Quantitative and Probabilistic Modeling in Pathway Logic

This paper presents a study of possible extensions of pathway logic to represent and reason about semiquantitative and probabilistic aspects of biological processes. The underlying theme is the annotation of reaction rules with affinity information that can be used in different simulation strategies. Several such strategies were implemented, and experiments carried out to test feasibility, and to compare results of different approaches. Dimerization in the ErbB signalling network, important in cancer biology, was used as a test case.