title: 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).
authors.affiliation: †Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Roehner
authors.affiliation: ‡Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: ‡Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States.
authors.forename: Tramy
authors.initials: T
authors.lastname: Nguyen
authors.affiliation: ‡Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States.
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Myers
mesh_terms: D066289:Data Curation; D008954:Models, Biological; D011381:Programming Languages; D049490:Systems Biology
keywords: SBML; SBOL; genetic design automation; modeling; standards