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

2012/06/30 by Adrien Basso-Blandin, Franck Delaplace
Computer Science · #cs.PL #cs.CE

paper · pdf · doi:10.4204/eptcs.100.3

published as EPTCS 100, 2012, pp. 29-47 · In Proceedings MeCBIC 2012, arXiv:1211.3476

arxiv created 2012/11/19 · arxiv updated 2012/11/20

Abstract

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.

Citations

• Proceedings 6th Workshop on Membrane Computing and Biologically Inspired Process Calculi