal in the script name). There were similar results with those alternative distributions in this model (not shown).

It takes 30 seconds to run, first in the control and then in the blocked condition. Note that a distal or constant tonic GABAA receptor distribution can be selected by setting the "distribution" variable circa line 66 in configure_sim.py which creates the tonic_GABAR_gbar.py. See code and below for details. Note (that running) the tonic_GABAAR_distal.py script is the main way vector (time-series) results (voltages, currents, conductances, etc.) are generated (the calcium suppression figure also relies on it). After the model has run, to interactively turn tonic GABAARs off, then (presumably after running or exploring some feature), back on at a constant, or alternatively distal distribution type at the NEURON-python prompt:

set_tonic(0)

g_region('d', 'exGABALeak', tonic_GABAAR_gbar) to set a constant distribution

or

g_piecewise_linear('d','exGABALeak', 200, tonic_GABAAR_gbar, 378.5, tonic_GABAAR_gbar)

or

g_piecewise_linear('d','exGABALeak', start_loc, tonic_GABAAR_gbar, end_loc, tonic_GABAAR_gbar)

Note that tonic_GABAAR_gbar is set to (a) default conductance of the GABAAR channels and after tonic_GABAR_distal.py is run you can access the V's, ica's, and cai's from the session_record dictionary which holds these elements in a dictionary that has keys of conductance state ('blocked' or 'control') of the constant or distal tonic GABAA Receptor (tGAR) maximum conductance and the distance to a dendritic location, and values of lists of voltage vectors recorded under those conditions. The names of the locations are stored in dendrite_names[distances]. Other session_record dicts have the time series of the quantities indicated in their names and have the same keys as the above described voltage dict. Here is a complete list of them: bAP_stimulation_session_record cai_session_record g_hva_session_record g_lva_session_record h_hva_session_record h_lva_session_record ica_hva_session_record ica_lva_session_record m_hva_session_record m_lva_session_record session_record. Note that soma_v_session_record and soma_AP_t_session_record also exist, with only the tonic GABAA Receptor status ('blocked' or 'control') key.

## generate LVA and HVA Ca channel kinetics traces interactively

If you want to examine the kinetics of channels manually, the states_times.py module can be used. For example to see the ion channel kinetics you can start an example run like:

python3 -i tonic_GABAAR_distal.py

and then after a short time it will stop and you can type on the python command line:

from plot_states_times import *

and plots of model ion channel kinetics will be displayed.

## recording locations

To generate a figure of the 25um spaced voltage and calcium recording locations in the apical dendrites run:

python3 -i recording_location_plots.py

Then save the image as a ps (Print to postscript in NEURON's Print & File Window Manager) to convert to other formats: