biobalm is a Python library for exploring the attractor landscape of large-scale Boolean networks with hundreds or thousands of variables. It combines symbolic (BDD) and automated (ASP) reasoning to efficiently construct a succession diagram of a Boolean network: an inclusion-based acyclic graph of the network's trap spaces. biobalm can then use this succession diagram to accelerate attractor search and infer control strategies for target trap spaces.
biobalm is on PyPI: TODO: PyPI release coming soon. Use git method (below).
pip install biobalm
The base installation allows you to generate succession diagrams and control strategies, plus some easier-to-find attractors. However, to enable the full attractor detection functionality, you need to also install pint and mole:
- Native binaries of
pintcan be obtained here. - Download
molehere, compile it (simply runmake), and make sure the result is in your$PATH.
You can also install the latest version of biobalm directly from github:
pip install git+https://github.com/jcrozum/biobalm.git@main
TODO: A publication describing biobalm in detail will be available soon. Until then, please link this github repository instead.
To learn more about how biobalm functions, you can explore the example notebooks listed below. Alternatively, biobalm's API documentation is also available online.
TODO: Usage examples coming soon.