This model is used to help interpret signals underlying GCaMP6f fluorescence.

input parameters are contained in a json file (inputs.json). information and units are provided in a inputs_units.txt

to run on a local machine, use driver.py. to specify which simulation, turn on the appropriate toggle within the inputs
file (e.g. "silentdend = 1")

to run on a remote machine, set up the simulations in run_all_sims_bash.sh. In this file, the specified job array
corresponds to the simulations run in run_all_sims_quest.py. these are the same as driver.py, but the task id number
turns on the appropriate simulation toggle (e.g. pindex = 10 turns on "silentdend").

within these driver files:
depending on the simulation, several parameters are updated before the model is setup (e.g. nablock ~= 0 for invitro)
these parameters also include stimulation parameters such as number of stimulations, time between stimulations, etc, to
be executed within protocols.py.

Then model_setup.py is executed.

Within this file:
    -certain parameters are adjusted from standard units (e.g. KD in nM) to neuron's default units (mM)
    -the morphology is read in
    -dendritic membrane conductances updated to reflect diameter fraction
    -spines are created and added to morphology
    -dendrites are made homogeneous (this toggle is on by default)
    -all mechanisms are added to sections via insert_channels.py
    -somatic membrane conductances updated to reflect diameter fraction
    -rxd species created, rxd reactions set up via setup_RxD.py
    -ampa and nmda channels added to spines via insert_syns

model_setup is identical for all simulations.

Next, protocols.py is executed. "sim" parameter (a boolean) determines what is executed (what protocol/stimulation to run) for each
simulation.

In driver.py, setup_neuron_gui.py is executed. in run_all_sims_quest.py, this toggle is turned off.
This allows one to view the simulation as it happens.

Lastly, the simulation is started via runmodel_func.py. This is also where output is set up via record.py. Output is a
dictionary, which can be used directly on a local machine, or is saved as a pickle file by default on a remote machine,
using the job array number and simulation name.

Also saved are the maximum df/f and maximum voltage values in every section, again identified by job and simulation name.

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Post-processing:

write-max-data.py
- using job number and sim name, and same inputs as simulation, this file plots the maximum voltage and df/f that every
section reached during that given simulation.
- it also plots the maximum df/f for every basal branch against distance from soma
- can also turn toggles on to save specific outputs to pickle, then plot this pickle file in plot_dspike_APs_waterfall.py


plot_quest_run.py
- reads in output dictionary using job id and simulation name
- runs sim_plots.py to read in components of output dictionary into plottable form
- can run multiple plotting files from there:
     - plot_figures.py = general summary information
     - plot_hotspots.py = detailed look at currents in soma and dendrite of interest (basal[19])


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mod files:

- gmax.mod, gmax_plot.mod, camax.mod and vmax.mod are for keeping track of maximum values, used in the neuron gui and
for plotting purposes only.
- the rest are ion channels, inserted within insert_channels.py
- gmax.mod allows for plotting of df/f