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BioDiVinE: A Framework for Parallel Analysis of Biological Models

Basic information
Original title:BioDiVinE: A Framework for Parallel Analysis of Biological Models
Authors:Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, Jan Láník, David Šafránek, Ma Hongwu
Further information
Citation:BARNAT, Jiří, Luboš BRIM, Ivana ČERNÁ, Sven DRAŽAN, Jana FABRIKOVÁ, Jan LÁNÍK, David ŠAFRÁNEK and Ma HONGWU. BioDiVinE: A Framework for Parallel Analysis of Biological Models. In Proceedings of 2nd International Workshop on Computational Models for Cell Processes. Neuveden: EPTCS, 2009. p. 31-45, 15 pp. ISSN 2075-2180.Export BibTeX
@inproceedings{850846,
author = {Barnat, Jiří and Brim, Luboš and Černá, Ivana and Dražan, Sven and Fabriková, Jana and Láník, Jan and Šafránek, David and Hongwu, Ma},
address = {Neuveden},
booktitle = {Proceedings of 2nd International Workshop on Computational Models for Cell Processes},
keywords = {model checking; multi-affine systems; dynamic systems; rectangular abstraction},
language = {eng},
location = {Neuveden},
pages = {31-45},
publisher = {EPTCS},
title = {BioDiVinE: A Framework for Parallel Analysis of Biological Models},
year = {2009}
}
Original language:English
Field:Informatics
Type:Article in Proceedings
Keywords:model checking; multi-affine systems; dynamic systems; rectangular abstraction

In this paper a novel tool BioDiVinE for parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study.

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