Synthetic Biology Open Language (SBOL) Version 2.3

Curtis Madsen 1 , Angel Goñi Moreno 2 , Umesh P 3 , Zachary Palchick 4 , Nicholas Roehner 5 , Christian Atallah 2 , Bryan Bartley 5 , Kiri Choi 6 , Robert Sidney Cox 7 , Thomas Gorochowski 8 , Raik Grünberg 9 , Chris Macklin 10 , James McLaughlin 2 , Xianwei Meng 11 , Tramy Nguyen 12 , Matthew Pocock 13 , Meher Samineni 12 , James Scott-Brown 14 , Ysis Tarter 10 , Michael Zhang 12 , Zhen Zhang 15 , Zach Zundel 12 , Jacob Bealhttp://orcid.org/https://orcid.org/0000-0002-1663-5102 5 , Michael Bissell 10 , Kevin Clancy 16 , John H. Gennari 6 , Goksel Misirli 17 , Chris Myers 12 , Ernst Oberortner 11 , Herbert Sauro 6 , and Anil Wipat 2
  • 1 Boston University, Boston, MA, USA
  • 2 Newcastle University, Newcastle, UK
  • 3 Kerala Technological University, Thiruvananthapuram, India
  • 4 Zymergen, Emeryville, CA, USA
  • 5 Raytheon BBN Technologies, Cambridge, MA, USA
  • 6 University of Washington, Seattle, WA, USA
  • 7 Prospect Bio, Brisbane, CA, USA
  • 8 University of Bristol, Bristol, UK
  • 9 KAUST, Thuwal, Saudi Arabia
  • 10 Amyris, Inc., Emeryville, CA, USA
  • 11 DOE Joint Genome Institute, Walnut Creek, CA, USA
  • 12 University of Utah, Salt Lake City, UT, USA
  • 13 Turing Ate My Hamster, Ltd., Newcastle, UK
  • 14 Imperial College, London, UK
  • 15 Utah State University, Logan, UT, USA
  • 16 BioCoder Consulting, Carlsbad, CA, USA
  • 17 Keele University, Keele, Staffordshire, UK

Abstract

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 is 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 2.3.0 of SBOL, which builds upon version 2.2.0 published in last year’s JIB Standards in Systems Biology special issue. In particular, SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.

If the inline PDF is not rendering correctly, you can download the PDF file here.

OPEN ACCESS

Journal + Issues

Search