A standard-enabled workflow for synthetic biology

Abstract
A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

Citation
Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, et al. (2017) A standard-enabled workflow for synthetic biology. Biochemical Society Transactions 45: 793–803. Available: http://dx.doi.org/10.1042/bst20160347.

Acknowledgements
This material is based on work supported by the National Science Foundation under grant nos CCF-1218095 and DBI-135604. T.E.G. is supported by BrisSynBio, a Biotechnology and Biological Sciences Research Council and Engineering and Physical Sciences Research Council Synthetic Biology Research Centre [BB/L01386X/1]. G.M. and A.W. have been supported by the Engineering and Physical Sciences Research Council (EPSRC) [grant EP/J02175X/1]. J.A.M. is supported by FUJIFILM DioSynth Biotechnologies. J.B. is supported, in part, by the National Science Foundation Expeditions in Computing Program Award #1522074 as part of the Living Computing Project. E.O. is supported under Contract No. DE-AC02-05CH11231 by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility. This document does not contain technology or technical data controlled under either the U.S. International Traffic in Arms Regulations or the U.S. Export Administration Regulations.

Publisher
Portland Press Ltd.

Journal
Biochemical Society Transactions

DOI
10.1042/bst20160347

PubMed ID
28620041

Additional Links
http://www.biochemsoctrans.org/content/45/3/793https://eprints.keele.ac.uk/4386/1/standard-enabled-workflow.pdf

Permanent link to this record