libSBOLj 2.0: A Java Library to Support SBOL 2.0

Zhen Zhang; Tramy Nguyen; Nicholas Roehner; Goksel Misirli; Matthew Pocock; Ernst Oberortner; Meher Samineni; Zach Zundel; Jacob Beal; Kevin Clancy; Anil Wipat; Chris J. Myers

doi:10.1109/LLS.2016.2546546

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libSBOLj 2.0: A Java Library to Support SBOL 2.0

Journal article

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libSBOLj 2.0: A Java Library to Support SBOL 2.0

Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Goksel Misirli, Matthew Pocock, Ernst Oberortner, Meher Samineni, Zach Zundel, Jacob Beal, Kevin Clancy, …

IEEE life sciences letters, Vol.1(4), pp.34-37

12/2015

DOI: 10.1109/LLS.2016.2546546

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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.

Application programming interfaces

Computational biology

Java

Software libraries

Software tools

Synthetic biology

Details

Title: Subtitle: libSBOLj 2.0: A Java Library to Support SBOL 2.0
Creators: Zhen Zhang - University of Utah
Tramy Nguyen - University of Utah
Nicholas Roehner - Boston University
Goksel Misirli - Newcastle University
Matthew Pocock - Turing Institute
Ernst Oberortner - Joint Genome Institute
Meher Samineni - University of Utah
Zach Zundel - University of Utah
Jacob Beal - RTX
Kevin Clancy - Thermo Fisher Scientific
Anil Wipat - Newcastle University
Chris J. Myers - University of Utah
Resource Type: Journal article
Publication Details: IEEE life sciences letters, Vol.1(4), pp.34-37
Publisher: IEEE
DOI: 10.1109/LLS.2016.2546546
ISSN: 2332-7685
eISSN: 2332-7685
Grant note: EP/J02175X/1 / Engineering and Physical Sciences Research Council (10.13039/501100000266) DBI-1356041; DBI-1355909 / National Science Foundation (10.13039/100000001)
Language: English
Date published: 12/2015
Academic Unit: Electrical and Computer Engineering
Record Identifier: 9984627300702771

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