Roehner Nicholas, Myers Chris J
Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States.
ACS Synth Biol. 2014 Feb 21;3(2):57-66. doi: 10.1021/sb400066m. Epub 2013 Sep 13.
Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.
最近，我们开始见证合成生物学的潜力，这里以经过基因工程改造的细菌和酵母为例，它们可用于生产生物燃料、制造药物前体，甚至侵入肿瘤细胞。然而，这些项目的成功往往在转化和应用于新项目时失败，缺乏结合DNA结构和功能描述的工程标准使这个问题更加严重。为满足这一需求，本文描述了一种将系统生物学标记语言（SBML）与合成生物学开放语言（SBOL）相连接的方法，SBML和SBOL分别是描述生化模型和DNA组件的现有标准。我们的方法首先用SBOL DNA组件注释SBML模型元素，如物种和反应。然后根据模型构建一个图，其中顶点对应模型中的元素，边对应这些元素之间的因果关系。最后，遍历该图，将注释性DNA组件组装成一个复合DNA组件，该组件用于注释模型本身，并可供其他复合模型和DNA组件引用。通过这种方式，我们的方法可用于构建一个用DNA组件注释的分层模型库。这样的库对于未来任何遗传技术映射算法都是有用的输入，该算法将自动完成合成DNA组件以满足行为规范的过程。我们的SBML到SBOL注释方法在我们最新版本的遗传设计自动化（GDA）软件工具iBioSim中得以实现。
