A Petri nets-based framework for whole-cell modeling. (December 2021)

• Record Type: Journal Article
• Authors: Liu, Fei; Assaf, George; Chen, Ming; Heiner, Monika
• Is Part Of: Bio systems. Volume 210(2021)
• Publication Date: 2021-12
• Subjects: Whole-cell modeling -- Systems biology -- Petri nets -- Modeling framework; Biological systems -- Periodicals; Biology -- Periodicals; Biology -- Periodicals; Evolution -- Periodicals; Biologie -- Périodiques; Évolution -- Périodiques; 570
• DOI: 10.1016/j.biosystems.2021.104533
• Languages: English
• ISSNs: 0303-2647

Abstract

Abstract: Whole-cell modeling aims to incorporate all main genes and processes, and their interactions of a cell in one model. Whole-cell modeling has been regarded as the central aim of systems biology but also as a grand challenge, which plays essential roles in current and future systems biology. In this paper, we analyze whole-cell modeling challenges and requirements and classify them into three aspects (or dimensions): heterogeneous biochemical networks, uncertainties in components, and representation of cell structure. We then explore how to use different Petri net classes to address different aspects of whole-cell modeling requirements. Based on these analyses, we present a Petri nets-based framework for whole-cell modeling, which not only addresses many whole-cell modeling requirements, but also offers a graphical, modular, and hierarchical modeling tool. We think this framework can offer a feasible modeling approach for whole-cell model construction.