Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

Diego Di Bernardo,Douglas Densmore,Lesia Bilitchenko,Emma Weeding,Sherine Cheung,J. Christopher Anderson,Adam Liu,Mariana Leguia,Bing Xia

doi:10.1371/journal.pone.0018882

Abstract

BackgroundSynthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts.ResultsWe illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively.ConclusionsEugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.

Highlights

In its development as an engineering field, synthetic biology is at a stage where encapsulation has been identified as a fundamental challenge [1], [2], [3], [4]
We present a domain specific programming language called Eugene meant to encapsulate biological Parts, Devices, and Rules paving the way for design space exploration, simulation, and automated assembly
One popular encapsulation view in synthetic biology is that DNA sequence information can be encapsulated as a Part

Summary

Introduction

In its development as an engineering field, synthetic biology is at a stage where encapsulation has been identified as a fundamental challenge [1], [2], [3], [4]. We present a domain specific programming language called Eugene meant to encapsulate biological Parts, Devices, and Rules paving the way for design space exploration, simulation, and automated assembly. Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts

Methods

Results

Conclusion