Biodivine Parametrised Boolean Networks

Rust library for working with parametrised Boolean networks. Supports:

• Read/Write Boolean network models from .aeon and .sbml formats.
• Basic static analysis, like monotonicity checking or network decomposition.
• Network parameters and partially unknown update functions.
• Fully symbolic asynchronous transition graphs.
• (Legacy) semi-symbolic asynchronous transition graphs.

To learn more, check out the documentation in our tutorial module.

PBN to colour graph dump

To analyse (very) small networks, it can be useful to dump them as explicit coloured graphs. There is a binary for that as well.

First, run cargo build --release.

You can then find the binary in target/release/dump-graph. The binary takes .aeon model on standard input and dumps the graph to standard output. So to convert a PBN to its coloured asynchronous transition graph, simply call dump-graph < ~/path/to/model.aeon > graph_file.txt.

Since the graph is explicit, expect the output size to be unmanageable for PBNs with roughly >10 variables and >1000 valid parametrisations (with parametrisations being the bigger problem).

You can test the functionality on aeon_models/g2a_*.aeon models which should all be sufficiently small.