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Modeling Biomolecular Site Dynamics pp 141–160Cite as

Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1945))

Abstract

ML-Rules is a rule-based language for multi-level modeling and simulation. ML-Rules supports dynamic nesting of entities and applying arbitrary functions on entity attributes and content, as well as for defining kinetics of reactions. This allows describing and simulating complex cellular dynamics operating at different organizational levels, e.g., to combine intra-, inter-, and cellular dynamics, like the proliferation of cells, or to include compartmental dynamics like merging and splitting of mitochondria or endocytosis. The expressiveness of the language is bought with additional efforts in executing ML-Rules models. Therefore, various simulators have been developed from which the user and automatic procedures can select. The experiment specification language SESSL facilitates design, execution, and reuse of simulation experiments. The chapter illuminates the specific features of ML-Rules as a rule-based modeling language, the implications for an efficient execution, and shows ML-Rules at work.

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Notes

  1. 1.

    Other rule-based languages, e.g., ML-Space [14], opted for accessing attributes by names.

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Authors and Affiliations

  1. Institute of Computer Science, University of Rostock, Rostock, Germany

    Tobias Helms, Tom Warnke & Adelinde M. Uhrmacher

Authors
  1. Tobias Helms
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  2. Tom Warnke
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  3. Adelinde M. Uhrmacher
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Corresponding author

Correspondence to Adelinde M. Uhrmacher .

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Editors and Affiliations

  1. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA

    William S. Hlavacek

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Helms, T., Warnke, T., Uhrmacher, A.M. (2019). Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules. In: Hlavacek, W. (eds) Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, vol 1945. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9102-0_6

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  • DOI: https://doi.org/10.1007/978-1-4939-9102-0_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9100-6

  • Online ISBN: 978-1-4939-9102-0

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