title: A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.
abstract: Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.
authors.forename: Tramy
authors.initials: T
authors.lastname: Nguyen
authors.affiliation: Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Roehner
authors.forename: Zach
authors.initials: Z
authors.lastname: Zundel
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Myers
mesh_terms: D008954:Models, Biological; D011381:Programming Languages; D058615:Synthetic Biology / Q000592:standards*; D049490:Systems Biology / Q000592:standards*
keywords: SBML; SBOL; genetic design automation; modeling; standards