将系统生物学标记语言（SBML）自动翻译成β-结合物。

An automatic translation of SBML into Beta-binders.

作者信息

Ciocchetta Federica, Priami Corrado, Quaglia Paola

机构信息

University of Edinburgh, Scotland, UK.

出版信息

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):80-90. doi: 10.1109/TCBB.2007.70219.

DOI:10.1109/TCBB.2007.70219

PMID:18245877

Abstract

A translation of Systems Biology Markup Language (SBML) into a process algebra is proposed in order to allow the formal specification, the simulation and the formal analysis of biological models. Beta-binders, a language with a quantitative stochastic extension, is chosen for the translation. The proposed translation focuses on the main components of SBML models, as species and reactions. Furthermore, it satisfies the compositional property, i.e. the translation of the whole model is obtained by composing the translation of the subcomponents. An automatic translator tool of SBML models into Beta-binders has been implemented as well. Finally, the translation of a simple model is reported.

摘要

为了实现生物模型的形式化规范、模拟和形式化分析，提出了一种将系统生物学标记语言（SBML）转换为进程代数的方法。翻译选用了具有定量随机扩展的语言Beta-binders。所提出的转换重点关注SBML模型的主要组件，如物种和反应。此外，它满足组合特性，即整个模型的转换是通过组合子组件的转换得到的。还实现了一个将SBML模型自动转换为Beta-binders的工具。最后，报告了一个简单模型的转换情况。