A Generic Language for Biological Systems based on Bigraphs

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 B^Σ_R-calculi sharing a small set of familiar operators and operations, and provide them with a simple operational semantics. We show that B^Σ_R-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 B^Σ_R-processes. Finally, to illustrate the usage of B^Σ_R, we show that with non-aliasing semantics the κ-calculus may be faithfully captured as a B^Σ_R-calculus.