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Hiding the combinatorial state space explosion of biomodels through colored Petri nets

Diana-Elena Gratie, Ion Petre, Hiding the combinatorial state space explosion of biomodels through colored Petri nets. Annals of University of Bucharest LXI, 23–41, 2014.

Abstract:

Model refinement is an important step in the model implementation cycle that deals with adding details to an existing model. Several ways of implementing model refinement have been discussed in the literature, for rule-based models and for ODE models. We focus here on implementing model refinement in the framework of Petri nets, using the programming capabilities of colored Petri nets. We exemplify our strategy on a reaction-based model of the eukaryotic heat shock response. We conclude with an analysis of the initial and refined models, a proof that the two colored Petri net models we have built are bisimilar, and a discussion on how modeling biological systems with colored Petri nets scales with further expansions of the model.

BibTeX entry:

@ARTICLE{jGrPe14a,
  title = {Hiding the combinatorial state space explosion of biomodels through colored Petri nets},
  author = {Gratie, Diana-Elena and Petre, Ion},
  journal = {Annals of University of Bucharest},
  volume = {LXI},
  publisher = {Editura Universitatii din Bucuresti},
  pages = {23–41},
  year = {2014},
  keywords = {Model refinement; colored Petri nets; bisimilar; heat shock response.},
  ISSN = {1224-7170},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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