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Communicating Structure and Function in Synthetic Biology Diagrams

Lookup NU author(s): Dr Angel Goni-Moreno, James Alastair McLaughlin McLaughlin, Dr Curtis Madsen, Dr Matthew Pocock, Zach Zundel, Professor Anil Wipat

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Abstract

Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.

Publication metadata

Author(s): Beal J, Nguyen T, Gorochowski TE, Goni-Moreno A, Scott-Brown J, McLaughlin JA, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo Hair S, Clancy K, Luna A, Le Novere N, Palchick Z, Pocock M, Sauro H, Sexton JT, Tabor JJ, Voigt CA, Zundel Z, Myers C, Wipat A

Publication type: Article

Publication status: Published

Journal: ACS Synthetic Biology

Year: 2019

Volume: 8

Issue: 8

Pages: 1818-1825

Print publication date: 16/08/2019

Online publication date: 26/07/2019

Acceptance date: 30/03/2019

ISSN (electronic): 2161-5063

Publisher: American Chemical Society

URL: https://doi.org/10.1021/acssynbio.9b00139

DOI: 10.1021/acssynbio.9b00139

PubMed id: 31348656

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