A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language

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 b...

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Veröffentlicht in:ACS synthetic biology 2016-06, Vol.5 (6), p.479-486
Hauptverfasser: Nguyen, Tramy, Roehner, Nicholas, Zundel, Zach, Myers, Chris J
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Models, Biological
Programming Languages
Synthetic Biology - standards
Systems Biology - standards
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creator Nguyen, Tramy
Roehner, Nicholas
Zundel, Zach
Myers, Chris J
description 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.
doi_str_mv 10.1021/acssynbio.5b00212
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Systems Biology - standards
title A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
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