A Language for Biochemical Systems: Design and Formal Specification
A Language for Biochemical Systems: Design and Formal Specification
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生化系统语言：设计和形式规范
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发表时间：
2010
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通讯作者：
G. Plotkin
中科院分区：
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作者：
Michael Pedersen;G. Plotkin
本文介绍了一种生物化学系统（LBS）的语言，它结合了基于规则的建模方法与模块化。它是基于生物化学系统（CBS）的微积分，它提供了模块化的描述代谢，信号和调节网络之间的反应修饰的复合物，同时发生在一个层次的车厢和可能的跨室相互作用和运输。LBS的其他功能，针对实际和大规模的应用程序，包括物种表达式，以简洁的方式操纵大型复杂，参数化模块与子类型的概念，用于编写可重用的模块，和非确定性处理组合爆炸。这些功能都通过实例演示。LBS的正式规范，然后通过一个抽象的语法和一般的语义，这是一个结构上的参数有关的目标语义对象的具体选择。这种结构的具体情况下的Petri网，有色Petri网，常微分方程和连续时间马尔可夫链的例子也给出了。
This paper introduces a Language for Biochemical Systems (LBS) which combines rule-based approaches to modelling with modularity. It is based on the Calculus of Biochemical Systems (CBS) which affords modular descriptions of metabolic, signalling and regulatory networks in terms of reactions between modified complexes, occurring concurrently inside a hierarchy of compartments and with possible cross-compartment interactions and transport. Additional features of LBS, targeted towards practical and large-scale applications, include species expressions for manipulating large complexes in a concise manner, parameterised modules with a notion of subtyping for writing reusable modules, and nondeterminism for handling combinatorial explosion. These features are demonstrated through examples. A formal specification of LBS is then given through an abstract syntax and a general semantics which is parametric on a structure pertaining to the specific choice of target semantical objects. Examples of such structures for the specific cases of Petri nets, coloured Petri nets, ODEs and continuous time Markov chains are also given.