Biomaterial Database

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language. 2015

Nicholas Roehner, and Zhen Zhang, and Tramy Nguyen, and Chris J Myers

†Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States.

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).

UI	MeSH Term	Description	Entries
D008954	Models, Biological	Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.	Biological Model,Biological Models,Model, Biological,Models, Biologic,Biologic Model,Biologic Models,Model, Biologic
D011381	Programming Languages	Specific languages used to prepare computer programs.	Language, Programming,Languages, Programming,Programming Language
D049490	Systems Biology	Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.	Biology, Systems
D066289	Data Curation	Management activities required to maintain research data to ensure that they are fit for contemporary use and available for discovery and reuse.	Data Annotation,Data Archiving,Annotation, Data,Archiving, Data,Curation, Data