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A Petri nets-based framework for whole-cell modeling

  • 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.

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Metadaten
Author: Fei LiuORCiD, George Assaf, Ming Chen, Monika HeinerORCiD
URL:https://www.sciencedirect.com/science/article/abs/pii/S0303264721001738?via%3Dihub
DOI:https://doi.org/10.1016/j.biosystems.2021.104533
ISSN:0303-2647
ISSN:1872-8324
Title of the source (English):Biosystems
Document Type:Scientific journal article peer-reviewed
Language:English
Year of publication:2021
Tag:Modeling framework; Petri nets; Systems biology; Whole-cell modeling
Volume/Year:210
Article number:104533
Faculty/Chair:Fakultät 1 MINT - Mathematik, Informatik, Physik, Elektro- und Informationstechnik / FG Datenstrukturen und Softwarezuverlässigkeit
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