Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0

Robert Sidney Cox 1 , Curtis Madsen 2 , James McLaughlin 3 , Tramy Nguyen 4 , Nicholas Roehner 5 , Bryan Bartley 6 , Swapnil Bhatia 2 , Mike Bissell 7 , Kevin Clancy 8 , Thomas Gorochowski 9 , Raik Grünberg 10 , Augustin Luna 11 , Nicolas Le Novère 12 , Matthew Pocock 13 , Herbert Sauro 6 , John T. Sexton 14 , Guy-Bart Stan 15 , Jeffrey J. Tabor 14 , Christopher A. Voigt 16 , Zach Zundel 4 , Chris Myers 4 , Jacob Bealhttp://orcid.org/0000-0002-1663-5102 17  and Anil Wipat 18
  • 1 Kobe University, Kobe, Japan
  • 2 Boston University, Boston, MA, USA
  • 3 Newcastle University, Newcastle, United Kingdom of Great Britain and Northern Ireland
  • 4 University of Utah, Salt Lake City, USA
  • 5 Raytheon BBN Technologies, Cambridge, MA, USA
  • 6 University of Washington, Seattle, WA, USA
  • 7 Amyris, Inc., Emeryville, CA, USA
  • 8 Thermo Fisher Scientific, San Diego, CA, USA
  • 9 University of Bristol, Bristol, United Kingdom of Great Britain and Northern Ireland
  • 10 King Abdullah University of Science and Technology (KAUST), BESE, Thuwal 23955 - 6900, Saudi Arabia
  • 11 Harvard Medical School, Boston, MA, USA
  • 12 Babraham Institute, Cambridge, Cambridgeshire, United Kingdom of Great Britain and Northern Ireland
  • 13 Turing Ate My Hamster, Ltd., Newcastle, United Kingdom of Great Britain and Northern Ireland
  • 14 Rice University, Houston, TX, USA
  • 15 Imperial College, London, United Kingdom of Great Britain and Northern Ireland
  • 16 Massachusetts Institute of Technology, Cambridge, MA, USA
  • 17 Raytheon BBN Technologies, Cambridge, MA, USA
  • 18 Newcastle University, Newcastle, United Kingdom of Great Britain and Northern Ireland

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 2.0 of SBOL Visual, which builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs.

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Journal + Issues

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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