Synthetic Biology Open Language (SBOL) Version 2.1.0

Summary Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.

[1]  A. Cornish-Bowden Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. , 1985, Nucleic acids research.

[2]  Herbert M Sauro,et al.  Designing and engineering evolutionary robust genetic circuits , 2010, Journal of biological engineering.

[3]  Karen Eilbeck,et al.  Evolution of the Sequence Ontology terms and relationships , 2009, J. Biomed. Informatics.

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

[5]  M. Elowitz,et al.  Synthetic Biology: Integrated Gene Circuits , 2011, Science.

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

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

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

[9]  Mads Kaern,et al.  The engineering of gene regulatory networks. , 2003, Annual review of biomedical engineering.

[10]  H. Sauro,et al.  Standard Biological Parts Knowledgebase , 2011, PloS one.

[11]  Michael A. Savageau,et al.  Design principles for elementary gene circuits: Elements, methods, and examples. , 2001, Chaos.

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