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

Diana-Elena Gratie, Ion Petre

    Research output: Contribution to journalArticleScientificpeer-review


    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.
    Original languageUndefined/Unknown
    Pages (from-to)23–41
    JournalAnalele Universitatii Bucuresti
    Publication statusPublished - 2014
    MoE publication typeA1 Journal article-refereed

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