Hybrid modelling of biological systems using fuzzy continuous Petri nets. Issue 1 (15th December 2019)

• Record Type: Journal Article
• Authors: Liu, Fei; Sun, Wujie; Heiner, Monika; Gilbert, David
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 1(2021)
• Page Start: 438
• Page End: 450
• Publication Date: 2019-12-15
• Subjects: systems biology -- integrated modelling -- fuzzy continuous Petri nets -- uncertainties -- hybrid simulation; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbz114
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: 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.