This repository contains the Neuron and Arbor implementations and simulations of

1. A single basket cell
2. A single granule cell

1. The basket cell is a single soma model
2. The granule cell reads the morphology from output0_updated.swc in the morphologies directory

The basket and granule cells both have the following mechanisms inserted on the soma and dendrites:

1. borgka.mod
2. cagk.mod
3. cat.mod
4. ccanl.mod
5. gskch.mod
6. ichan2.mod
7. lca.mod
8. nca.mod

Various parameters can be set and will be read by Arbor and Neuron in param_basket.json and param_granule.json

A series of spikes is delivered to a synapse on the basket/granule cell. The spike times are read from param_basket.json and param_granule.json.

$ cd neuron
$ nrnivmodl modfiles
$ python2 test_granulecell.py ../param_granule.json
OR
$ python2 test_basketcell.py ../param_basket.json

Running the examples will generate a plot

Installing Arbor:

• Install Arbor from the following branch: https://github.com/noraabiakar/usc_collab/tree/testing/new-revpot
• For help installing Arbor refer to: https://arbor.readthedocs.io/en/latest/install.html

Compiling the example:

$ cd arbor/granule
OR
$ cd arbor/basket

$ mkdir build && cd build
$ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/arbor/installation -DCMAKE_BUILD_TYPE=release
$ make

Running the example:

$ ./granule ../../../param_granule.json
OR
$ ./basket ../../../param_basket.json

Plotting the results:

Running the examples will generate voltages.json. To plot the results, you can use the provided tsplot script:

$ python2 tsplot.py arbor/granule/build/voltages.json
OR
$ python2 tsplot.py arbor/basket/build/voltages.json