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Quantitative and Probabilistic Modeling in Pathway Logic

Abate, Alessandro
Bai, Yu
Sznajder, Natalie
Talcott, Carolyn
Tiwari, Ashish
Technical Report Identifier: EECS-2006-180
December 16, 2006

Abstract: 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 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.