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RKappa: Statistical Sampling Suite for Kappa Models

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Hybrid Systems Biology (HSB 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7699))

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Abstract

We present RKappa, a framework for the development and analysis of rule-based models within a mature, statistically empowered R environment. The infrastructure allows model editing, modification, parameter sampling, simulation, statistical analysis and visualisation without leaving the R environment. We demonstrate its effectiveness through its application to Global Sensitivity Analysis, exploring it in “parallel” and “concurrent” implementations.

The pipeline was designed for high performance computing platforms and aims to facilitate analysis of the behaviour of large-scale systems with limited knowledge of exact mechanisms and respectively sparse availability of parameter values. We illustrate it here with two biological examples. The package is available on github: https://github.com/lptolik/R4Kappa.

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Acknowledgments

AS was partially supported by RFBR, research project No. 14-44-03679 r_centr_a, and European Research Council (ERC) under grants 320823 RULE. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement nos. 241498 (EUROSPIN project), 242167 (SynSys-project) and 604102 (Human Brain Project). This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF) (http://www.ecdf.ed.ac.uk/). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).

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Authors and Affiliations

  1. Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russia

    Anatoly Sorokin

  2. The University of Edinburgh, Edinburgh, UK

    Anatoly Sorokin, 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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Corresponding author

Correspondence to Anatoly Sorokin .

Editor information

Editors and Affiliations

  1. "CNRS-VERIMAG, University of Grenoble-Alpes (UGA), Grenoble, France

    Oded Maler

  2. West Virginia University, Morgantown, West Virginia, USA

    Ádám Halász

  3. VERIMAG, Gieres, France

    Thao Dang

  4. University of Udine, Udine, Italy

    Carla Piazza

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Sorokin, A., Sorokina, O., Armstrong, J.D. (2015). RKappa: Statistical Sampling Suite for Kappa Models. In: Maler, O., Halász, Á., Dang, T., Piazza, C. (eds) Hybrid Systems Biology. HSB 2014. Lecture Notes in Computer Science(), vol 7699. Springer, Cham. https://doi.org/10.1007/978-3-319-27656-4_8

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  • DOI: https://doi.org/10.1007/978-3-319-27656-4_8

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-27655-7

  • Online ISBN: 978-3-319-27656-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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