Pathway Logic: Executable Models of Biological Networks

Abstract

In this paper we describe the use of the rewriting logic based Maude tool to model and analyze mammalian signaling pathways. We discuss the representation of the underlying biological concepts and events and describe the use of the new search and model checking capabilities of Maude 2.0 to analyze the modeled network. We also discuss the use of Maude's reflective capability for meta modeling and analyzing the models themselves. The idea of symbolic biological experiments opens up an exciting new world of challenging applications for formal methods in general and for rewriting logic based formalisms in particular.