A Generic Language for Biological Systems based on Bigraphs

Troels Christoffer Damgaard, Jean Krivine

    Publikation: Bog / Antologi / Rapport / Ph.D.-afhandlingRapportForskning

    Abstrakt

    Several efforts have shown that process calculi developed for reasoning about concurrent and mobile systems may be employed for modelling biological systems at the molecular level. In this paper, we initiate investigation of the meta-language framework bigraphical reactive systems, due to Milner et al., as a basis for developing rule-based languages for molecular biology. We describe a family of BΣR-calculi sharing a small set of familiar operators and operations, and provide them with a simple operational semantics. We show that BΣR-calculi and their reaction semantics correspond to a version of bigraphical reaction under non-aliasing contexts and with reaction rules extended to allow negative side-conditions for the subset of bigraphs corresponding to BΣR-processes. Finally, to illustrate the usage of BΣR, we show that with non-aliasing semantics the κ-calculus may be faithfully captured as a BΣR-calculus.
    OriginalsprogEngelsk
    UdgivelsesstedCopenhagen
    ForlagIT-Universitetet i København
    Vol/bindTR-2008-115
    Antal sider37
    StatusUdgivet - 2008
    NavnIT University Technical Report Series
    NummerTR-2008-115
    ISSN1600-6100

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