Department of Computer Science, University of Bradford, Richmond Building, Bradford BD7 1DP, UK.
School of Computing Science, Newcastle University, Science Square, Newcastle upon Tyne NE4 5TG, UK.
J R Soc Interface. 2023 May;20(202):20230019. doi: 10.1098/rsif.2023.0019. Epub 2023 May 10.
The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological systems. In particular, formal verification, complementary approach to standard computational techniques such as simulation, is used to validate the system correctness and obtain critical information about system behaviour. In this study, we survey the most frequently used computational modelling approaches and formal verification techniques for computational biology. We compare a number of verification tools and software suites used to analyse biological systems and biochemical networks, and to verify a wide range of biological properties. For users who have no expertise in formal verification, we present a novel methodology that allows them to easily apply formal verification techniques to analyse their biological or biochemical system of interest.
使用计算建模方法对生物系统进行形式化，作为对基于数学方法的替代，最近受到了广泛关注，因为计算模型为生物系统提供了更深入的机制理解。特别是，形式验证是对模拟等标准计算技术的补充方法，用于验证系统的正确性，并获得有关系统行为的关键信息。在本研究中，我们调查了计算生物学中最常用的计算建模方法和形式验证技术。我们比较了用于分析生物系统和生化网络以及验证广泛的生物学特性的许多验证工具和软件套件。对于没有形式验证专业知识的用户，我们提出了一种新方法，允许他们轻松地将形式验证技术应用于分析他们感兴趣的生物或生化系统。
