BioDiVinE: A Framework for Parallel Analysis of Biological Models

BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor 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 tec...

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Main Authors: David Šafránek, Jan Láník, Jana Fabriková, Sven Dražan, Ivana Černá, Luboš Brim, Jiří Barnat, Hongwu Ma
Format: Article
Language:English
Published: Open Publishing Association 2009-10-01
Series:Electronic Proceedings in Theoretical Computer Science
Online Access:http://arxiv.org/pdf/0910.0928v1
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spelling doaj-b0bd8ba67c8c46f7994e69d016802d992020-11-24T20:57:54ZengOpen Publishing AssociationElectronic Proceedings in Theoretical Computer Science2075-21802009-10-016Proc. COMPMOD 2009314510.4204/EPTCS.6.3BioDiVinE: A Framework for Parallel Analysis of Biological ModelsDavid ŠafránekJan LáníkJana FabrikováSven DražanIvana ČernáLuboš BrimJiří BarnatHongwu MaIn this paper a novel tool BioDiVinEfor 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. http://arxiv.org/pdf/0910.0928v1
collection DOAJ
language English
format Article
sources DOAJ
author David Šafránek
Jan Láník
Jana Fabriková
Sven Dražan
Ivana Černá
Luboš Brim
Jiří Barnat
Hongwu Ma
spellingShingle David Šafránek
Jan Láník
Jana Fabriková
Sven Dražan
Ivana Černá
Luboš Brim
Jiří Barnat
Hongwu Ma
BioDiVinE: A Framework for Parallel Analysis of Biological Models
Electronic Proceedings in Theoretical Computer Science
author_facet David Šafránek
Jan Láník
Jana Fabriková
Sven Dražan
Ivana Černá
Luboš Brim
Jiří Barnat
Hongwu Ma
author_sort David Šafránek
title BioDiVinE: A Framework for Parallel Analysis of Biological Models
title_short BioDiVinE: A Framework for Parallel Analysis of Biological Models
title_full BioDiVinE: A Framework for Parallel Analysis of Biological Models
title_fullStr BioDiVinE: A Framework for Parallel Analysis of Biological Models
title_full_unstemmed BioDiVinE: A Framework for Parallel Analysis of Biological Models
title_sort biodivine: a framework for parallel analysis of biological models
publisher Open Publishing Association
series Electronic Proceedings in Theoretical Computer Science
issn 2075-2180
publishDate 2009-10-01
description In this paper a novel tool BioDiVinEfor 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.
url http://arxiv.org/pdf/0910.0928v1
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AT janafabrikova biodivineaframeworkforparallelanalysisofbiologicalmodels
AT svendrazan biodivineaframeworkforparallelanalysisofbiologicalmodels
AT ivanacerna biodivineaframeworkforparallelanalysisofbiologicalmodels
AT lubosbrim biodivineaframeworkforparallelanalysisofbiologicalmodels
AT jiribarnat biodivineaframeworkforparallelanalysisofbiologicalmodels
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