Rewriting Logic and Symbolic Systems Biology applied to EGF Signaling Pathway

The idea of symbolic biological experiments opens up an exciting new world of challenging applications for formal methods. Pathway Logic is a step towards a vision of symbolic systems biology. In this paper we describe the Pathway Logic approach to the modeling and analysis of signal transduction, and the use of the Pathway Logic Assistant (PLA) tool to browse and query these models. The epidermal growth factor (EGF) signaling pathway is used to illustrate the concepts. In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a variety of formal tools are used to query these models.