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Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)

Lookup NU author(s): James Alastair McLaughlin McLaughlin, Dr Matthew Pocock

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Abstract

As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of combinatorial design space. To this end, we present a community accepted extension of the SBOL data standard that allows for the efficient and flexible encoding of combinatorial designs. This extension includes data structures for representing genetic designs with "variable" components that can be implemented by choosing one of many linked designs for existing genetic parts or constructs. We demonstrate the representational power of the SBOL combinatorial design extension through case studies on metabolic pathway design and genetic circuit design, and we report the expansion of the SBOLDesigner software tool to support users in creating and modifying combinatorial designs in SBOL.

Publication metadata

Author(s): Roehner N, Bartley B, Beal J, McLaughlin J, Pocock M, Zhang M, Zundel Z, Myers CJ

Publication type: Article

Publication status: Published

Journal: ACS Synthetic Biology

Year: 2019

Volume: 8

Issue: 7

Pages: 1519-1523

Online publication date: 17/06/2019

Acceptance date: 02/04/2019

ISSN (electronic): 2161-5063

Publisher: American Chemical Society

URL: https://doi.org/10.1021/acssynbio.9b00092

DOI: 10.1021/acssynbio.9b00092

PubMed id: 31260271

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