Journal article
Synthetic Biology Open Language (SBOL) Version 2.3
Journal of integrative bioinformatics, Vol.16(2), 20190025
06/13/2019
DOI: 10.1515/jib-2019-0025
PMCID: PMC6798821
PMID: 31199770
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.
Details
- Title: Subtitle
- Synthetic Biology Open Language (SBOL) Version 2.3
- Creators
- Curtis Madsen - Boston UniversityAngel Goñi Moreno - Newcastle University, Newcastle, UKUmesh P - A P J Abdul Kalam Technological UniversityZachary Palchick - ZogenixNicholas Roehner - RTXChristian Atallah - Newcastle UniversityBryan Bartley - RTXKiri Choi - University of WashingtonRobert Sidney CoxThomas Gorochowski - University of BristolRaik Grünberg - King Abdullah University of Science and TechnologyChris Macklin - AmyrisJames McLaughlin - Newcastle UniversityXianwei Meng - Joint Genome InstituteTramy Nguyen - University of UtahMatthew Pocock - Turing InstituteMeher Samineni - University of UtahJames Scott-Brown - Imperial College LondonYsis Tarter - AmyrisMichael Zhang - University of UtahZhen Zhang - Utah State UniversityZach Zundel - University of UtahJacob Beal - RTXMichael Bissell - AmyrisKevin Clancy - BioCoder Consulting, Carlsbad, CA, USAJohn H Gennari - University of WashingtonGoksel Misirli - Keele UniversityChris Myers - University of UtahErnst Oberortner - Joint Genome InstituteHerbert Sauro - University of WashingtonAnil Wipat - Newcastle University
- Resource Type
- Journal article
- Publication Details
- Journal of integrative bioinformatics, Vol.16(2), 20190025
- DOI
- 10.1515/jib-2019-0025
- PMID
- 31199770
- PMCID
- PMC6798821
- NLM abbreviation
- J Integr Bioinform
- ISSN
- 1613-4516
- eISSN
- 1613-4516
- Grant note
- BB/L01386X/1 / Biotechnology and Biological Sciences Research Council
- Language
- English
- Date published
- 06/13/2019
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627242502771
Metrics
4 Record Views