eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems

TROJÁK, Matej, David ŠAFRÁNEK, Branislav BROZMANN and Luboš BRIM. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. Online. In I. Petre, A. Păun. 20th International Conference on Computational Methods in Systems Biology. LNBI 13447. Neuveden: Springer, 2022, p. 302-309. ISBN 978-3-031-15033-3. Available from: https://dx.doi.org/10.1007/978-3-031-15034-0_17.

Basic information

• Original name: eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems
• Authors: TROJÁK, Matej (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Branislav BROZMANN (703 Slovakia, belonging to the institution) and Luboš BRIM (203 Czech Republic, belonging to the institution).
• Edition: LNBI 13447. Neuveden, 20th International Conference on Computational Methods in Systems Biology, p. 302-309, 8 pp. 2022.
• Publisher: Springer

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Netherlands
• Confidentiality degree: is not subject to a state or trade secret
• Publication form: electronic version available online
• WWW: URL
• Impact factor: Impact factor: 0.402 in 2005
• RIV identification code: RIV/00216224:14330/22:00129141
• Organization unit: Faculty of Informatics
• ISBN: 978-3-031-15033-3
• ISSN: 0302-9743
• Doi: http://dx.doi.org/10.1007/978-3-031-15034-0_17
• Keywords in English: rule-based modelling; regulations; SBML; Galaxy tool
• Tags: firank_B
• Tags: International impact, Reviewed

Abstract

eBCSgen is a software tool for developing and analysing models written in Biochemical Space Language (BCSL). BCSL is a rule-based language designed for the description of biological systems with rewriting rules in the form of behavioural patterns. This tool paper describes a new version of the tool, implementing the support for regulations, a mechanism suitable for reducing the branching behaviour of concurrent systems. Additionally, the presented version provides export to SBML, and support for CTL model checking. The paper artefact is available via https://doi.org/10.5281/zenodo.6644973.

Links

• GA22-10845S, research and development project: Name: Studium role polyhydroxyalkanoátů u bakterie Schlegelella thermodepolymerans – slibného bakteriálního kandidáta pro biotechnologie nové generace (Acronym: PHAST)

Investor: Czech Science Foundation, Unraveling the role of polyhydroxyalkanoates in Schlegelella thermodepolymerans – promising environmental bacterium for next generation biotechnology

• MUNI/A/1145/2021, interní kód MU: Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace XI. (Acronym: SV-FI MAV XI.)

Investor: Masaryk University