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.

翻译：生物调控网络可通过计算模型进行表示，这些模型能够研究并分析生物行为，从而加深对特定生物过程的理解。然而，随着新信息的获取，生物学模型可能需要修正以兼容这些新数据。当前模型修正工具较为稀缺，且常缺乏与更广泛分析工作流整合的灵活性。本文提出pyModRev——模型修正工具ModRev的增强版本，它能够验证布尔调控模型的一致性，并在发现不一致时定位最小修复方案。pyModRev支持基于稳态观测和时间序列数据的模型验证，可同时考虑不同更新机制。该工具兼容多种模型格式，并以Python包形式发布至PyPI，便于与其他模型分析工具集成，显著提升了逻辑建模领域的可访问性与实用性。