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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References
Anaconda software distribution (2020). https://docs.anaconda.com/
Afgan, E., et al.: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(W1), 537–544 (2018)
Bornstein, B.J., Keating, S.M., Jouraku, A., Hucka, M.: libSBML: an API library for SBML. Bioinformatics 24(6), 880–881 (2008)
Calzone, L., Fages, F., Soliman, S.: BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14), 1805–1807 (2006)
Casagrande, A.: pyModelChecking (2022). https://pypi.org/project/pyModelChecking
Clarke, E.M.: Model checking. In: Ramesh, S., Sivakumar, G. (eds.) FSTTCS 1997. LNCS, vol. 1346, pp. 54–56. Springer, Heidelberg (1997). https://doi.org/10.1007/BFb0058022
Danos, V., Laneve, C.: Formal molecular biology. Theoret. Comput. Sci. 325, 69–110 (2004)
Grüning, B., et al.: Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat. Methods 15(7), 475–476 (2018)
Harris, L.A., et al.: BioNetGen 2.2: advances in rule-based modeling. Bioinformatics 32, 3366–3368 (2016)
Hasson, H., Jonsson, B.: A logic for reasoning about time and probability. FAOC 6, 512–535 (1994)
Hucka, M., et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003)
Lopez, C.F., Muhlich, J.L., Bachman, J.A., Sorger, P.K.: Programming biological models in python using PySB. Mol. Syst. Biol. 9, 646 (2013)
Maus, C., Rybacki, S., Uhrmacher, A.M.: Rule-based multi-level modeling of cell biological systems. BMC Syst. Biol. 5(1), 1–20 (2011). https://doi.org/10.1186/1752-0509-5-166
Pearson, G., et al.: Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions. Endocr. Rev. 22(2), 153–183 (2001)
Pedersen, M., Phillips, A., Plotkin, G.D.: A high-level language for rule-based modelling. Plos One 10(6), 1–26 (2015)
Romers, J.C., Krantz, M.: rxncon 2.0: a language for executable molecular systems biology. bioRxiv (2017)
Troják, M.: eBCSgen: a bioconda package (2022). https://anaconda.org/bioconda/ebcsgen
Troják, M., Šafránek, D., Mertová, L., Brim, L.: eBCSgen: a software tool for biochemical space language. In: Abate, A., Petrov, T., Wolf, V. (eds.) CMSB 2020. LNCS, vol. 12314, pp. 356–361. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-60327-4_20
Troják, M., Šafránek, D., Mertová, L., Brim, L.: Parameter synthesis and robustness analysis of rule-based models. In: Lee, R., Jha, S., Mavridou, A., Giannakopoulou, D. (eds.) NFM 2020. LNCS, vol. 12229, pp. 41–59. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-55754-6_3
Troják, M., Pastva, S., Šafránek, D., Brim, L.: Regulated multiset rewriting systems (2021). https://arxiv.org/abs/2111.13036
Troják, M., Šafránek, D., Brim, L.: Biochemical space language in relation to multiset rewriting systems (2022). https://arxiv.org/abs/2201.08817
Troják, M., Šafránek, D., Mertová, L., Brim, L.: Executable biochemical space for specification and analysis of biochemical systems. PLoS ONE 15(9), 1–24 (2020)
Zhang, F., Meier-Schellersheim, M.: Multistate, multicomponent and multicompartment species package for SBML level 3. COMBINE Specifications (2017)
Zimmer, R.H., Millar, A.J., Plotkin, G.D., Zardilis, A.: Chromar, a language of parametrised objects. Theor. Comput. Sci. (2017)
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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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