Soma-dendrite motor neuron model

Overview

Two compartment motor neuron (MN) pool model based on (Elias and Kohn, 2013). Every MN is comprised by a cylindrical soma and dendrite. The dendrites of the MNs include L-type Ca2+ channels to simulate the effect of persistent inward currents. The output is coupled with a model of motor unit (MU) twitch for force production. The model support the injection of current in the soma or dendrite, plus synaptic excitatory inputs (generated based on Avrillon et al, 2023 and Farina and Negro, 2015). The code is implemented in Brian2.

Table of Contents

• Installation
• Quick start
• Contributing
• License
• Citation
• Acknowledgments
• Contact

Installation

This toolbox is installable via pip with: sh pip install git+https://github.com/imendezguerra/soma_den_mn_model

To install it in editable mode, please clone the repository in your project's folder and run: sh pip install -e ./soma_den_mn_model Once the toolbox has been installed you can just import the corresponding packages as: python from soma_den_mn_model.configs import S_MN_Config

Prerequisites

When installing the package, pip will automatically install the required packages stored in requirements.txt.

If you decide to clone the repository, then you can replicate the environment with: conda env create -f environment.yml The file was constructed without the build so it should be compatible with Os, Windows, and Linux.

Local setup guide

To set up the project locally do the following:

1. Clone the repository: sh git clone https://github.com/imendezguerra/soma_den_mn_model.git
2. Navigate to the project directory: sh cd soma_den_mn_model
3. Create the conda environment from the environment.yml file: sh conda env create -f environment.yml
4. Activate the environment: sh conda activate soma_den_mn_model

Quick start

The package is composed of the following modules: - configs.py: Child dataclasses with properties for S, FR, and FF motor neurons. - inputs.py: Class to generate synaptic excitatory inputs (dynamics of the excitatory neurotransmitter, unitless). - pool.py: Class with functions to simulate a motor neuron pool.

The tutorials folder contains examples of how to use the package, including: - example_injected_dendrite.ipynb: Dendrite current injection to a 100 MN pool - example_injected_soma.ipynb: Soma current injection to a 100 MN pool - example_synaptic_dendrite.ipynb: Synaptic excitatory inputs (dendrite compartment) to a 100 MN pool

Contributing

We welcome contributions! Here’s how you can contribute:

1. Fork the repository.
2. Create a feature branch (git checkout -b feature/newfeature).
3. Commit your changes (git commit -m 'Add some newfeature').
4. Push to the branch (git push origin feature/newfeature).
5. Open a pull request.

License

This project is licensed under the MIT License.

Citation

If you use this code in your research, please cite this repository:

sh @software{Mendez_Guerra_soma_den_mn_model, author = {Mendez Guerra, Irene}, title = {{Soma-dendrite motor neuron model}}, url = {https://github.com/imendezguerra/soma_den_mn_model}, version = {1.0} }

Contact

For any questions or inquiries, please contact us at: sh Irene Mendez Guerra irene.mendez17@imperial.ac.uk