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Modeling Biomolecular Site Dynamics pp 161–177Cite as

Using Python for Spatially Resolved Modeling with Simmune

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

Abstract

Mechanistic models are an important tool to gain insights about the quantitative behavior of cell-biological signal transduction networks. Here we show how Simmune can be used in conjunction with IPython to create repeatable, self-contained analyses of signal transduction processes in spatially inhomogeneous environments.

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References

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Acknowledgements

We would like to thank Anke Knauf and Nicolas W. Lounsbury from the Laboratory of Immune System Biology for critically reading the manuscript. This work was supported by the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health.

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Authors and Affiliations

  1. Computational Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA

    Bastian R. Angermann & Martin Meier-Schellersheim

Authors
  1. Bastian R. Angermann
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  2. Martin Meier-Schellersheim
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Corresponding author

Correspondence to Martin Meier-Schellersheim .

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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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Angermann, B.R., Meier-Schellersheim, M. (2019). Using Python for Spatially Resolved Modeling with Simmune. 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_7

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  • DOI: https://doi.org/10.1007/978-1-4939-9102-0_7

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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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