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Extending boolean regulatory network models with answer set programming

机译:使用答案集编程扩展布尔规则网络模型

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摘要

Because of their simplicity, boolean networks are a popular formalism to model gene regulatory networks. However, they have their limitations, including their inability to formally and unambiguously define network behaviour, and their lack of the possibility to model meta interactions, i.e., interactions that target other interactions. In this paper we develop an answer set programming (ASP) framework that supports threshold boolean network semantics and extends it with the capability to model meta interactions. The framework is easy to use but sufficiently flexible to express intricate interactions that go beyond threshold network semantics as we illustrate with an example of a Mammalian cell cycle network. Moreover, readily available answer set solvers can be used to find the steady states of the network.
机译:由于其简单性,布尔网络是一种流行的形式主义,用于对基因调控网络进行建模。但是,它们有其局限性,包括无法正式和明确地定义网络行为,并且缺乏建模元交互(即以其他交互为目标的交互)的可能性。在本文中,我们开发了一个答案集编程(ASP)框架,该框架支持阈值布尔网络语义,并通过对元交互进行建模的功能对其进行了扩展。该框架易于使用,但具有足够的灵活性,可以表达超出阈值网络语义的复杂交互,如我们以哺乳动物细胞周期网络为例进行说明。此外,可以使用随时可用的答案集求解器来查找网络的稳态。

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