Containment in Rule-Based Models

Authors:
C. D. Thompson-Walsh;J. Hayman;G. Winskel
Affiliations:
Computer Laboratory, University of Cambridge, United Kingdom;Computer Laboratory, University of Cambridge, United Kingdom;Computer Laboratory, University of Cambridge, United Kingdom
Venue:
Electronic Notes in Theoretical Computer Science (ENTCS)
Year:
2012

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Abstract

Recently, there has been substantial interest in using rule-based modelling approaches, such as the Kappa modelling language, to attack the combinatorial intractability of many biochemical systems. These approaches have allowed several novel static analyses to be developed, which motivates broadening their expressivity. In this paper, we build upon prior work giving Kappa an SPO-rewriting semantics to add containment structure, to model the various ways in which biological mixtures are partitioned and enclosed by membranes.