Paper Info
Title
Modeling Biological Systems With Delays In Bio-Pepa
Abstract
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed, or to provide abstraction of some behavior of the system resulting more compact models. In this paper we enrich the stochastic process algebra Bio-PEPA, with the possibility of assigning delays to actions, yielding a new non-Markovian process algebra: Bio-PEPAd. This is a conservative extension meaning that the original syntax of Bio-PEPA is retained and the delay specification which can now be associated with actions may be added to existing Bio-PEPA models. The semantics of the firing of the actions with delays is the delay-as-duration approach, earlier presented in papers on the stochastic simulation of biological systems with delays. These semantics of the algebra are given in the Starting-Terminating style, meaning that the state and the completion of an action are observed as two separate events, as required by delays. Furthermore we outline how to perform stochastic simulation of Bio-PEPAd systems and how to automatically translate a BioPEPAd system into a set of Delay Differential Equations, the deterministic framework for modeling of biological systems with delays. We end the paper with two example models of biological systems with delays to illustrate the approach.
Year
DOI
Venue
2010
10.4204/EPTCS.40.7
ELECTRONIC PROCEEDINGS IN THEORETICAL COMPUTER SCIENCE
Keywords
Field
DocType
delay differential equation,quantitative method,biological systems,stochastic simulation
Stochastic simulation,Abstraction,Theoretical computer science,Conservative extension,Delay differential equation,Syntax,Process calculus,PEPA,Semantics,Mathematics
Journal
Issue
ISSN
Citations 
40
2075-2180
5
PageRank 
References 
Authors
0.43
14
2
Name
Order
Citations
PageRank
Giulio Caravagna115616.46
Jane Hillston21657125.09