D 2022

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

TROJÁK, Matej, David ŠAFRÁNEK, Branislav BROZMANN and Luboš BRIM

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

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

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

Keywords in English

rule-based modelling; regulations; SBML; Galaxy tool

Tags

Tags

International impact, Reviewed
Změněno: 6/1/2023 09:59, prof. RNDr. Luboš Brim, CSc.

Abstract

V originále

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