Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language

Abstract

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

Nicholas Roehner
Nicholas Roehner
Raytheon BBN Technologies, Researcher
Zhen Zhang
Zhen Zhang
Utah State University, Assistant Professor
Tramy Nguyen
Tramy Nguyen
Raytheon BBN Technologies, Research Scientist/Software Engineer

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