bnet2hoa 0.1.0

Generate the state space of a Boolean network in HOA format

BNET2HOA: Boolean network into HOA format

This tool takes as input a Boolean network expressed in the .bnet format (as used, e.g., by pyboolnet and BNetToPrime). Then, it builds a HOA automaton (https://adl.github.io/hoaf/) that captures the network's state-transition graph under a hybrid (aka generalised asynchronous) update paradigm. The automaton takes as input n atomic propositions, one for each variable in the Boolean network. If the i-th proposition is set to true, the next state will update the i-th variable. Therefore:

• Setting every AP true at every step results in the synchronous updating scheme.
• Setting exactly one AP true at every step results in the "traditional" asynchronous updating scheme.

Options

• --allow-stutter: Treat the input where all APs are false as a no-op (no update function is applied). Since BNs are usually not allowed to stutter, by default the tool treats this input as a synchronous update.

Dependencies

This tool depends on BNetToPrime. We always look for it in the system's PATH first. If there is no executable with that name, and we are running in Linux or macOS, we may try to use a bundled executable as a last resort. Notice that:

• We only bundle binaries for linux-x86_64 and darwin-arm64.
• The Linux binary was compiled with glibc 2.39.
• We do not plan to support issues related to bundled binaries. BNetToPrime is quite easy to compile for other platforms.