Electrical Engineering
      and Computer Sciences

Electrical Engineering and Computer Sciences

COLLEGE OF ENGINEERING

UC Berkeley

Quantitative and Probabilistic Modeling in Pathway Logic

Alessandro Abate, Yu Bai, Natalie Sznajder, Carolyn Talcott and Ashish Tiwari

EECS Department
University of California, Berkeley
Technical Report No. UCB/EECS-2006-180
December 16, 2006

http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-180.pdf

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.


BibTeX citation:

@techreport{Abate:EECS-2006-180,
    Author = {Abate, Alessandro and Bai, Yu and Sznajder, Natalie and Talcott, Carolyn and Tiwari, Ashish},
    Title = {Quantitative and Probabilistic Modeling in Pathway Logic},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2006},
    Month = {Dec},
    URL = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-180.html},
    Number = {UCB/EECS-2006-180},
    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.}
}

EndNote citation:

%0 Report
%A Abate, Alessandro
%A Bai, Yu
%A Sznajder, Natalie
%A Talcott, Carolyn
%A Tiwari, Ashish
%T Quantitative and Probabilistic Modeling in Pathway Logic
%I EECS Department, University of California, Berkeley
%D 2006
%8 December 16
%@ UCB/EECS-2006-180
%U http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-180.html
%F Abate:EECS-2006-180