programming_formalisms_project_summer_2024
The Programming Formalisms project of summer 2024.
Goal
To simulate bacterial movement in 2D space.
One way to model bacterial movement is the run and tumble model, where 'run' is going straight in a direction, and 'tumble' is picking a random direction. The 'run' lasts longer when a bacterium finds more and more nutrients (e.g. dissolved sugars), and lasts shorter when finding less and less nutrients.
Image from coursehero
Usage
from bacsim.simulation import run_experiment
run_experiment("parameter_filename.txt", "results_filename.csv")Internal links
Files used for continuous integration scripts
| Filename | Descriptions |
|---|---|
| mlc_config.json | Configuration of the link checker |
| .spellcheck.yml | Configuration of the spell checker, use pyspelling -c .spellcheck.yml to do spellcheck locally |
| .wordlist.txt | Whitelisted words for the spell checker, use pyspelling -c .spellcheck.yml to do spellcheck locally |
| .pylintrc | Configuration file for pylint |
| pyproject.toml | Configuration file of this package |
External links
References
- [Wang et al., 2011] Wang, Charles CN, et al. "Simulation of bacterial chemotaxis by the random run and tumble model." 2011 IEEE 11th International Conference on Bioinformatics and Bioengineering. IEEE, 2011.