基于时态逻辑模式的细胞交互网络动态模型查询
Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
摘要：
近年来，细胞相互作用网络的动力学模型变得越来越大。基于模型检查的形式化验证提供了一种强大的技术来跟上这种规模和复杂性的增加。然而，模型检查方法的应用受到了阻碍，因为非专家用户很难在时序逻辑中提出适当的问题。为了处理这个问题，我们建议使用的模式，即，高层次的查询模板，捕获反复出现的生物问题，并可以自动转换为时序逻辑。已开发的一套模式的适用性进行了研究，通过分析的全球监管机构控制大肠杆菌的碳饥饿反应的网络的扩展模型。
英文摘要：
Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The application of model-checking approaches is hampered, however, by the difficulty for non-expert users to formulate appropriate questions in temporal logic. In order to deal with this problem, we propose the use of patterns, that is, high-level query templates that capture recurring biological questions and that can be automatically translated into temporal logic. The applicability of the developed set of patterns has been investigated by the analysis of an extended model of the network of global regulators controlling the carbon starvation response in Escherichia coli.
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