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

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• RIV identification code: RIV/00216224:14330/09:00028618
• Organization unit: Faculty of Informatics
• ISSN: 2075-2180
• Keywords in English: model checking; multi-affine systems; dynamic systems; rectangular abstraction
• Tags: International impact, Reviewed

Abstract

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.

Abstract (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.

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