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libSBOLj3: a graph-based library for design and data exchange in synthetic biology.

Mısırlı, Göksel

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Abstract

The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBOLj3 to facilitate data exchange and provide interoperability between computer-aided design and automation tools using this standard. The library adopts a graph-based approach. Tool developers can extend these graphs with application-specific information and use detailed validation reports to identify errors and interoperability issues and apply best practice rules. The libSBOLj3 library is implemented in Java and can be downloaded or used as a Maven dependency. The open-source project, code examples and documentation about accessing and using the library are available via GitHub at https://github.com/SynBioDex/libSBOLj3. [Abstract copyright: © The Author(s) 2023. Published by Oxford University Press.]

Journal Article Type Article
Acceptance Date Aug 23, 2023
Online Publication Date Aug 25, 2023
Publication Date Aug 1, 2023
Deposit Date Sep 4, 2023
Publicly Available Date Sep 6, 2023
Journal Bioinformatics
Print ISSN 1367-4803
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 39
Issue 8
Article Number btad525
Pages 3
DOI https://doi.org/10.1093/bioinformatics/btad525
Keywords Computational Mathematics; Computational Theory and Mathematics; Computer Science Applications; MolecularSynthetic Biology; Biochemistry; Statistics and Probability, Gene Library, Language, Automation, Documentation
Publisher URL https://academic.oup.com/bioinformatics/article/39/8/btad525/7251028?login=true

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