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Review Article

A standard-enabled workflow for synthetic biology

Chris J. Myers, Jacob Beal, Thomas E. Gorochowski, Hiroyuki Kuwahara, Curtis Madsen, James Alastair McLaughlin, Göksel Mısırlı, Tramy Nguyen, Ernst Oberortner, Meher Samineni, Anil Wipat, Michael Zhang, Zach Zundel
Biochemical Society Transactions Jun 15, 2017, 45 (3) 793-803; DOI: 10.1042/BST20160347
Chris J. Myers
Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A.
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  • For correspondence: myers@ece.utah.edu
Jacob Beal
Information and Knowledge Technologies, Raytheon BBN Technologies, 10 Moulton Street, Cambridge, MA 02138, U.S.A.
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Thomas E. Gorochowski
BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K.
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Hiroyuki Kuwahara
King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955, Saudi Arabia
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Curtis Madsen
Department of Electrical and Computer Engineering, Boston University, 8 St. Mary's Street, Office #324, Boston, MA 02215, U.S.A.
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James Alastair McLaughlin
School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
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Göksel Mısırlı
School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
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Tramy Nguyen
Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A.
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Ernst Oberortner
DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, U.S.A.
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Meher Samineni
Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A.
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Anil Wipat
School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
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Michael Zhang
Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A.
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Zach Zundel
Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A.
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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.

  • standards
  • synthetic biological circuits
  • synthetic biology
  • Abbreviations

    API,
    application programming interface;
    BOOST,
    Build-Optimization Software Tools;
    CDS,
    coding sequence;
    COMBINE,
    COmputational Modeling in BIology NEtwork;
    CRISPR,
    clustered regularly interspaced short palindromic repeats;
    JBEI,
    Joint BioEnergy Institute;
    LIMS,
    Laboratory Information Management System;
    RDF,
    resource description framework;
    SBGN,
    Systems Biology Graphical Notation;
    SBML,
    Systems Biology Markup Language;
    SBOL,
    Synthetic Biology Open Language;
    SBOLv,
    SBOL Visual;
    SED-ML,
    Simulation Experiment Description Markup Language;
    SO,
    Sequence Ontology
    • © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society
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    June 2017

    Volume: 45 Issue: 3

    Biochemical Society Transactions: 45 (3)
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    A standard-enabled workflow for synthetic biology
    Chris J. Myers, Jacob Beal, Thomas E. Gorochowski, Hiroyuki Kuwahara, Curtis Madsen, James Alastair McLaughlin, Göksel Mısırlı, Tramy Nguyen, Ernst Oberortner, Meher Samineni, Anil Wipat, Michael Zhang, Zach Zundel
    Biochemical Society Transactions Jun 2017, 45 (3) 793-803; DOI: 10.1042/BST20160347
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    A standard-enabled workflow for synthetic biology
    Chris J. Myers, Jacob Beal, Thomas E. Gorochowski, Hiroyuki Kuwahara, Curtis Madsen, James Alastair McLaughlin, Göksel Mısırlı, Tramy Nguyen, Ernst Oberortner, Meher Samineni, Anil Wipat, Michael Zhang, Zach Zundel
    Biochemical Society Transactions Jun 2017, 45 (3) 793-803; DOI: 10.1042/BST20160347

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    • Article
      • Abstract
      • Introduction
      • Synthetic Biology Open Language
      • Supporting reproduction and reuse with SBOL
      • Software support for SBOL
      • A standard-enabled workflow for synthetic biology
      • Conclusion
      • Funding
      • Competing Interests
      • References
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    Keywords

    standards
    synthetic biological circuits
    synthetic biology

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