A Generic Language for Biological Systems based on Bigraphs
TR-2008-115, Authors: Troels C. Damgaard and Jean Krivine
Troels C. Damgaard and Jean Krivine
December 2008
Abstract
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.
Technical report TR-2008-115 in IT University Technical Report Series, December 2008.
Available as PDF.