Using Petri Net Tools to Study Properties and Dynamics of Biological Systems
- Affiliations of the authors: Department of Management Information Systems, University of Haifa, Haifa, Israel (MP); Stanford Medical Informatics, Stanford University Medical School, Stanford, CA (DR); Department of Genetics, Stanford University, Stanford, CA (RBA)
- Correspondence and reprints: Mor Peleg, PhD, Department of Management Information Systems, Rabin Building, University of Haifa, Haifa 31905, Israel; e-mail: <morpeleg{at}mis.hevra.haifa.ac.il>
- Received 13 June 2004
- Accepted 10 October 2004
Abstract
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.
Footnotes
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Supported by the Burroughs Wellcome Fund.
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The authors thank Samson Tu for his many insightful suggestions and comments. They thank Tod Courtney and the Mobius development team and Piotr Liguzinsky and the Cell Illustrator team for their efforts in explaining the differences in simulation results obtained for the gemcitabine example. The authors also thank the anonymous reviewers for their helpful suggestions.
