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Hybrid modelling of biological systems using fuzzy continuous Petri nets

  • Integrated modelling of biological systems is challenged by composing components with sufficient kinetic data and components with insufficient kinetic data or components built only using experts’ experience and knowledge. Fuzzy continuous Petri nets (FCPNs) combine continuous Petri nets with fuzzy inference systems, and thus offer an hybrid uncertain/certain approach to integrated modelling of such biological systems with uncertainties. In this paper, we give a formal definition and a corresponding simulation algorithm of FCPNs, and briefly introduce the FCPN tool that we have developed for implementing FCPNs. We then present a methodology and workflow utilizing FCPNs to achieve hybrid (uncertain/certain) modelling of biological systems illustrated with a case study of the Mercaptopurine metabolic pathway. We hope this research will promote the wider application of FCPNs and address the uncertain/certain integrated modelling challenge in the systems biology area.

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Metadaten
Author: Fei LiuORCiD, Wujie Sun, Monika HeinerORCiD, David Gilbert
DOI:https://doi.org/10.1093/bib/bbz114
Title of the source (English):Briefings in Bioinformatics
Document Type:Scientific journal article peer-reviewed
Language:English
Year of publication:2019
Tag:fuzzy continuous Petri nets; hybrid simulation; integrated modelling; systems biology; uncertainties
Volume/Year:22(2021)
Article Number:1
Number of pages:13
First Page:438
Last Page:450
Faculty/Chair:Fakultät 1 MINT - Mathematik, Informatik, Physik, Elektro- und Informationstechnik / FG Datenstrukturen und Softwarezuverlässigkeit
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