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

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Book cover Computational Methods in Systems Biology (CMSB 2022)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13447))

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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.

This work has been supported by the Czech Science Foundation grant 22-10845S.

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Notes

  1. 1.

    https://biodivine-vm.fi.muni.cz/galaxy/.

  2. 2.

    https://biodivine.fi.muni.cz/galaxy/eBCSgen/tutorial.

  3. 3.

    https://biodivine.fi.muni.cz/galaxy/eBCSgen/case-studies/cmsb-2022-regulations.

  4. 4.

    https://biodivine.fi.muni.cz/galaxy/eBCSgen/case-studies/cmsb-2022.

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Authors and Affiliations

  1. Systems Biology Laboratory, Masaryk University, Brno, Czech Republic

    Matej Troják, David Šafránek, Branislav Brozmann & Luboš Brim

Authors
  1. Matej Troják
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  2. David Šafránek
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  3. Branislav Brozmann
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  4. Luboš Brim
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Corresponding author

Correspondence to Matej Troják .

Editor information

Editors and Affiliations

  1. University of Turku, Turku, Finland

    Ion Petre

  2. University of Bucharest, Bucharest, Romania

    Andrei Păun

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Troják, M., Šafránek, D., Brozmann, B., Brim, L. (2022). eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. In: Petre, I., Păun, A. (eds) Computational Methods in Systems Biology. CMSB 2022. Lecture Notes in Computer Science(), vol 13447. Springer, Cham. https://doi.org/10.1007/978-3-031-15034-0_17

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  • DOI: https://doi.org/10.1007/978-3-031-15034-0_17

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-15033-3

  • Online ISBN: 978-3-031-15034-0

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