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libSBOLj 2.0: A Java Library to Support SBOL 2.0

Lookup NU author(s): Dr Goksel Misirli, Zach Zundel, Professor Anil Wipat, Professor Christopher Myers

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Abstract

© 2014 IEEE.The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic design automation tools. The latest version of the standard, SBOL 2.0, enables the annotation of a large variety of biological components (e.g., DNA, RNA, proteins, complexes, small molecules, etc.) and their interactions. SBOL 2.0 also allows researchers to organize components into hierarchical modules, to specify their intended functions, and to link modules to models that describe their behavior mathematically. To support the use of SBOL 2.0, we have developed the libSBOLj 2.0 Java library, which provides an easy to use Application Programming Interface (API) for developers, including manipulation of SBOL constructs, serialization to and from an RDF/XML file format, and migration support in the form of conversion from the prior SBOL 1.1 standard to SBOL 2.0. This letter describes the libSBOLj 2.0 library and key engineering decisions involved in its design.


Publication metadata

Author(s): Zhang Z, Nguyen T, Roehner N, Misirli G, Pocock M, Oberortner E, Samineni M, Zundel Z, Beal J, Clancy K, Wipat A, Myers CJ

Publication type: Article

Publication status: Published

Journal: IEEE Life Sciences Letters

Year: 2016

Volume: 1

Issue: 4

Pages: 34-37

Print publication date: 01/12/2015

Acceptance date: 01/01/1900

ISSN (electronic): 2332-7685

Publisher: Institute of Electrical and Electronics Engineers Inc.

URL: http://doi.org/10.1109/LLS.2016.2546546

DOI: 10.1109/LLS.2016.2546546


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