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<html>
  <p/>
  This document describes how to interactively run the model that was
  used in the paper
  <p/>

  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

  <p/>
  If instead you would like to regenerate the figures in the paper
  please consult the <a href="./readme.html">readme.html</a>
  <p/>
  After installing NEURON, compile the mod files in this archives root
  folder with
  <p/>
  nrnivmodl mod_files <p/>
  <h2> To run interactively </h2>
  <p/>
  python3 -i tonic_GABAAR_distal.py
  <p/>
  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).
  <p/>
  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 <b>tonic_GABAAR_distal.py</b> 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:
  <p/>
    set_tonic(0)
  <p/>
  g_region('d', 'exGABALeak', tonic_GABAAR_gbar) to set a constant distribution
  <p/>
  or
  <p/>
  g_piecewise_linear('d','exGABALeak', 200, tonic_GABAAR_gbar, 378.5, tonic_GABAAR_gbar)
  <p/>
  or <p/>
  g_piecewise_linear('d','exGABALeak', start_loc, tonic_GABAAR_gbar, end_loc, tonic_GABAAR_gbar)
  <p/>
  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.
  <p/>
  <h2>generate LVA
  and HVA Ca channel kinetics traces
  interactively </h2>
  <p/> 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:
  <p/>
  python3 -i tonic_GABAAR_distal.py
  <p/> and then after a short time it will stop and you can type on
  the python command line:
  <p/>
  from plot_states_times import *
  <p/>
  and plots of model ion channel kinetics will be displayed.
<h2> recording locations </h2>
  <p/>
  To generate a figure of the 25um spaced voltage and calcium
  recording locations in the apical dendrites run:
  <p/>
  python3 -i recording_location_plots.py
  <p/> Then save the image as a ps (Print to postscript in NEURON's Print & File Window Manager) to convert to other formats:<p/>
  <img src="./images/recording_locations.png" width=400>

</html>