BioDiVinE: A Framework for Parallel Analysis of Biological Models

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. ISSN 2075-2180.

Basic information

Original name

BioDiVinE: A Framework for Parallel Analysis of Biological Models

Name in Czech

BioDiVinE: Framework pro analýzu biologických modelů

Authors

BARNAT, Jiří (203 Czech Republic, belonging to the institution), Luboš BRIM (203 Czech Republic, belonging to the institution), Ivana ČERNÁ (203 Czech Republic, belonging to the institution), Sven DRAŽAN (203 Czech Republic, belonging to the institution), Jana FABRIKOVÁ (203 Czech Republic, belonging to the institution), Jan LÁNÍK (203 Czech Republic, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution) and Ma HONGWU (826 United Kingdom of Great Britain and Northern Ireland)

Edition

Neuveden, Proceedings of 2nd International Workshop on Computational Models for Cell Processes, p. 31-45, 15 pp. 2009

Publisher

EPTCS

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Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14330/09:00028618

Organization unit

Faculty of Informatics

ISSN

Keywords in English

model checking; multi-affine systems; dynamic systems; rectangular abstraction

Tags

International impact, Reviewed

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Abstract

V originále

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.

In Czech

V článku je představen nástroj BioDiVinE pro paralelní analýzu biologických modelů. Nástroj umožňuje analýzu kvalitativních temporálních vlastností dynamiky prostřednictvím obdélníkové abstrakce. Použití je demonstrováno prostřednictvím případové studie na reálném biologickém modelu bakterie E.Coli.

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Links

GA201/09/1389, research and development project	Name: Verifikace a analýza velmi velkých počítačových systémů Investor: Czech Science Foundation, Verification and Analysis of Large-Scale Computer Systems
GP201/09/P497, research and development project	Name: Automatizovaná formální verifikace s využitím soudobého hardware Investor: Czech Science Foundation, Automated formal verification using modern hardware
MSM0021622419, plan (intention)	Name: Vysoce paralelní a distribuované výpočetní systémy Investor: Ministry of Education, Youth and Sports of the CR, Highly Parallel and Distributed Computing Systems
1ET408050503, research and development project	Name: Techniky automatické verifikace a validace softwarových a hardwarových systémů Investor: Academy of Sciences of the Czech Republic, Techniques for automatic verification and validation of software nad hardware systems