Journal of Integrative Bioinformatics (Jun 2021)
Synthetic biology open language visual (SBOL Visual) version 2.3
- Baig Hasan,
- Fontanarossa Pedro,
- Kulkarni Vishwesh,
- McLaughlin James,
- Vaidyanathan Prashant,
- Bartley Bryan,
- Bhakta Shyam,
- Bhatia Swapnil,
- Bissell Mike,
- Clancy Kevin,
- Cox Robert Sidney,
- Goñi Moreno Angel,
- Gorochowski Thomas,
- Grunberg Raik,
- Lee Jihwan,
- Luna Augustin,
- Madsen Curtis,
- Misirli Goksel,
- Nguyen Tramy,
- Le Novere Nicolas,
- Palchick Zachary,
- Pocock Matthew,
- Roehner Nicholas,
- Sauro Herbert,
- Scott-Brown James,
- Sexton John T.,
- Stan Guy-Bart,
- Tabor Jeffrey J.,
- Terry Logan,
- Vazquez Vilar Marta,
- Voigt Christopher A.,
- Wipat Anil,
- Zong David,
- Zundel Zach,
- Beal Jacob,
- Myers Chris
Affiliations
- Baig Hasan
- University of Connecticut, Storrs, USA
- Fontanarossa Pedro
- University of Utah, Salt Lake City, USA
- Kulkarni Vishwesh
- University of Warwick, Coventry, USA
- McLaughlin James
- Newcastle University, Newcastle upon Tyne, UK
- Vaidyanathan Prashant
- Microsoft Research, Cambridge, UK
- Bartley Bryan
- Raytheon BBN Technologies, Cambridge, USA
- Bhakta Shyam
- Rice University, Houston, USA
- Bhatia Swapnil
- Boston University, Boston, USA
- Bissell Mike
- Shipyard Toolchains LLC, Emeryville, USA
- Clancy Kevin
- Thermo Fisher Scientific, San Diego, USA
- Cox Robert Sidney
- Kobe University, Kobe, Japan
- Goñi Moreno Angel
- Newcastle University, Newcastle upon Tyne, UK
- Gorochowski Thomas
- University of Bristol, Bristol, UK
- Grunberg Raik
- KAUST, Thuwal, Saudi Arabia
- Lee Jihwan
- Rice University, Houston, USA
- Luna Augustin
- Harvard Medical School, Boston, USA
- Madsen Curtis
- Boston University, Boston, USA
- Misirli Goksel
- Keele University, Keele, UK
- Nguyen Tramy
- Raytheon BBN Technologies, Cambridge, USA
- Le Novere Nicolas
- Babraham Institute, Cambridge, UK
- Palchick Zachary
- Zymergen, Emeryville, USA
- Pocock Matthew
- Turing Ate My Hamster, Ltd., Newcastle, UK
- Roehner Nicholas
- Raytheon BBN Technologies, Cambridge, USA
- Sauro Herbert
- University of Washington, Seattle, USA
- Scott-Brown James
- University of Oxford, Oxford, UK
- Sexton John T.
- Rice University, Houston, USA
- Stan Guy-Bart
- Imperial College, London, UK
- Tabor Jeffrey J.
- Rice University, Houston, USA
- Terry Logan
- University of Utah, Salt Lake City, USA
- Vazquez Vilar Marta
- Universitat Politecnica de Valencia, Valencia, Spain
- Voigt Christopher A.
- MIT, Cambridge, USA
- Wipat Anil
- Newcastle University, Newcastle upon Tyne, UK
- Zong David
- Rice University, Houston, USA
- Zundel Zach
- University of Utah, Salt Lake City, USA
- Beal Jacob
- Raytheon BBN Technologies, Cambridge, USA
- Myers Chris
- University of Colorado Boulder, Boulder, USA
- DOI
- https://doi.org/10.1515/jib-2020-0045
- Journal volume & issue
-
Vol. 18,
no. 3
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 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level “interactions with interactions,” such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new “unspecified interaction” glyph is added for visualizing interactions whose nature is unknown, the “insulator” glyph is deprecated in favor of a new “inert DNA spacer” glyph, and the polypeptide region glyph is recommended for showing 2A sequences.
Keywords
