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The Tenth q-bio Summer School - Albuquerque: Lecture 1

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Introduction to modeling signal transduction using rules

James R. Faeder, University of Pittsburgh School of Medicine

This lecture will describe the challenges faced in developing detailed models of biochemical networks, which encompass large numbers of interacting components. Although simpler coarse-grained models are often useful for gaining insight into biological mechanisms, such detailed models are necessary to understand how molecular components work in the network context and essential to developing the ability to manipulate such networks for practical benefits. The rule-based modeling (RBM) approach, in which biological molecules can be represented as structured objects whose interactions are governed by rules that describe their biochemical interactions, is the basis for addressing multiple scaling issues that arise in the development of large scale models. Currently available software tools for RBM, such as BioNetGen, Kappa, and Simmune, enable the specification and simulation of large scale models, and these tools are in widespread use by the modeling community. I will review some of the developments that gave rise to those capabilities, and then I will present several applications of the approach which yield new insights into the mechanisms that govern cell fate decisions.

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