Communicating Structure and Function in Synthetic Biology Diagrams

Jacob Beal; Tramy Nguyen; Thomas E Gorochowski; Angel Goñi-Moreno; James Scott-Brown; James Alastair McLaughlin; Curtis Madsen; Benjamin Aleritsch; Bryan Bartley; Shyam Bhakta; Mike Bissell; Sebastian Castillo Hair; Kevin Clancy; Augustin Luna; Nicolas Le Novère; Zach Palchick; Matthew Pocock; Herbert Sauro; John T Sexton; Jeffrey J Tabor; Christopher A Voigt; Zach Zundel; Chris Myers; Anil Wipat

doi:10.1021/acssynbio.9b00139

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Communicating Structure and Function in Synthetic Biology Diagrams

Journal article

Peer reviewed

Communicating Structure and Function in Synthetic Biology Diagrams

Jacob Beal, Tramy Nguyen, Thomas E Gorochowski, Angel Goñi-Moreno, James Scott-Brown, James Alastair McLaughlin, Curtis Madsen, Benjamin Aleritsch, Bryan Bartley, Shyam Bhakta, …

ACS synthetic biology, Vol.8(8), pp.1818-1825

08/16/2019

DOI: 10.1021/acssynbio.9b00139

PMCID: PMC8023477

PMID: 31348656

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https://research-information.bris.ac.uk/en/publications/3d79131a-380b-4351-8b18-ad3a9358f46eView

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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.

Models, Theoretical

Programming Languages

Software

Synthetic Biology - methods

Details

Title: Subtitle: Communicating Structure and Function in Synthetic Biology Diagrams
Creators: Jacob Beal - RTX (United States)
Tramy Nguyen - University of Utah
Thomas E Gorochowski - University of Bristol
Angel Goñi-Moreno - Newcastle University
James Scott-Brown - University of Oxford
James Alastair McLaughlin - Newcastle University
Curtis Madsen - Boston University
Benjamin Aleritsch - Technical University of Munich
Bryan Bartley - RTX (United States)
Shyam Bhakta - Rice University
Mike Bissell - Amyris (United States)
Sebastian Castillo Hair - Rice University
Kevin Clancy - BioCoder Consulting , Carlsbad 92008 , California , United States
Augustin Luna - Harvard University
Nicolas Le Novère - aSciStance Ltd. , Cambridge CB22 3LF , U.K
Zach Palchick - Zogenix (United States)
Matthew Pocock - Turing Institute
Herbert Sauro - University of Washington
John T Sexton - Rice University
Jeffrey J Tabor - Rice University
Christopher A Voigt - IIT@MIT
Zach Zundel - University of Utah
Chris Myers - University of Utah
Anil Wipat - Newcastle University
Resource Type: Journal article
Publication Details: ACS synthetic biology, Vol.8(8), pp.1818-1825
DOI: 10.1021/acssynbio.9b00139
PMID: 31348656
PMCID: PMC8023477
NLM abbreviation: ACS Synth Biol
ISSN: 2161-5063
eISSN: 2161-5063
Grant note: BB/L01386X/1 / Biotechnology and Biological Sciences Research Council R01 GM123032 / NIGMS NIH HHS U41 HG006623 / NHGRI NIH HHS P41 GM103504 / NIGMS NIH HHS
Language: English
Date published: 08/16/2019
Academic Unit: Electrical and Computer Engineering
Record Identifier: 9984627312202771

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