Bactos.jl

Agent-based modelling of bacterial motility and chemotaxis in Julia.

Features

• Built on Agents.jl
• Bacterial motility in 1, 2 and 3 dimensions with customizable motile patterns.
• Chemotaxis with different tunable models (Brown-Berg, Brumley, Celani, Xie).
• Integration of differential equations in parallel with agent stepping via DifferentialEquations.jl, using finite differences.
• Easy evaluation of quantities of interest (mean-squared displacement, autocorrelation functions...).

Limitations

• The length of the integration timestep also sets the sensing timescale in chemotaxis models (i.e. the time over which a microbe integrates environmental signals).
• Reorientations are always assumed to be instantaneous.
• No hydrodynamic interactions.

Future directions

• Swimming in flow fields.
• More behavioral strategies (chemokinesis, infotaxis...).
• Extended set of core functionalities (encounters, interactions...).
• Complex environments (non-spherical obstacles).
• Steric interactions and non-spherical microbes.

Citation

If you use this package in work that leads to a publication, please cite the GitHub repository:

@misc{Foffi2022,
    author = {Foffi, R.},
    title = {Bactos.jl},
    year = {2022},
    publisher = {GitHub},
    journal = {GitHub repository},
    howpublished = {\url{https://github.com/mastrof/Bactos.jl}}
}

Acknowledgements

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 955910.