Distributed Computing Inspired by Biology

Repository containing all scripts and demo notebooks associated with the submitted paper:

Függer, M., Nowak, T., Thuillier, K. (2025). Distributed Computing Inspired by Biology. Seminars in Cell and Developmental Biology.

Requirements

Python 3 requirements are described in requirements.txt

numpy
networkx
scipy
mobspy
jupyterlab
ipykernel
ipywidgets

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

Jupyter Notebook

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 .

Figures and Videos

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.

Paper's Figures

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.

Supplementary Videos

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

Make videos

Videos will be generated in the out-videos directory.