The Bond-Calculus: A Process Algebra for Complex Biological Interaction Dynamics
The Bond-Calculus: A Process Algebra for Complex Biological Interaction Dynamics
复制标题
债券微积分：复杂生物相互作用动力学的过程代数
DOI：
--
复制
发表时间：
2018
期刊：
影响因子：
--
通讯作者：
I. Stark
中科院分区：
文献类型：
--
作者：
Thomas Wright;I. Stark
我们提出了键合演算，这是一种用于模拟生物和化学系统的进程代数，具有非线性动力学、多向相互作用和试剂的动态成键。基于微分方程式的数学模型在模拟和理解生物系统的动力学方面起到了很大的作用。定量过程代数旨在建立对生物系统的更高级别的描述，捕捉其行为背后的代理人和相互作用，并可编译为一系列较低级别的数学模型。键合演算建立在Kwiatkowski、Banks和Stark的连续圆周率演算的基础上，增加了基于亲和力模式和一般动力学定律的灵活的多路通信操作。我们发展了一种基于向量场和线性算子的合成语义，并用它来定义该系统的时间演化。这使得能够通过生成微分方程式或随机模拟来进行模拟和分析。最后，我们将我们的框架应用于一个现有的生物学模型：库兹涅佐夫的经典肿瘤免疫相互作用模型。
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been instrumental in modelling and understanding the dynamics of biological systems. Quantitative process algebras aim to build higher level descriptions of biological systems, capturing the agents and interactions underlying their behaviour, and can be compiled down to a range of lower level mathematical models. The bond-calculus builds upon the work of Kwiatkowski, Banks, and Stark's continuous pi-calculus by adding a flexible multiway communication operation based on affinity patterns and general kinetic laws. We develop a compositional semantics based on vector fields and linear operators, which we use to define the time evolution of this system. This enables simulation and analysis via differential equation generation or stochastic simulation. Finally, we apply our framework to an existing biological model: Kuznetsov's classic model of tumour immune interactions.
影响因子：
8.8
作者：
Soufiene Benkirane;J. Hillston;C. McCaig;R. Norman;C. Shankland
通讯作者：
Soufiene Benkirane;J. Hillston;C. McCaig;R. Norman;C. Shankland
影响因子：
1.1
作者：
Ciocchetta, Federica;Hillston, Jane
通讯作者：
Hillston, Jane
影响因子：
3.5
作者：
KUZNETSOV, VA;MAKALKIN, IA;PERELSON, AS
通讯作者：
PERELSON, AS