Roehner Nicholas, Zhang Zhen, Nguyen Tramy, Myers Chris J
†Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States.
‡Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States.
ACS Synth Biol. 2015 Aug 21;4(8):873-9. doi: 10.1021/sb5003289. Epub 2015 Apr 9.
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).
在合成生物学的背景下，模型生成是基于基因设计构建生化模型的自动化过程。本文讨论了基因设计自动化（GDA）软件工具中模型生成的用例，并介绍了使该过程有用的标准和模型注释的基础概念。最后，本文展示了GDA软件工具iBioSim中模型生成的实现，并提供了一个从用合成生物学开放语言（SBOL）编写的4输入与门传感器设计生成系统生物学标记语言（SBML）模型的示例。
