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Theoretical and Applied Aspects of Systems Biology pp 3–26Cite as

Bio-modeling Using Petri Nets: A Computational Approach

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Abstract

Petri nets have been widely used to model and analyze biological system. The formalism comprises different types of paradigms, integrating qualitative and quantitative (i.e., stochastic, continuous, or hybrid) modeling and analysis techniques. In this chapter, we describe the Petri net formalism and a broad view of its structure and characteristics applied in the modeling process in systems biology. We present the different net classes of the formalism, its color extension, and model analysis. The objective is to provide a discussion on the Petri net formalism as basis for research in computational biology.

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Acknowledgments

This work was supported by Fundação de Amparo a Pesquisa do Estado de Goiás (FAPEG) and CNPq.

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Authors and Affiliations

  1. Pontifical Catholic University of Goias, Goiânia, Brazil

    Rafael V. Carvalho & Clarimar J. Coelho

  2. Leiden University, Leiden, The Netherlands

    Fons J. Verbeek

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  1. Rafael V. Carvalho
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  2. Fons J. Verbeek
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  3. Clarimar J. Coelho
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Editors and Affiliations

  1. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil

    Fabricio Alves Barbosa da Silva

  2. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil

    Nicolas Carels

  3. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil

    Floriano Paes Silva Junior

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Carvalho, R.V., Verbeek, F.J., Coelho, C.J. (2018). Bio-modeling Using Petri Nets: A Computational Approach. In: Alves Barbosa da Silva, F., Carels, N., Paes Silva Junior, F. (eds) Theoretical and Applied Aspects of Systems Biology. Computational Biology, vol 27. Springer, Cham. https://doi.org/10.1007/978-3-319-74974-7_1

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