Liu F, Heiner M, Gilbert D. Protocol for biomodel engineering of unilevel to multilevel biological models using colored Petri nets.
STAR Protoc 2023;
4:102651. [PMID:
38103198 PMCID:
PMC10751555 DOI:
10.1016/j.xpro.2023.102651]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/26/2023] [Accepted: 09/27/2023] [Indexed: 12/18/2023] Open
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.
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