VisBOL2-Improving Web-Based Visualization for Synthetic Biology Designs

Benjamin Hatch; Linhao Meng; Jeanet Mante; James A McLaughlin; James Scott-Brown; Chris J Myers

doi:10.1021/acssynbio.1c00147

VisBOL2-Improving Web-Based Visualization for Synthetic Biology Designs

ACS Synth Biol. 2021 Aug 20;10(8):2111-2115. doi: 10.1021/acssynbio.1c00147. Epub 2021 Jul 29.

Authors

Benjamin Hatch¹, Linhao Meng², Jeanet Mante³, James A McLaughlin⁴, James Scott-Brown⁵, Chris J Myers³

Affiliations

¹ University of Utah, Salt Lake City, Utah 84112, United States.
² Eindhoven University of Technology, Eindhoven, 5612 AZ, Netherlands.
³ University of Colorado Boulder, Boulder, Colorado 80309, United States.
⁴ EMBL-EBI, Cambridge, CB10 1SD, United Kingdom.
⁵ University of Oxford, Oxford, OX1 2JD, United Kingdom.

PMID: 34324811
DOI: 10.1021/acssynbio.1c00147

Abstract

VisBOL is a web-based visualization tool used to depict genetic circuit designs. This tool depicts simple DNA circuits adequately, but it has become increasingly outdated as new versions of SBOL Visual were released. This paper introduces VisBOL2, a heavily redesigned version of VisBOL that makes a number of improvements to the original VisBOL, including proper functional interaction rendering, dynamic viewing, a more maintainable code base, and modularity that facilitates compatibility with other software tools. This modularity is demonstrated by incorporating VisBOL2 into a sequence visualization plugin for SynBioHub.

Keywords: SBOL; SBOL Visual; sequence visualization; synthetic biology; visualization.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Gene Regulatory Networks*
Models, Genetic*
Software*
Synthetic Biology*