Literature DB >> 31199770

Synthetic Biology Open Language (SBOL) Version 2.3.

Curtis Madsen1, Angel Goñi Moreno2, Umesh P3, Zachary Palchick4, Nicholas Roehner5, Christian Atallah2, Bryan Bartley5, Kiri Choi6, Robert Sidney Cox7, Thomas Gorochowski8, Raik Grünberg9, Chris Macklin10, James McLaughlin2, Xianwei Meng11, Tramy Nguyen12, Matthew Pocock13, Meher Samineni12, James Scott-Brown14, Ysis Tarter10, Michael Zhang12, Zhen Zhang15, Zach Zundel12, Jacob Beal5, Michael Bissell10, Kevin Clancy16, John H Gennari6, Goksel Misirli17, Chris Myers12, Ernst Oberortner11, Herbert Sauro6, Anil Wipat2.   

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.

Keywords:  Standards; Synthetic Biology; Synthetic Biology Open Language

Mesh:

Year:  2019        PMID: 31199770      PMCID: PMC6798821          DOI: 10.1515/jib-2019-0025

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


  6 in total

Review 1.  Biological Materials: The Next Frontier for Cell-Free Synthetic Biology.

Authors:  Richard J R Kelwick; Alexander J Webb; Paul S Freemont
Journal:  Front Bioeng Biotechnol       Date:  2020-05-12

2.  DisCoTune: versatile auxiliary plasmids for the production of disulphide-containing proteins and peptides in the E. coli T7 system.

Authors:  Andreas B Bertelsen; Celeste Menuet Hackney; Carolyn N Bayer; Lau D Kjelgaard; Maja Rennig; Brian Christensen; Esben Skipper Sørensen; Helena Safavi-Hemami; Tune Wulff; Lars Ellgaard; Morten H H Nørholm
Journal:  Microb Biotechnol       Date:  2021-08-18       Impact factor: 5.813

3.  A Network Approach to Genetic Circuit Designs.

Authors:  Matthew Crowther; Anil Wipat; Ángel Goñi-Moreno
Journal:  ACS Synth Biol       Date:  2022-08-31       Impact factor: 5.249

4.  A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication.

Authors:  Yerko Ortiz; Javier Carrión; Rafael Lahoz-Beltrá; Martín Gutiérrez
Journal:  Front Bioeng Biotechnol       Date:  2021-05-10

5.  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

6.  Towards standardization guidelines for in silico approaches in personalized medicine.

Authors:  Søren Brunak; Catherine Bjerre Collin; Katharina Eva Ó Cathaoir; Martin Golebiewski; Marc Kirschner; Ingrid Kockum; Heike Moser; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2020-07-24
  6 in total

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