Talcott, C. (2008). Pathway Logic. In: Bernardo, M., Degano, P., Zavattaro, G. (eds) Formal Methods for Computational Systems Biology. SFM 2008. Lecture Notes in Computer Science, vol 5016. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68894-5_2
Pathway Logic (PL) is an approach to modeling and analysis of biological processes based on rewriting logic. This tutorial describes the use of PL to model signal transduction processes. It begins with a general discussion of Symbolic Systems Biology, followed by some background on rewriting logic and signal transduction. The representation and analysis of a small model Ras and Raf activation is presented in some detail. This is followed by discussion of a curated model of early signaling events in response to Epidermal Growth Factor stimulation.