Demo notebooks and scripts associated with the paper Distributed Computing Inspired by Biology.

Cite:

Függer, M., Nowak, T., & Thuillier, K. (2025, November). Distributed computing inspired by biology. In Seminars in Cell & Developmental Biology (Vol. 175, p. 103666). Academic Press. DOI: 10.1016/j.semcdb.2025.103666

Python 3 requirements are listed in requirements.txt. A virtual Python 3 environment with all dependencies can be installed with:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

We provide a jupyter notebook (notebook.ipynb) to showcase the bio-inspired algorithms discussed in the associated paper.

It can be visualized at https://nbviewer.org/github/BioDisCo/dc_bio/tree/main/.

It can also be executed online (without any installation), using Binder .

Use make to generate all figures and supplementary videos.

Remarks: Generated figures may differ from the paper ones. Indeed, the scripts heavily rely on numpy.random and random packages. While, we define fixed seeds for everything, the behaviors of these pseudo-random algorithms may changed depending on the user OS, and the OS and packages versions.

Warning: all Python requirements should be installed.

Python 3 scripts generating the associated paper figures are stored in src. All figures can be generated using:

make figures

Figures will be generated in the out-figures directory.

ffmeg is required to generated the supplementary videos. They can be generated using:

make videos

Videos will be generated in the out-videos directory.