ElegansBot 1.0.1

Newtonian Mechanics Model for C. elegans Locomotion

ElegansBot

Newtonian Mechanics Model for C. elegans Locomotion

Requirements

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

Tested Environment

• Windows 10
• python 3.8.18
• numpy 1.19.0
• numba 0.54.0
  • scipy 1.5.0
• matplotlib 3.4.2

Usage

1. Install ElegansBot by pip install 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 wish to use ElegansBot with a pre-determined $\theta_{\mathrm{ctrl}}$ (target body angle), it's recommended to utilize the "run" method of an instance of the "Worm" class.
   • 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.

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.

Local Demo

Execute the following command:

python elegansbot.py

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.

Citation

• If ElegansBot has been significant in your research, and you would like to acknowledge this work in your academic publication, please consider citing the following paper (this citation may be updated in the future):

Chung, T., Chang, I., & Kim, S. (2023). ElegansBot: Development of equation of motion deciphering locomotion including omega turns of Caenorhabditis elegans (p. 2023.09.26.559644). bioRxiv. https://doi.org/10.1101/2023.09.26.559644