Literature DB >> 26528570

Synthetic Biology Open Language (SBOL) Version 2.0.0.

Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H Gennari, Chris Myers, Anil Wipat, Herbert Sauro.   

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 2.0 of SBOL, introducing a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard also includes rules and best practices on how to use this data model and populate it with relevant design details. The publication of this specification is intended to make these capabilities more widely accessible to potential developers and users in the synthetic biology community and beyond.

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Year:  2015        PMID: 26528570     DOI: 10.2390/biecoll-jib-2015-272

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


  7 in total

1.  Vivarium: an interface and engine for integrative multiscale modeling in computational biology.

Authors:  Eran Agmon; Ryan K Spangler; Christopher J Skalnik; William Poole; Shayn M Peirce; Jerry H Morrison; Markus W Covert
Journal:  Bioinformatics       Date:  2022-02-04       Impact factor: 6.937

2.  GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data.

Authors:  Marta Vazquez-Vilar; Alfredo Quijano-Rubio; Asun Fernandez-Del-Carmen; Alejandro Sarrion-Perdigones; Rocio Ochoa-Fernandez; Peio Ziarsolo; José Blanca; Antonio Granell; Diego Orzaez
Journal:  Nucleic Acids Res       Date:  2017-02-28       Impact factor: 16.971

Review 3.  Biocircuits in plants and eukaryotic algae.

Authors:  Mayna da Silveira Gomide; Matheus de Castro Leitão; Cíntia Marques Coelho
Journal:  Front Plant Sci       Date:  2022-09-23       Impact factor: 6.627

Review 4.  Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants.

Authors:  Camilla Beate Hill; Tobias Czauderna; Matthias Klapperstück; Ute Roessner; Falk Schreiber
Journal:  Front Bioeng Biotechnol       Date:  2015-10-21

Review 5.  Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle.

Authors:  Pablo Carbonell; Andrew Currin; Adrian J Jervis; Nicholas J W Rattray; Neil Swainston; Cunyu Yan; Eriko Takano; Rainer Breitling
Journal:  Nat Prod Rep       Date:  2016-05-17       Impact factor: 13.423

6.  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

Review 7.  Beyond natural: synthetic expansions of botanical form and function.

Authors:  Nicola J Patron
Journal:  New Phytol       Date:  2020-04-23       Impact factor: 10.323

  7 in total

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