A standard-enabled workflow for synthetic biology

Handle URI:
http://hdl.handle.net/10754/625613
Title:
A standard-enabled workflow for synthetic biology
Authors:
Myers, Chris J.; Beal, Jacob; Gorochowski, Thomas E.; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach
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.
KAUST Department:
Computational Bioscience Research Center (CBRC)
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.
Publisher:
Portland Press Ltd.
Journal:
Biochemical Society Transactions
Issue Date:
15-Jun-2017
DOI:
10.1042/bst20160347
Type:
Article
ISSN:
0300-5127; 1470-8752
Sponsors:
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.
Additional Links:
http://www.biochemsoctrans.org/content/45/3/793
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorMyers, Chris J.en
dc.contributor.authorBeal, Jacoben
dc.contributor.authorGorochowski, Thomas E.en
dc.contributor.authorKuwahara, Hiroyukien
dc.contributor.authorMadsen, Curtisen
dc.contributor.authorMcLaughlin, James Alastairen
dc.contributor.authorMısırlı, Gökselen
dc.contributor.authorNguyen, Tramyen
dc.contributor.authorOberortner, Ernsten
dc.contributor.authorSamineni, Meheren
dc.contributor.authorWipat, Anilen
dc.contributor.authorZhang, Michaelen
dc.contributor.authorZundel, Zachen
dc.date.accessioned2017-10-03T12:49:29Z-
dc.date.available2017-10-03T12:49:29Z-
dc.date.issued2017-06-15en
dc.identifier.citationMyers 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.en
dc.identifier.issn0300-5127en
dc.identifier.issn1470-8752en
dc.identifier.doi10.1042/bst20160347en
dc.identifier.urihttp://hdl.handle.net/10754/625613-
dc.description.abstractA 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.en
dc.description.sponsorshipThis 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.en
dc.publisherPortland Press Ltd.en
dc.relation.urlhttp://www.biochemsoctrans.org/content/45/3/793en
dc.subjectstandardsen
dc.subjectSynthetic Biologyen
dc.subjectSynthetic Biological Circuitsen
dc.titleA standard-enabled workflow for synthetic biologyen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBiochemical Society Transactionsen
dc.contributor.institutionDepartment of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A.en
dc.contributor.institutionDepartment of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A. myers@ece.utah.edu.en
dc.contributor.institutionInformation and Knowledge Technologies, Raytheon BBN Technologies, 10 Moulton Street, Cambridge, MA 02138, U.S.A.en
dc.contributor.institutionBrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K.en
dc.contributor.institutionDepartment of Electrical and Computer Engineering, Boston University, 8 St. Mary's Street, Office #324, Boston, MA 02215, U.S.A.en
dc.contributor.institutionSchool of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.en
dc.contributor.institutionDOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, U.S.A.en
kaust.authorKuwahara, Hiroyukien
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