A standard-enabled workflow for synthetic biology.

Mısırlı, G; Nguyen, T; Oberortner, E; Samineni, M; Wipat, A; Zhang, M; Zundel, Z; Madsen, C; McLaughlin, JA; Myers, CJ; Beal, J; Gorochowski, TE; Kuwahara, H

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

Mısırlı, G., Nguyen, T., Oberortner, E., Samineni, M., Wipat, A., Zhang, M., Zundel, Z., Madsen, C., McLaughlin, J., Myers, C., Beal, J., Gorochowski, T., & Kuwahara, H. (2017). A standard-enabled workflow for synthetic biology. Transactions, 793 - 803. https://doi.org/10.1042/BST20160347

• Acceptance Date: Jun 15, 2017
• Publication Date: Jun 15, 2017
• Journal: Biochemical Society Transactions
• Print ISSN: 1470-8752
• Publisher: Portland Press
• Pages: 793 - 803
• DOI: https://doi.org/10.1042/BST20160347
• Keywords: standards, synthetic biological circuits, synthetic biology
• Public URL: https://keele-repository.worktribe.com/output/410023
• Publisher URL: http://www.biochemsoctrans.org/content/45/3/793