Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

Curtis Madsen 1 , Angel Goni Moreno 2 , Zachary Palchick 3 , Umesh P 4 , Nicholas Roehner 5 , Bryan Bartley 5 , Swapnil Bhatia 1 , Shyam Bhakta 6 , Mike Bissell 7 , Kevin Clancy 8 , Robert Sidney Cox 9 , Thomas Gorochowski 10 , Raik Grunberg 11 , Augustin Luna 12 , James McLaughlin 2 , Tramy Nguyen 13 , Nicolas Le Novere 14 , Matthew Pocock 15 , Herbert Sauro 16 , James Scott-Brown 17 , John T. Sexton 6 , Guy-Bart Stan 17 , Jeffrey J. Tabor 6 , Christopher A. Voigt 18 , Zach Zundel 13 , Chris Myers 13 , Jacob Bealhttp://orcid.org/https://orcid.org/0000-0002-1663-5102 5 , and Anil Wipat 2
  • 1 Boston University, Boston, MA, USA
  • 2 Newcastle University, Newcastle, UK
  • 3 Zymergen, Emeryville, CA, USA
  • 4 Kerala Technological University, Thiruvananthapuram, India
  • 5 Raytheon BBN Technologies, Cambridge, MA, USA
  • 6 Rice University, Houston, TX, USA
  • 7 Amyris, Inc., Emeryville, CA, USA
  • 8 Thermo Fisher Scientific, San Diego, CA, USA
  • 9 Kobe University, Kobe, Japan
  • 10 University of Bristol, Bristol, UK
  • 11 KAUST, Thuwal, Saudi Arabia
  • 12 Harvard Medical School, Boston, MA, USA
  • 13 University of Utah, Salt Late City, UT, USA
  • 14 Babraham Institute, Cambridge, UK
  • 15 Turing Ate My Hamster, Ltd., Newcastle, UK
  • 16 University of Washington, Seattle, WA, USA
  • 17 Imperial College, London, UK
  • 18 MIT, Cambridge, MA, USA

Abstract

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species . Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.

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