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

TL;DR

GUBS is a rule-based language designed for specifying behaviors of synthetic biological devices, accounting for open system dynamics and hidden actions to enhance design safety.

Contribution

The paper introduces GUBS, a novel domain-specific language for behavioral specification of open biological systems, with a semantics that considers hidden actions.

Findings

GUBS enables partial behavioral descriptions of biological devices.

The language's semantics incorporate hidden actions affecting system behavior.

A compilation framework improves safety in synthetic biological design.

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.