Protocol for biomodel engineering of unilevel to multilevel biological models using colored Petri nets

Fei Liu; Monika Heiner; David Gilbert

doi:10.1016/j.xpro.2023.102651

Protocol for biomodel engineering of unilevel to multilevel biological models using colored Petri nets

STAR Protoc. 2023 Dec 15;4(4):102651. doi: 10.1016/j.xpro.2023.102651. Epub 2023 Dec 8.

Authors

Fei Liu¹, Monika Heiner², David Gilbert³

Affiliations

¹ School of Software Engineering, South China University of Technology, Guangzhou, Guangdong 510006, P.R. China. Electronic address: feiliu@scut.edu.cn.
² Department of Computing Science, Brandenburg University of Technology Cottbus-Senftenberg, D03013 Cottbus, Germany.
³ Department of Computing Science, Brunel University London, UB8 3PH London, UK.

Abstract

Biological systems inherently span multiple levels, which can pose challenges in spatial representation for modelers. We present a protocol that utilizes colored Petri nets to construct and analyze biological models of systems, encompassing both unilevel and multilevel scenarios. We detail a modeling workflow exploiting the PetriNuts platform comprising a set of tools linked together via common file formats. We describe steps for modeling preparation, component-level modeling and analysis, followed by system-level modeling and analysis, and model use.

Keywords: Bioinformatics; Computer sciences; Systems biology.

MeSH terms

Computer Simulation
Models, Biological*