VERIFICATION AND TESTING OF BIOLOGICAL MODELS

Author

Clark, Allan ; Hillston, Jane ; Gilmore, Stephen ; Kemper, Peter

Author_Institution

Sch. of Inf., Univ. of Edinburgh, Edinburgh, UK

fYear

2010

fDate

5-8 Dec. 2010

Firstpage

620

Lastpage

630

Abstract

Simulation modeling in systems biology embarks on discrete event simulation only for cases of small cardinalities of entities and uses continuous simulation otherwise. Modern modeling environments like Bio-PEPA support both types of simulation within a single modeling formalism. Developing models for complex dynamic phenomena is not trivial in practice and requires careful verification and testing. In this paper, we describe relevant steps in the verification and testing of a TNFα-mediated NF-κB signal transduction pathway model and discuss to what extent automated techniques help a practitioner to derive a suitable model.

Keywords

biology computing; cellular biophysics; discrete event simulation; performance evaluation; process algebra; stochastic processes; TNFα-mediated NF-κB signal transduction pathway model; bio-PEPA; biological system; continuous simulation; discrete event simulation; simulation modeling; single modeling formalism; Analytical models; Biological system modeling; Computational modeling; Equations; Mathematical model; Numerical models; Stochastic processes;

fLanguage

English

Publisher

ieee

Conference_Titel

Simulation Conference (WSC), Proceedings of the 2010 Winter

Conference_Location

Baltimore, MD

ISSN

0891-7736

Print_ISBN

978-1-4244-9866-6

Type

conf

DOI

10.1109/WSC.2010.5679126

Filename

5679126