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eBCSgen: A Software Tool for Biochemical Space Language

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Book cover Computational Methods in Systems Biology (CMSB 2020)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 12314))

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Abstract

eBCSgen is a tool for development and analysis of models written in Biochemical Space Language (BCSL). BCSL is a rule-based language for biological systems designed to combine compact description with a specific level of abstraction which makes it accessible to users from life sciences. Currently, eBCSgen represents the only tool completely supporting BCSL. It has the form of a command line interface which is integrated into Galaxy – a web-based bioinformatics platform automating data-driven and model-based analysis pipelines.

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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.

    The model files and computed analysis results are available here:

    https://biodivine.fi.muni.cz/galaxy/eBCSgen/case-studies/cmsb-2020.

    The results for simplified analysis are also publicly available:

    https://biodivine.fi.muni.cz/galaxy/eBCSgen/case-studies/nfm-2020.

References

  1. Afgan, E., et al.: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(W1), W537–W544 (2018)

    Article  Google Scholar 

  2. Barbuti, R., et al.: An intermediate language for the stochastic simulation of biological systems. TCS 410(33–34), 3085–3109 (2009)

    Article  MathSciNet  Google Scholar 

  3. Boutillier, P., et al.: The Kappa platform for rule-based modeling. Bioinformatics 34(13), i583–i592 (2018)

    Article  Google Scholar 

  4. Calzone, L., et al.: BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14), 1805–1807 (2006)

    Article  Google Scholar 

  5. Chabrier-Rivier, N., Fages, F., Soliman, S.: The biochemical abstract machine BIOCHAM. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS, vol. 3082, pp. 172–191. Springer, Heidelberg (2005). https://doi.org/10.1007/978-3-540-25974-9_14

    Chapter  Google Scholar 

  6. Danos, V., Laneve, C.: Formal molecular biology. Theor. Comput. Sci. 325, 69–110 (2004)

    Article  MathSciNet  Google Scholar 

  7. Daws, C.: Symbolic and parametric model checking of discrete-time Markov chains. In: Liu, Z., Araki, K. (eds.) ICTAC 2004. LNCS, vol. 3407, pp. 280–294. Springer, Heidelberg (2005). https://doi.org/10.1007/978-3-540-31862-0_21

    Chapter  MATH  Google Scholar 

  8. Dehnert, C., Junges, S., Katoen, J.P., Volk, M.: A STORM is coming: a modern probabilistic model checker. In: Majumdar, R., Kunčak, V. (eds.) CAV 2017. LNCS, vol. 10427, pp. 592–600. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-63390-9_31

    Chapter  Google Scholar 

  9. Děd, T., et al.: Formal biochemical space with semantics in Kappa and BNGL. Electr. Notes Theor. Comput. Sci. 326, 27–49 (2016)

    Article  Google Scholar 

  10. Harris, L.A., et al.: BioNetGen 2.2: advances in rule-based modeling. Bioinformatics 32(21), 3366–3368 (2016)

    Google Scholar 

  11. Hasson, H., Jonsson, B.: A logic for reasoning about time and probability. FAOC 6, 512–535 (1994)

    Google Scholar 

  12. Honorato-Zimmer, R., et al.: Chromar, a language of parameterised agents. Theor. Comput. Sci. 765, 97–119 (2019)

    Article  MathSciNet  Google Scholar 

  13. Lanotte, R., et al.: Parametric probabilistic transition systems for system design and analysis. FAOC 19(1), 93–109 (2007)

    MATH  Google Scholar 

  14. Lopez, C.F., et al.: Programming biological models in Python using PySB. Mol. Syst. Biol. 9(1), 646 (2013)

    Article  Google Scholar 

  15. Miyoshi, F., et al.: A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in Cyanobacteria. J. Biol. Rhythms 22(1), 69–80 (2007)

    Article  Google Scholar 

  16. Pedersen, M., et al.: A high-level language for rule-based modelling. PloS One 10(6), e0114296 (2015)

    Article  Google Scholar 

  17. Romers, J.C., Krantz, M.: rxncon 2.0: a language for executable molecular systems biology. bioRxiv (2017)

    Google Scholar 

  18. Troják, M., et al.: Executable biochemical space for specification and analysis of biochemical systems. arXiv 2002.00731 (2020)

    Google Scholar 

  19. Troják, M., et al.: Parameter synthesis and robustness analysis of rule-based models. In: NASA Formal Methods Symposium (2020, published). https://doi.org/10.1007/978-3-030-55754-6_3

  20. Xu, W., et al.: RuleBender: a visual interface for rule-based modeling. Bioinformatics 27(12), 1721–1722 (2011)

    Article  Google Scholar 

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Author information

Authors and Affiliations

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

    Matej Troják, David Šafránek, Lukrécia Mertová & Luboš Brim

Authors
  1. Matej Troják
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  2. David Šafránek
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  3. Lukrécia Mertová
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  4. Luboš Brim
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Corresponding author

Correspondence to Matej Troják .

Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Oxford, Oxford, UK

    Alessandro Abate

  2. Department of Computer and Information Science, University of Konstanz, Konstanz, Germany

    Tatjana Petrov

  3. Department of Computer Science, Saarland University, Saarbrücken, Germany

    Verena Wolf

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Troják, M., Šafránek, D., Mertová, L., Brim, L. (2020). eBCSgen: A Software Tool for Biochemical Space Language. In: Abate, A., Petrov, T., Wolf, V. (eds) Computational Methods in Systems Biology. CMSB 2020. Lecture Notes in Computer Science(), vol 12314. Springer, Cham. https://doi.org/10.1007/978-3-030-60327-4_20

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  • DOI: https://doi.org/10.1007/978-3-030-60327-4_20

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-60326-7

  • Online ISBN: 978-3-030-60327-4

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