Modeling Cellular Signaling Systems: An Abstraction-Refinement Approach
File version
Accepted Manuscript (AM)
Author(s)
Olarte, Carlos
Rueda, Camilo
Valencia, Frank D
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Rocha, MP
Rodriguez, JMC
FdezRiverola, F
Valencia, A
Date
Size
File type(s)
Location
Salamanca, Spain
License
Abstract
The molecular mechanisms of cell communication with the environment involve many concurrent processes governing dynamically the cell function. This concurrent behavior makes traditional methods, such as differential equations, unsatisfactory as a modeling strategy since they do not scale well when a more detailed view of the system is required. Concurrent Constraint Programming (CCP) is a declarative model of concurrency closely related to logic for specifying reactive systems, i.e., systems that continuously react with the environment. Agents in CCP interact by telling and asking information represented as constraints (e.g., x > 42). In this paper we describe a modeling strategy for cellular signaling systems based on a temporal and probabilistic extension of CCP. Starting from an abstract model, we build refinements adding further details coming from experimentation or abstract assumptions. The advantages of our approach are: due to the notion of partial information as constraints in CCP, the model can be straightforwardly extended when more information is available; qualitative and quantitative information can be represented by means of probabilistic constructs of the language; finally, the model is a runnable specification and can be executed, thus allowing for the simulation of the system. We outline the use of this methodology to model the interaction of G-protein-coupled receptors with their respective G-proteins that activates signaling pathways inside the cell. We also present simulation results obtained from an implementation of the framework. © 2011 Springer-Verlag Berlin Heidelberg.
Journal Title
Conference Title
5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011)
Book Title
Edition
Volume
93
Issue
Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement
© 2011 Springer. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher. The original publication is available at www.springerlink.com
Item Access Status
Note
Access the data
Related item(s)
Subject
Science & Technology
Technology
Life Sciences & Biomedicine
Computer Science, Artificial Intelligence
Computer Science, Information Systems
Persistent link to this record
Citation
Hermith, D; Olarte, C; Rueda, C; Valencia, FD, Modeling Cellular Signaling Systems: An Abstraction-Refinement Approach, 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), 2011, 93, pp. 321-328