Quantitative model refinement in four different frameworks, with applications to the heat shock response

Diana-Elena Gratie, Bogdan Iancu, Sepinoud Azimi Rashti, Ion Petre

    Research output: Chapter in Book/Conference proceedingChapterScientificpeer-review

    3 Citations (Scopus)

    Abstract

    Quantitative model refinement is an essential step in the model development cycle. Starting with a high level, abstract representation of a biological system, one often needs to add details to this representation to reflect changes in its constituent elements. Any such refinement step has two aspects: one structural and one quantitative. The structural aspect of the refinement defines an increase in the resolution of its representation, while the quantitative one specifies a numerical setup for the model that ensures its fit preservation at every refinement step. We discuss in this paper the implementation of quantitative model refinement in four extensively used bio-modelling frameworks: ODE-based models, rule-based models, Petri net models, and guarded command language models, emphasizing the specificity for every model implementation. We argue that quantitative model refinement is framework-independent, being implementable in all chosen frameworks despite their different underlying modelling paradigms. Quantitative model refinement is an essential step in the model development cycle. Starting with a high level, abstract representation of a biological system, one often needs to add details to this representation to reflect changes in its constituent elements. Any such refinement step has two aspects: one structural and one quantitative. The structural aspect of the refinement defines an increase in the resolution of its representation, while the quantitative one specifies a numerical setup for the model that ensures its fit preservation at every refinement step. We discuss in this paper the implementation of quantitative model refinement in four extensively used bio-modelling frameworks: ODE-based models, rule-based models, Petri net models, and guarded command language models, emphasizing the specificity for every model implementation. We argue that quantitative model refinement is framework-independent, being implementable in all chosen frameworks despite their different underlying modelling paradigms.
    Original languageUndefined/Unknown
    Title of host publicationFrom Action Systems to Distributed Systems
    EditorsLuigia Petre, Emil Sekerinski
    PublisherCRC Press
    Pages201–214
    ISBN (Electronic)978-1-4987-0159-4
    ISBN (Print)978-1-4987-0158-7
    DOIs
    Publication statusPublished - 2016
    MoE publication typeA3 Part of a book or another research book

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