Synthetic Biology Open Language (SBOL) Version 2.1.0

Jacob Beal 1 , Robert Sidney Cox 2 , Raik Grünberg 3 , James McLaughlin 4 , Tramy Nguyen 5 , Bryan Bartley 6 , Michael Bissell 7 , Kiri Choi 6 , Kevin Clancy 8 , Chris Macklin 7 , Curtis Madsen 9 , Goksel Misirli 4 , Ernst Oberortner 10 , Matthew Pocock 11 , Nicholas Roehner 9 , Meher Samineni 5 , Michael Zhang 5 , Zhen Zhang 12 , Zach Zundel 5 , John H. Gennari 6 , Chris Myers 5 , Herbert Sauro 6  and Anil Wipat 4
  • 1 Raytheon BBN Technologies, Cambridge, United States of America
  • 2 Kobe University, Kobe, Japan
  • 3 King Abdullah University for Science and Technology, Thuwal, Saudi Arabia
  • 4 Newcastle University, Newcastle, United Kingdom of Great Britain and Northern Ireland
  • 5 University of Utah, Salt Lake City, United States of America
  • 6 University of Washington, Seattle, United States of America
  • 7 Amyris, Inc., Emeryville, United States of America
  • 8 ThermoFisher Scientific, Waltham, United States of America
  • 9 Boston University, Boston, United States of America
  • 10 DOE Joint Genome Institute, Walnut Creek, United States of America
  • 11 Turing Ate My Hamster LTD, Backworth, United Kingdom of Great Britain and Northern Ireland
  • 12 University of South Florida, Tampa, United States of America

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.

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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