Formal Executable Models of Cell Signaling Primitives

We have discussed key features of intra-cellular signaling processes as computational primitives and shown how they can be modeled, executed and analyzed using pathway logic. This is intended to lay the ground for deeper formal studies of the relations between the building blocks and composition mechanisms of biological processes and foundations of computing. Pathway logic has a knowledge base of over 1000 rules and 600 basic components and is used to analyze signaling in different cell types. Questions of interest include effects of perturbations (knockouts, knockins) and finding upstream and downstream effects of given components.