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We use computational modeling and formal analysis techniques to study temporal behavior of a discrete logical model of the naïve T cell differentiation. The model is analyzed formally and automatically by performing temporal logic queries via statistical model checking. While the model can be verified and then further explored using Monte Carlo simulations, model checking allows for much more efficient...
Recent work has presented logical models and showed the benefits of applying logical approaches to studying the dynamics of biological networks. In this work, we develop a methodology for automating the design of such models by utilizing methods and algorithms from the field of electronic design automation. We anticipate that automated discrete model development will greatly improve the efficiency...
We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intra-cellular biochemistry. Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less...
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