Functional synthesis of genetic regulatory networks

Authors:
Jacob Beal;Aaron Adler
Affiliations:
Raytheon BBN Technologies, Cambridge, MA, USA;Raytheon BBN Technologies, Cambridge, MA, USA
Venue:
Proceedings of the 1st annual workshop on Functional programming concepts in domain-specific languages
Year:
2013

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Abstract

As synthetic biologists improve their ability to engineer complex computations in living organisms, there is increasing interest in using programming languages to assist in the design and composition of biological constructs. In this paper, we argue that there is a natural fit between functional programming and genetic regulatory networks, exploring this connection in depth through the example of BioProto, a piggyback DSL on the Proto general-purpose spatial language. In particular, we present the first formalization of BioProto syntax and semantics, and compare these to the formal syntax and semantics of the parent language Proto. Finally, we examine the pragmatics of implementing BioProto and challenges to proving correctness of BioProto programs.