Spillover

This repository contains simulation files used in the publication Trpevski, et al. "Glutamate spillover provides robust all-or-none behavior of plateau potentials in multicompartment models of striatal projection neurons", Authorea. March 29, 2023. DOI: 10.22541/au.168012861.16093883/v1

The simulations are implemented in Python 3, using the NEURON simulator through its Python 3 interface. This README file provides instructions for running the simulation scripts and reproducing the figures in the paper.

Requirements

• NEURON simulator
• Python 3
• Required Python packages (list them here)

Usage

The repository contains the following files:

• fig_2B.py and fig_2B_hm.py for reproducing plots in Fig. 2B.
• iv.py for generating Fig. 3.
• single_run.py for running a single simulation with clustered inputs.
• nmda_plateaus.py for obtaining results for variable cluster size (as in Fig. 2).
• alpha_mpi.py and eta_mpi.py for generating full simulated data, which were run on the Fenix Infrastructure resorces for 5 hours with the setup in the files alpha.sh and eta.sh, respectively.
• analyze_alpha.py and analyze_eta.py for analyzing the full simulated data.

The simulation code is organized around two classes:

• d1msn.py for the cell (inherits from the general class neuron_cls.py)
• spillover_experiment.py for the experiment performed with the cell (inherits from the general class experiment.py)

All parameters in the neuron model and the simulations are set in the parameters.py file.

Running a Simulation

To run an elementary simulation, such as single_run.py, follow these steps:

1. Create a neuron using the d1msn class.
2. Create an experiment with that neuron using the spillover_experiment class.
3. Set up the input to the neuron using the insert_synapses() method. Important arguments for this method are:
   • noise_SPN - inserts the background noise
   • my_spillover - creates a cluster of synapses with extrasynaptic NMDARs
   • no_spillover - creates a cluster of synapses without extrasynaptic NMDARs
4. Set up the recording via the set_up_recording() method.
5. Run the simulation via the simulate() method.
6. Plot the results via the plot_results() method.

Results

The results of the simulations are provided in the results folder. This includes the simulated data used in the fig_2B.py and fig_2B_hm.py scripts.

DOI

The DOI for the publication is DOI: [10.3389/fncel.2023.1196182]

License

The code is released under GNU General Public License v3.0.

References

• [NEURON Simulator documentation link]