Journal
BIOCHEMICAL SOCIETY TRANSACTIONS
Volume 45, Issue -, Pages 793-803Publisher
PORTLAND PRESS LTD
DOI: 10.1042/BST20160347
Keywords
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Categories
Funding
- National Science Foundation [CCF-1218095, DBI-135604]
- BrisSynBio
- Biotechnology and Biological Sciences Research Council and Engineering
- Physical Sciences Research Council Synthetic Biology Research Centre [BB/L01386X/1]
- Engineering and Physical Sciences Research Council (EPSRC) [EP/J02175X/1]
- FUJIFILM DioSynth Biotechnologies
- National Science Foundation Expeditions in Computing Program Award [1522074]
- U.S. Department of Energy Joint Genome Institute [DE-AC02-05CH11231]
- DOE Office of Science User Facility
- BBSRC [BB/L01386X/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/L01386X/1] Funding Source: researchfish
- Division of Computing and Communication Foundations
- Direct For Computer & Info Scie & Enginr [1522074] Funding Source: National Science Foundation
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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.
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