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https://github.com/digital-c-fiber/neuron-c-fiber

Simulation of C-fiber with the simulation environment NEURON

https://github.com/digital-c-fiber/neuron-c-fiber

Science Score: 39.0%

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Repository

Simulation of C-fiber with the simulation environment NEURON

Basic Info
  • Host: GitHub
  • Owner: Digital-C-Fiber
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 39.1 KB
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  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed 5 months ago
Metadata Files
Readme

ReadMe.md

Computational Model of a C-fiber

This computational model simulates the biophysical properties of C-fibers, a class of unmyelinated sensory nerve fibers involved in pain perception. The model incorporates detailed ion channel dynamics, including sodium and potassium channels. It was translated to Python and adapted to run on a high-performance computing cluster (HPC).

Requirements:

  • NEURON v7.8 or higher
  • (For PSO-based optimization) Access to a High-Performance Cluster

Installation and Usage:

  1. Install NEURON: Follow the official installation guide: https://www.neuron.yale.edu/neuron/
  2. Compile mod-files: Navigate to the MODTigerholm folder and compile the mod files: nrnivmodl MODTigerholm
  3. Run the Model To execute the model, use: import main
    main.run()

File Structure:

Model Files:

  • main.py: Creates the nerve cell, runs the simulation, and saves results
  • run.py: Example script to run the model
  • defineCell.py: Functions for creating the cell
  • dataProcessing.py: Functions for data processing: getFilename(), getData() and calculateLatency()
  • stimulationProtocols.py: Predefined stimulation protocols

Optimization Files:

  • particleSwarm2.py, particleSwarm2GEPSO.py, particleSwarm2RPSO.py: Different implementations of the Particle Swarm Optimization (PSO) algorithm
  • evaluate.py: Functions for evaluating PSO-generated parameter sets

Plotting:

  • plot.py: Functions for visualizing results

Mechanisms:

  • All ion channel mechanism files (.mod files) are located in MOD_Tigerholm/

Citation:

If you use this model in your research, please cite the following publication(s):

"Maxion, A., et al. (2023). A modeling study to dissect the potential role of voltage-gated ion channels in activity-dependent conduction velocity changes as identified in small fiber neuropathy patients. Frontiers in Computational Neuroscience, 17. https://doi.org/10.3389/fncom.2023.1265958"

License:

This project is licensed under the Apache License 2.0.

Owner

  • Name: Digital-C-Fiber
  • Login: Digital-C-Fiber
  • Kind: organization

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