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

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.