Fuzzy Matching for Cellular Signaling Networks in a Choroidal Melanoma Model.

Symbolic systems biology aims to explore biological processes as whole systems instead of independent elements. The goal is to define formal models that capture biologists’ reasoning. Pathway Logic (PL) is a system for the development of executable formal models of biomolecular processes. PL uses forwards/backwards collections that assemble a connected set of rules from a rule knowledge base in order to model a system specified by an initial state. For this to succeed the rules must contain component states that have the same level of detail, while at the same time, the knowledge base must capture as much detail as possible. In this paper, we propose a new way to perform matching in the rewriting process in Maude language. We introduce a basic concept of fuzzy match or fuzzy instantiates to which we will use to check requirements imposed by controls in the forward collection and to check if the change part of a rule applies forwards or backwards.