复杂反应机理的BlenX-based组分模拟
BlenX-based compositional modeling of complex reaction mechanisms
摘要：
分子相互作用以一种迷人的方式连接在一起，导致生物系统的复杂行为。理论建模为理解这种网络的动态和功能提供了一个有用的框架。生物网络的复杂性需要概念工具来管理一组可能的相互作用的组合爆炸。一个合适的攻击复杂性的概念工具是组合性，已经成功地用于进程代数领域来建模计算机系统。我们依赖于BlenX程序设计语言，起源于β-binders过程演算，指定和模拟高层次的生物电路的描述。BlenX的Gillespie随机框架要求将唯象函数分解为基本的基本反应。在这项研究中显示了复杂的反应机制到BlenX模板的系统解包。缺失参数的估计/推导和随机过程代数的组成模型建设中出现的挑战进行了讨论。生物钟的一个例子，作为BlenX组合的案例研究。
英文摘要：
Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.
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