Sharing Structure and Function in Biological Design with SBOL 2.0.

The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.

[1]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R. Weiss,et al.  Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks , 2011, PloS one.

[3]  Michael Bissell,et al.  Genotype Specification Language. , 2016, ACS synthetic biology.

[4]  Christopher A. Voigt,et al.  Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates , 2013, Nature chemical biology.

[5]  Ernst Oberortner,et al.  A Rule-Based Design Specification Language for Synthetic Biology , 2014, ACM J. Emerg. Technol. Comput. Syst..

[6]  Chris J Myers,et al.  A methodology to annotate systems biology markup language models with the synthetic biology open language. , 2014, ACS synthetic biology.

[7]  Matthew R. Pocock,et al.  SBOL Visual: A Graphical Language for Genetic Designs , 2015, PLoS biology.

[8]  Michael Hucka,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core , 2010, J. Integr. Bioinform..

[9]  Chris J Myers,et al.  A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language. , 2016, ACS synthetic biology.

[10]  Zhen Zhang,et al.  Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language. , 2015, ACS synthetic biology.

[11]  R. Weiss,et al.  Cancer Cells Multi-Input RNAi-Based Logic Circuit for Identification of Specific , 2011 .

[12]  Michael B Elowitz,et al.  Synthetic biology of multicellular systems: new platforms and applications for animal cells and organisms. , 2014, ACS synthetic biology.

[13]  W. J. Hedley,et al.  A short introduction to CellML , 2001, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[14]  Kwang-Hyun Cho,et al.  Encyclopedia of Systems Biology , 2013, Springer New York.

[15]  G. Stephanopoulos,et al.  Metabolic engineering: past and future. , 2013, Annual review of chemical and biomolecular engineering.

[16]  Chris J. Myers,et al.  Tablet—next generation sequence assembly visualization , 2009, Bioinform..

[17]  C Burks,et al.  The GenBank genetic sequence data bank. , 1988, Nucleic acids research.

[18]  Timothy S. Ham,et al.  Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools , 2012, Nucleic acids research.

[19]  Christopher A. Voigt,et al.  Genetic circuit design automation , 2016, Science.

[20]  Douglas Densmore,et al.  Interactive assembly algorithms for molecular cloning , 2014, Nature Methods.

[21]  Yeo Joon Yoon,et al.  Reinvigorating natural product combinatorial biosynthesis with synthetic biology. , 2015, Nature chemical biology.

[22]  Jacob Beal,et al.  Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0 , 2018, J. Integr. Bioinform..

[23]  Prashant Vaidyanathan,et al.  A Framework for Genetic Logic Synthesis , 2015, Proceedings of the IEEE.

[24]  Allan Kuchinsky,et al.  The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.

[25]  James W. Fickett,et al.  The GenBank genetic sequence databank , 1986, Nucleic Acids Res..

[26]  Zhang Yan,et al.  Recent advances in synthetic biology , 2015 .

[27]  Emma M. B. Weeding,et al.  Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems , 2011, PloS one.

[28]  E. Prud hommeaux,et al.  SPARQL query language for RDF , 2011 .

[29]  Zhen Zhang,et al.  Synthetic Biology Open Language (SBOL) Version 2.0.0 , 2015, J. Integr. Bioinform..

[30]  Christopher A. Voigt,et al.  Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca , 2012, Proceedings of the National Academy of Sciences.

[31]  A. Arkin,et al.  Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems , 2012, Biotechnology journal.

[32]  T. Ellis,et al.  Bricks and blueprints: methods and standards for DNA assembly , 2015, Nature Reviews Molecular Cell Biology.

[33]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[34]  Manuel Porcar,et al.  iGEM 2.0—refoundations for engineering biology , 2014, Nature Biotechnology.

[35]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[36]  Y. Benenson.  Biomolecular computing systems: principles, progress and potential , 2012, Nature Reviews Genetics.

[37]  Jacob Beal,et al.  Proposed data model for the next version of the synthetic biology open language. , 2015, ACS synthetic biology.

[38]  William J. Slattery.  An index of U.S. voluntary engineering standards : covering those standards, specifications, test methods, and recommended practices issued by National Standardization Organizations in the United States , 1971 .

[39]  Zhen Zhang,et al.  libSBOLj 2.0: A Java Library to Support SBOL 2.0 , 2015, IEEE Life Sciences Letters.

[40]  Christopher A. Voigt,et al.  Genetic programs constructed from layered logic gates in single cells , 2012, Nature.

[41]  Gary D Bader,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[42]  Edda Klipp,et al.  Systems Biology , 1994 .

[43]  Rodrigo Weber dos Santos,et al.  CellML and associated tools and techniques , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[44]  Christopher A. Voigt,et al.  Characterization of 582 natural and synthetic terminators and quantification of their design constraints , 2013, Nature Methods.

[45]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[46]  Rainer Breitling,et al.  Steps towards the synthetic biology of polyketide biosynthesis , 2014, FEMS microbiology letters.

[47]  Ieee Standards Board.  IEEE standard verilog hardware description language , 2001 .

[48]  Christopher A. Voigt,et al.  Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters , 2013, Molecular Systems Biology.

[49]  Galdzicki Michal,et al.  SBOL: A community standard for communicating designs in synthetic biology , 2013 .