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Using Python for Spatially Resolved Modeling with Simmune

  • Bastian R. Angermann
  • Martin Meier-SchellersheimEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Mechanistic modeling GPCR signaling Gradient sensing IPython 

Notes

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.

References

  1. 1.
    Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M (2012) Computational modeling of cellular signaling processes embedded into dynamic spatial contexts. Nat Methods 9:283–289CrossRefGoogle Scholar
  2. 2.
    Cheng HC, Angermann BR, Zhang F, Meier-Schellersheim M (2014) NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. BMC Syst Biol 8:70CrossRefGoogle Scholar
  3. 3.
    Zhang F, Angermann BR, Meier-Schellersheim M (2013) The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions. Bioinformatics 29:1229–1230CrossRefGoogle Scholar
  4. 4.
    Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. Sci STKE 2006:re6Google Scholar
  5. 5.
    Perez F, Granger BE (2007) IPython: a system for interactive scientific computing. Comput Sci Eng 9:21–29CrossRefGoogle Scholar
  6. 6.
    Marks F, Klingmüller U, Müller-Decker K (2009) Cellular signal processing: an introduction to the molecular mechanisms of signal transduction. Garland Science, New YorkGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Bastian R. Angermann
    • 1
  • Martin Meier-Schellersheim
    • 1
    Email author
  1. 1.Computational Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUSA

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