pyModRev: a Python Tool for Model Revision of Boolean Networks
For researchers using Boolean network models in biology, pyModRev provides a more accessible and flexible tool for model revision, though it is an incremental improvement over the existing ModRev tool.
pyModRev is a Python tool for revising Boolean network models to maintain consistency with new biological data, supporting both steady-state and time-series observations. It improves accessibility and integration with other tools by being available as a Python package.
Biological regulatory networks can be represented by computational models, which allow the study and analysis of biological behaviours, therefore providing a better understanding of a given biological process. However, as new information is acquired, biological models may need to be revised in order to also account for this new information. Current model revision tools are scarce and often lack the flexibility to integrate with broader analysis workflows. Here, we present pyModRev, an enhanced iteration of the model revision tool ModRev, capable of verifying the consistency of Boolean regulatory models, and finding minimal repairs in case of inconsistency. pyModRev supports model validation against both steady state observations as well as time-series data, being able to consider different update schemes simultaneously. pyModRev supports different model formats, and is available as a Python package in PyPI, for easy integration with other model analysis tools, significantly improving accessibility and utility for the logical modelling community.