GUBS, a Behaviour-Based Language for Design in Synthetic Biology

Abstract

In this article, we propose a domain specific language, GUBS (Genomic Unified Behaviour Specification), dedicated to the behavioural specification of synthetic biological devices, viewed as discrete open dynamical systems. GUBS is a rule-based declarative language. In contrast to a closed system, a program is always a partial description of the behaviour of the system. The semantics of the language accounts the existence of some hidden non-specified actions that possibly alter the behaviour of the programmed devices. The compilation framework follows a scheme similar to automated theorem proving, aiming at improving synthetic biological design safety.