GUBS a Language for Synthetic Biology: Specification and Compilation

• Published in: Unconventional Computation and Natural Computation Vol. 8553; pp. 40 - 53
• Main Authors: Basso-Blandin, Adrien, Delaplace, Franck
• Format: Book Chapter
• Language: English
• Published: Switzerland Springer International Publishing AG 2014; Springer International Publishing
• Series: Lecture Notes in Computer Science
• Subjects: Biological Component; Compilation Process; Computer science; Domain Specific Language; Kripke Model; Pattern recognition; Synthetic Biology; User interface design & usability
• ISBN: 9783319081229; 3319081225
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-319-08123-6_4

The field of synthetic biology is looking forward principles and tools to make the biological devices inter-operable and programmable with, as long-term goal, the design of de-novo synthetic genome [14]. In this endeavour, computer-aided-design (CAD) environments play a central role by providing the required features to engineer systems: specification, analysis, and tuning [9,17,20,12]. Scaling up the complexity of devices necessitates to harness the development of CAD environments based on an automatic conversion of the design specification into DNA sequences, like compilers for programming languages. Currently, domain specific languages for synthetic biology mainly address the design of structure, namely the biological component assembly, where programming relates to DNA sequence description. Although the structural description is an indispensable step in the design-to-manufacture chain and provide an accurate description of devices, the required size of program for sequence description likely makes the task error-prone and infeasible. In this context, high level programming language for synthetic biology is announced as a key milestone for the second wave of synthetic biology to overcome the complexity of such large synthetic system design. We have proposed a domain specific language, Gubs [5] (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 (trigged by the environment for example) that possibly alter the behaviour of the programmed devices. Here we describe in detail the compilation framework,Ggc(Gubs Genetic Compiler), an automated compiler translating a program into biological components usable in living cells. The compilation process assemble biological components from a database to behaviourally cover the behaviour described by a program.