libSBOLj 2.0: A Java Library to Support SBOL 2.0

Misirli

Abstract

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.

Citation

Misirli. (2016). libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 34 - 37. https://doi.org/10.1109/LLS.2016.2546546

• Acceptance Date: Feb 27, 2016
• Publication Date: Mar 24, 2016
• Journal: IEEE Life Sciences Letters
• Publisher: Institute of Electrical and Electronics Engineers (IEEE)
• Pages: 34 - 37
• DOI: https://doi.org/10.1109/LLS.2016.2546546
• Keywords: Application programming interfaces; Computational biology; Java; Software libraries; Software tools; Synthetic biology; Application programming interfaces; computational biology; software libraries; software tools; synthetic biology
• Publisher URL: http://ieeexplore.ieee.org/document/7440806/authors?ctx=authors