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RKappa: Software for Analyzing Rule-Based Models

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Modeling Biomolecular Site Dynamics

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

Abstract

RKappa is a framework for the development, simulation, and analysis of rule-based models within the mature statistically empowered R environment. It is designed for model editing, parameter identification, simulation, sensitivity analysis, and visualization. The framework is optimized for high-performance computing platforms and facilitates analysis of large-scale systems biology models where knowledge of exact mechanisms is limited and parameter values are uncertain.

The RKappa software is an open-source (GLP3 license) package for R, which is freely available online (https://github.com/lptolik/R4Kappa).

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Author information

Authors and Affiliations

  1. Institute of Cell Biophysics, Russian Academy of Sciences, Moscow Region, Russia

    Anatoly Sorokin

  2. Moscow Institute of Physics and Technology, Moscow Region, Russia

    Anatoly Sorokin

  3. School of Informatics, University of Edinburgh, Edinburgh, UK

    Oksana Sorokina & J. Douglas Armstrong

Authors
  1. Anatoly Sorokin
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  2. Oksana Sorokina
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  3. J. Douglas Armstrong
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Editor information

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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Sorokin, A., Sorokina, O., Douglas Armstrong, J. (2019). RKappa: Software for Analyzing Rule-Based Models. 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_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9102-0_17

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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

  • eBook Packages: Springer Protocols

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