Synthetic biology open language visual (SBOL visual) version 2.2

Hasan Baig 1 , Pedro Fontanarrosahttp://orcid.org/https://orcid.org/0000-0002-0535-2684 2 , Vishwesh Kulkarni 3 , James McLaughlin 4 , Prashant Vaidyanathan 5 , Bryan Bartley 6 , Swapnil Bhatia 7 , Shyam Bhakta 8 , Michael Bissell 9 , Kevin Clancy 10 , Robert Sidney Cox 11 , Angel Goñi Moreno 4 , Thomas Gorochowski 12 , Raik Grunberg 13 , Augustin Luna 14 , Curtis Madsen 7 , Goksel Misirli 15 , Tramy Nguyen 6 , Nicolas Le Novere 16 , Zachary Palchick 17 , Matthew Pocock 18 , Nicholas Roehner 6 , Herbert Sauro 19 , James Scott-Brown 20 , John T. Sexton 8 , Guy-Bart Stan 21 , Jeffrey J. Tabor 8 , Marta Vazquez Vilar 22 , Christopher A. Voigt 23 , Anil Wipat 4 , David Zonghttp://orcid.org/https://orcid.org/0000-0002-8157-4780 8 , Zach Zundel 2 , Jacob Bealhttp://orcid.org/https://orcid.org/0000-0002-1663-5102 6 ,  and Chris Myers 2
  • 1 University of Connecticut, Storrs, USA
  • 2 University of Utah, Salt Lake City, USA
  • 3 University of Warwick, Coventry, UK
  • 4 Newcastle University, Newcastle upon Tyne, UK
  • 5 Microsoft Research, Cambridge, UK
  • 6 Raytheon BBN Technologies, Cambridge, USA
  • 7 Boston University, Boston, USA
  • 8 Rice University, Houston, USA
  • 9 Shipyard Toolchains LLC, Emeryville, USA
  • 10 Thermo Fisher Scientific, San Diego, USA
  • 11 Kobe University, Kobe, Japan
  • 12 University of Bristol, Bristol, UK
  • 13 KAUST, Thuwal, Saudi Arabia
  • 14 Harvard Medical School, Boston, USA
  • 15 Keele University, Keele, UK
  • 16 Babraham Institute, Cambridge, UK
  • 17 Zymergen, Emeryville, USA
  • 18 Turing Ate My Hamster, Ltd., Newcastle, UK
  • 19 University of Washington, Seattle, USA
  • 20 University of Oxford, Oxford, UK
  • 21 Imperial College, London, UK
  • 22 Universitat Politecnica de Valencia, Valencia, Spain
  • 23 MIT, Cambridge, 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 2.2 of SBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First, the grounding of molecular species glyphs is changed from BioPAX to SBO, aligning with the use of SBO terms for interaction glyphs. Second, new glyphs are added for proteins, introns, and polypeptide regions (e. g., protein domains), the prior recommended macromolecule glyph is deprecated in favor of its alternative, and small polygons are introduced as alternative glyphs for simple chemicals.

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The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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