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
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
Technical report TR-2008-115 in IT University Technical Report Series, December 2008.
Available as PDF.