BoolDog

A Python package for integrated Boolean and semi-quantitative network modelling.

CI Status

Tests

OS \ Python	3.12	3.13
Ubuntu
macOS
Windows

Tutorials

tutorial-basic OS \ Python 3.12 3.13 Ubuntu macOS Windows

tutorial-advanced OS \ Python 3.12 3.13 Ubuntu macOS Windows

Documentation

For installation, usage, and examples, see the documentation at nib-si.github.io/BoolDog

Citation

Bleker, C., Zagorščak, M., Blejec, A., Gruden, K. & Županič, A. BoolDog: integrated Boolean and semi-quantitative network modelling in Python. bioRxiv 10.64898/2026.03.16.711264 (2026).

@article{bleker2026booldog,
  title   = {BoolDog: integrated Boolean and semi-quantitative network modelling in Python},
  author  = {Bleker, Carissa and Zagor{\v{s}}{\v{c}}ak, Maja and Blejec, Andrej and Gruden, Kristina and {\v{Z}}upani{\v{c}}, An{\v{z}}e},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.03.16.711264}
}

Development version

Development version of BoolDog can be installed from GitHub.

To install:

git clone https://github.com/NIB-SI/BoolDog.git
cd BoolDoG
pip install .

To install with all optional extras (networks, SBML-qual, BioModels):

pip install .[all]

To remove:

pip uninstall booldog

Docker

A standalone Dockerfile at the repo root builds a container with BoolDog and its all extras installed. For a container that instead extends the CoLoMoTo Docker image (bundled with its own tools and a Jupyter notebook environment), see colomoto/README.md.

Benchmarks

Performance/scalability characterisation of BoolDog runtime against model size and regulatory in-degree is in benchmarks/README.md.

Contributing

See CONTRIBUTING.md.