biobalm 0.2.0

Boolean Attractor Landscape Mapper

Boolean Attractor Landscape Mapper (biobalm)

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.

Installation

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 pint can be obtained here.
• Download mole here, compile it (simply run make), 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

Referencing biobalm

TODO: A publication describing biobalm in detail will be available soon. Until then, please link this github repository instead.

Using biobalm

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.