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Communicating Structure and Function in Synthetic Biology Diagrams

Research output: Contribution to journalArticle (Academic Journal)

  • Jacob Beal
  • Tramy Nguyen
  • Thomas Gorochowskihttp://orcid.org/0000-0003-1702-786X
  • 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 Tabor
  • Christopher Voigt
  • Zach Zundel
  • Chris Myers
  • Anil Wipat
Original languageEnglish
Pages (from-to)1818-1825
Number of pages8
JournalACS Synthetic Biology
Volume8
Early online date26 Jul 2019
DOIs
DateAccepted/In press - 26 Jul 2019
DateE-pub ahead of print - 26 Jul 2019
DatePublished (current) - 26 Jul 2019

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.

    Research areas

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

    Structured keywords

  • Bristol BioDesign Institute
  • BrisSynBio

Documents

Documents

  • Full-text PDF (author accepted manuscript)

    Rights statement: This is the author accepted manuscript (AAM). The final published version (version of record) is available online via American Chemical Society at https://pubs.acs.org/doi/10.1021/acssynbio.9b00139# . Please refer to any applicable terms of use of the publisher

    Accepted author manuscript, 1.06 MB, PDF document

    Embargo ends: 26/07/20

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DOI

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