A b s t r a c t Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats.
REF surveyed various Petri Net implementations to study the properties and dynamics of biological systems.
Using Petri Net Tools to Study Properties and Dynamics of Biological Systems
Journal of the American Medical Informatics Association : JAMIA
Journal of the American Medical Informatics Association : JAMIA
Computer Science Medicine