Literature DB >> 28187407

Synthetic Biology Open Language (SBOL) Version 2.1.0.

Jacob Beal, Robert Sidney Cox, Raik Grünberg, James McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John Gennari, Chris Myers, Herbert Sauro, Anil Wipat.   

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 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.

Entities:  

Mesh:

Year:  2016        PMID: 28187407     DOI: 10.2390/biecoll-jib-2016-291

Source DB:  PubMed          Journal:  J Integr Bioinform        ISSN: 1613-4516


  3 in total

1.  Tellurium: An extensible python-based modeling environment for systems and synthetic biology.

Authors:  Kiri Choi; J Kyle Medley; Matthias König; Kaylene Stocking; Lucian Smith; Stanley Gu; Herbert M Sauro
Journal:  Biosystems       Date:  2018-07-25       Impact factor: 1.973

2.  Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Authors:  Falk Schreiber; Gary D Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; Chris Myers; David Nickerson; Björn Sommer; Dagmar Walthemath
Journal:  J Integr Bioinform       Date:  2016-12-18

3.  The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.

Authors:  James Alastair McLaughlin; Jacob Beal; Göksel Mısırlı; Raik Grünberg; Bryan A Bartley; James Scott-Brown; Prashant Vaidyanathan; Pedro Fontanarrosa; Ernst Oberortner; Anil Wipat; Thomas E Gorochowski; Chris J Myers
Journal:  Front Bioeng Biotechnol       Date:  2020-09-11
  3 in total

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