from pathways databases to network models of switching behavior从路径数据库转换行为的网络模型.pdfVIP

Education From Pathways Databases to Network Models of Switching Behavior * Baltazar D. Aguda , Andrew B. Goryachev Introduction resources on the Internet. Note that we are not concerned The excitement in today’s biology is driven by the huge here with computational methods of determining or amounts of information generated by high-throughput data- inferring network topology, or connectivity from omics data— acquisition technologies, and by the expectation that these on this topic the reader is referred to an article of Qi and Ge datasets will soon provide detailed understanding of life’s [3] that appeared in this journal recently. processes. Ultimately, these datasets have to be integrated In this article, we illustrate how one extracts a reduced into a framework that facilitates the study of the dynamics network model from a large preliminary network obtained arising from networks of physico–chemical interactions from databases. The model extraction procedure is explained orchestrating the physiology of a biological cell. The in the context of a specific biological question about a cell bioinformatics community is actively responding to this call cycle checkpoint called the ‘‘restriction point’’ (R point)— for integration in terms of frameworks of pathways databases that is, what is the smallest subset of interactions in the given [1,2]. This paper addresses the use of these databases as network that can account for the switching behavior sources of dynamical models for biological phenomena. We associated with this checkpoint? A method of qualitative focus here on models that are based on molecular