msn-model

Computational model of a striatial medium spiny neuron (MSN).

The model is implemented in NEURON. The associated Python files use NEURON to build a MSN and simulate various experimental conditions. The Python examples here were designed with the intention to provide some understanding of the various steps involved in building and manipulating a neuron model. After studying each example it should be possible to combine these to simulate experiments and assess specific hypotheses.

2021-2022 Antonio González

Credits

The original NEURON model (msn/mechanisms/*.mod), cell morphologies (msn/morphologies/*.swc), and best-fit parameters (msn/parameters/*.pkl) are from Lindroos and Hellgren Kotaleski [Lindroos2021], available from ModelDB (model ID 266775). See also [Lindroos2018]. Some of the Python code used to simulate MSNs is derived from code by the same authors available on GitHub; where applicable, the documentation in the individual files acknowledges this fact.

Requirements

• Python 3 (>= 3.7)
• Numpy
• Pandas
• Matplotlib
• NEURON
• scikit-learn (optional: needed only for some of the examples provided)

How to use it

1. Install NEURON with Python; refer to NEURON's website for details.
2. Run nrnivmodl inside the directory msn/mechanisms to compile the .mod files; see NEURON's website.
3. Run the example scripts provided (e.g. python example_1_build.py). These files should be self explanatory.

Links

• The source code is on GitHub.

References

[Lindroos2018]: Lindroos R, Dorst MC, Du K, Filipović M, Keller D, Ketzef M, Kozlov AK, Kumar A, Lindahl M, Nair AG, Pérez-Fernández J, Grillner S, Silberberg G & Hellgren Kotaleski J (2018). Basal ganglia neuromodulation over multiple temporal and structural scales-simulations of direct pathway MSNs investigate the fast onset of dopaminergic effects and predict the role of Kv4.2. Front Neural Circuits 12, 3 (https://doi.org/10.3389/fncir.2018.00003).

[Lindroos2021]: Lindroos R & Hellgren Kotaleski J (2021). Predicting complex spikes in striatal projection neurons of the direct pathway following neuromodulation by acetylcholine and dopamine. Eur J Neurosci 53, 2117–2134 (https://doi.org/10.1111/ejn.14891).