Communicating Structure and Function in Synthetic Biology Diagrams

Jacob Beal, Tramy Nguyen, Thomas Gorochowski, Angel Goni-Moreno, James Scott-Brown, James McLaughlin, Curtis Madsen, Benjamin Aleritsch, Bryan Bartley, Shyam Bhakta, Mike Bissell, Sebastian Castillo Hair, Kevin Clancy, Augustin Luna, Nicolas Le Novere, Zach Palchick, Matthew Pocock, Herbert Sauro, John Sexton, Jeffrey TaborChristopher Voigt, Zach Zundel, Chris Myers, Anil Wipat

Research output: Contribution to journalArticle (Academic Journal)peer-review

6 Citations (Scopus)
52 Downloads (Pure)

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.
Original languageEnglish
Pages (from-to)1818-1825
Number of pages8
JournalACS Synthetic Biology
Volume8
Early online date26 Jul 2019
DOIs
Publication statusPublished - 26 Jul 2019

Structured keywords

  • Bristol BioDesign Institute
  • BrisSynBio

Keywords

  • Synthetic Biology
  • Visualization
  • Diagrams
  • Synthetic Biology Open Language

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