GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology

Adrien Basso-Blandin
(IBISC Lab)
Franck Delaplace
(IBISC Lab)

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

In Gabriel Ciobanu: Proceedings 6th Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2012), Newcastle, UK, 8th September 2012, Electronic Proceedings in Theoretical Computer Science 100, pp. 29–47.
Published: 15th November 2012.

ArXived at: http://dx.doi.org/10.4204/EPTCS.100.3 bibtex PDF
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