Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena

Mura, Ivan (2007) Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena. UNSPECIFIED. (Unpublished)

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    This paper proposes a simplification of the stochastic Petri nets graphical notation with the purpose of defining a more compact and clearer graphical way of building formal models of biological phenomena. Three biological examples are first presented, then modeled with the classical SPN modeling formalism, and their key modeling patterns distilled to identify the main features that need to be represented in a stochastic model. The key features are then the object of the original part of the paper, in which a simplified and more concise, although formal, graphical notation, is proposed, and applied to the selected examples. The paper demonstrates the effectiveness of the simplified notation in producing more compact and understandable models of biological phenomena, still retaining the nice properties of Stochastic Petri Nets, i.e., their flexible abstraction level and formal semantics.

    Item Type: Departmental Technical Report
    Department or Research center: CoSBi (Center for Computational and Systems Biology)
    Subjects: Q Science > QA Mathematics > QA076 Computer software > QA076.7 Programming Languages - Semantics
    Report Number: TR-19-2007
    Repository staff approval on: 01 Dec 2009

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