Journal article
A standard-enabled workflow for synthetic biology
Biochemical Society transactions, Vol.45(3), pp.793-803
06/15/2017
DOI: 10.1042/BST20160347
PMID: 28620041
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.
Details
- Title: Subtitle
- A standard-enabled workflow for synthetic biology
- Creators
- Chris J. Myers - University of UtahJacob Beal - RaytheonThomas E. Gorochowski - University of BristolHiroyuki Kuwahara - King Abdullah University of Science and TechnologyCurtis Madsen - Boston UniversityJames Alastair McLaughlin - Newcastle UniversityGoksel Misirli - Newcastle UniversityTramy Nguyen - University of UtahErnst Oberortner - Joint Genome InstituteMeher Samineni - University of UtahAnil Wipat - Newcastle UniversityMichael Zhang - University of UtahZach Zundel - University of Utah
- Resource Type
- Journal article
- Publication Details
- Biochemical Society transactions, Vol.45(3), pp.793-803
- Publisher
- Portland Press Ltd
- DOI
- 10.1042/BST20160347
- PMID
- 28620041
- ISSN
- 0300-5127
- eISSN
- 1470-8752
- Number of pages
- 11
- Grant note
- FUJIFILM DioSynth Biotechnologies 1522074 / Direct For Computer & Info Scie & Enginr; National Science Foundation (NSF); NSF - Directorate for Computer & Information Science & Engineering (CISE) EP/J02175X/1 / Engineering and Physical Sciences Research Council (EPSRC); UK Research & Innovation (UKRI); Engineering & Physical Sciences Research Council (EPSRC) DE-AC02-05CH11231 / U.S. Department of Energy Joint Genome Institute; United States Department of Energy (DOE) CCF-1218095; DBI-135604 / National Science Foundation; National Science Foundation (NSF) BB/L01386X/1 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) BB/L01386X/1 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) Biotechnology and Biological Sciences Research Council and Engineering; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) BB/L01386X/1 / Physical Sciences Research Council Synthetic Biology Research Centre DOE Office of Science User Facility; United States Department of Energy (DOE) BrisSynBio 1522074 / National Science Foundation Expeditions in Computing Program Award
- Language
- English
- Date published
- 06/15/2017
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627321202771
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