title: Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device.
abstract: The concept of co-design is common in engineering, where it is necessary, for example, to determine the optimal partitioning between hardware and software of the implementation of a system features. Here we propose to adapt co-design methodologies for synthetic biology. As a test case, we have designed an environmental sensing device that detects the presence of three chemicals, and returns an output only if at least two of the three chemicals are present. We show that the logical operations can be implemented in three different design domains: (1) the transcriptional domain using synthetically designed hybrid promoters, (2) the protein domain using bi-molecular fluorescence complementation, and (3) the fluorescence domain using spectral unmixing and relying on electronic processing. We discuss how these heterogeneous design strategies could be formalized to develop co-design algorithms capable of identifying optimal designs meeting user specifications.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg VA, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Ball
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Lux
authors.forename: Russell R
authors.initials: RR
authors.lastname: Graef
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Peterson
authors.forename: Jane D
authors.initials: JD
authors.lastname: Valenti
authors.forename: John
authors.initials: J
authors.lastname: Dileo
authors.forename: Jean
authors.initials: J
authors.lastname: Peccoud
mesh_terms: D000465:Algorithms; D057005:Bioengineering; D019295:Computational Biology; D004784:Environmental Monitoring / Q000295:instrumentation*; D004867:Equipment Design; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006801:Humans; D011401:Promoter Regions, Genetic; D013050:Spectrometry, Fluorescence; D058615:Synthetic Biology / Q000295:instrumentation*; D049490:Systems Biology; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D049452:Green Fluorescent Proteins