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Open Source Science

https://github.com/biodisco/dc_bio

https://github.com/biodisco/dc_bio

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.9%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: BioDisCo
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 708 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

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 text numpy networkx scipy mobspy jupyterlab ipykernel ipywidgets A virtual Python 3 environment with all dependencies can be installed with: bash 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 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: bash 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: bash Make videos Videos will be generated in the out-videos directory.

Owner

  • Name: BioDisCo
  • Login: BioDisCo
  • Kind: organization

GitHub Events

Total
  • Push event: 19
Last Year
  • Push event: 19