ElegansBot

Newtonian Mechanics Model for C. elegans Locomotion

omega_turn.mp4

(Left: Experimental video from [1], Right: ElegansBot)

[1] Broekmans, O. D., Rodgers, J. B., Ryu, W. S., & Stephens, G. J. (2016). Resolving coiled shapes reveals new reorientation behaviors in C. elegans. ELife, 5, e17227. https://doi.org/10.7554/eLife.17227

Web Demo

• https://taegonchung.github.io/elegansbot/
  • Use the sliders to observe the worm's movement changes.
    • Water-Agar Slider: Adjust this to modify the ground's frictional coefficients.
    • Swim-Crawl Slider: This slider alters the period and linear wave number of C. elegans' locomotion.

Requirements

• Python (version 3)
• NumPy
• Numba
  • SciPy (required as a dependency of numba)
• Matplotlib

(Optional)

• FFmpeg (for saving a video.)
• Jupyter Notebook (for interactive block coding)

Tested Environment

Please, check "https://github.com/TaegonChung/ElegansBot/tested_environments.txt".

Usage

1. Install library by pip install elegansbot or conda install conda-forge::elegansbot.
2. Use from elegansbot import Worm to import the library.
3. Refer to the detailed instructions in the docstring of the "Worm" class. Below is a brief overview of potential use-cases:
   • If you want to determine $\theta_{\mathrm{ctrl}}$ dynamically, it's advised to update "act" (equivalent to theta_ctrl) manually and then invoke the "steps" method on an instance of the "Worm" class.
   • If you wish to use ElegansBot with a pre-determined $\theta_{\mathrm{ctrl}}$ (kymogram), it's recommended to utilize the "run" method of an instance of the "Worm" class.

Examples

You may want to check out examples in the "examples/" directory.
For instance, you can execute the example code with:
python examples/example01.py

Files:

• examples/example01.py : Dynamic input
• examples/example02.py : Kymogram input
• examples/example03.py : Kymogram input (Omega-turn)
• examples/example04.py : Kymogram input (Delta-turn)
• examples/example05.py : Frictional forces, power, and behavioral classification

Local Demo

Execute the following command:

python -m elegansbot.elegansbot

File Description

• elegansbot.py : Main code
• Video_S1_omega_turn.avi : Video from the supplementary section of our paper.
• Video_S2_delta_turn.avi : Another video from the supplementary section of our paper.

Citing ElegansBot

• If ElegansBot has been significant in your research, and you would like to acknowledge this work in your academic publication, we suggest citing the following paper:

Taegon Chung, Iksoo Chang, Sangyeol Kim (2024) Development of equation of motion deciphering locomotion including omega turns of Caenorhabditis elegans eLife 12:RP92562 https://doi.org/10.7554/eLife.92562