A Simple Calculus for Proteins and Cells
A Simple Calculus for Proteins and Cells
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蛋白质和细胞的简单微积分
DOI：
10.1016/j.entcs.2007.05.013
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发表时间：
2007
期刊：
影响因子：
--
通讯作者：
Fabien Tarissan
中科院分区：
文献类型：
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作者：
C. Laneve;Fabien Tarissan
利用过程演算来表示生物系统已经导致了不同演算的设计，如膜演算[Luca Cardelli]。膜结石。在CMSB，页257-278,2004]和-微积分[Vincent Danos和Cosimo Laneve。正式的分子生物学。理论计算机科学，2004(1):69-110。这两种方法都被证明对不同类型的生物系统建模是有用的。为了统一这两个方向，我们引入了生物κ演算，这是一种描述蛋白质和细胞的简单演算，其中键通过共享名称表示，相互作用在结构域水平上建模。蛋白质与蛋白质之间的相互作用最多只能是二元的，而细胞之间的相互作用必须符合排序约束。我们定义了bioκ-微积分的语义，分析了其性质，并通过模拟两个重要的例子：信号通路和病毒感染来讨论其表达性。
The use of process calculi to represent biological systems has led to the design of different calculi such as brane calculi [Luca Cardelli. Brane calculi. In CMSB, pages 257–278, 2004] and κ-calculus [Vincent Danos and Cosimo Laneve. Formal molecular biology. Theoritical Computer Science, 325(1):69–110, 2004]. Both have proved to be useful to model different types of biological systems. As an attempt to unify the two directions, we introduce the bioκ-calculus, a simple calculus for describing proteins and cells, in which bonds are represented by means of shared names and interactions are modelled at the domain level. Protein-protein interactions have to be at most binary and cell interactions have to fit with sort constraints. We define the semantics of bioκ-calculus, analyse its properties, and discuss its expressiveness by modelling two significant examples: a signalling pathway and a virus infection.