biodivine-aeon 0.2.0a0

Python bindings for the tool AEON.

Biodivine/AEON.py

This repository contains AEON.py, the Python bindings for the AEON tool, which can be used for symbolic analysis of (partially specified) Boolean networks. In particular, it allows solving attractor detection and source-target control problems on large, non-trivial networks. Furthermore, these problems can be addressed even in networks with logical parameters or partially unknown dynamics.

Installation

The package is available through PyPI for all major operating systems (Windows, Linux and macOS). To install it, you can simply run:

pip install biodivine-aeon

Documentation

For new users, we recommend familiarising with the three Jupyter notebooks below, which summarise most of the major functionality of AEON.py:

• Symbolic computation using BDDs
• Working with parametrised Boolean networks
• AEON.py example project

Subsequently, the manual of the standalone AEON tool (which AEON.py is based on) can be also helpful to understand some of the high-level concepts.

More advanced users can inspect a detailed API documentation available here. Note that this is a documentation generated for the Rust codebase, which is then exported into Python using the PyO3 tool. As such, note that some names may be different in the exported Python library (observe the name attribute on most structs that is used for this reason). Nevertheless, the documentation should describe all available methods and data structures.