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libSBOLj 2.0: A Java Library to Support SBOL 2.0

By Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Göksel Misirli, Matthew Pocock, Ernst Oberortner, Meher Samineni, Zach Zundel, Jacob Beal, Kevin Clancy, Anil Wipat, and Chris J. Myers
Published March 24, 2016.

libSBOLj 2.0: A Java Library to Support SBOL 2.0

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.

View the full article at IEEE Xplore

About the Life Sciences Letters

IEEE Life Sciences Letters (LSL) is a new digital, peer reviewed open access journal. The LSL publication will focus on shorter papers with a quick turnaround, in the area of personalized medicine, pharmaceutical engineering, synthetic biology, and systems biology. Learn more about the scope here. Information for authors can be found here.


Paolo BonatoInterim Editor-in-Chief
Paolo Bonato

Senior Editors

Leroy HoodSenior Editor for Personalized Medicine
Leroy Hood

Richard D. BraatzSenior Editor for Pharmaceutical Engineering
Richard D. Braatz

Ron WeissSenior Editor for Synthetic Biology
Ron Weiss

Hiroaki KitanoSenior Editor for Systems Biology
Hiroaki Kitano

For biographies and the list of all of the editors, click here.