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Simulating Stochastic Dynamic Interactions with Spatial Information and Flux

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Theory and Practice of Natural Computing (TPNC 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10071))

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Abstract

We present a conservative extension to rule based modeling languages with constructs for component attributes and functions that modify these attributes; the language has a stochastic semantics, and it is equipped with flux analysis. We show that the constructs of this language, called \(\mathsf {M}\), bring an ease especially in modeling biological systems, where spatial information is of essence. We discuss the language on models from molecular biology such as membrane diffusion systems, and actin polymerization networks, as well as models from ecology, where spatial behavior of animals as in bird flocks and fish schools are studied.

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Notes

  1. 1.

    Prototype modules that implement the language components are available for download at our website. http://sites.google.com/site/ozankahramanogullari/M.

  2. 2.

    https://www.youtube.com/watch?v=38KCf8nHQz0.

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Author information

Authors and Affiliations

  1. Department of Mathematics, University of Trento, Trento, Italy

    Ozan Kahramanoğulları

  2. Centre for Computational and Systems Biology, The Micrososft Research - University of Trento, Rovereto, Italy

    Ozan Kahramanoğulları

Authors
  1. Ozan Kahramanoğulları
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Editor information

Editors and Affiliations

  1. Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  2. Tohoku University, Sendai, Japan

    Takaaki Mizuki

  3. University of Extremadura, Cáceres, Spain

    Miguel A. Vega-Rodríguez

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Kahramanoğulları, O. (2016). Simulating Stochastic Dynamic Interactions with Spatial Information and Flux. In: Martín-Vide, C., Mizuki, T., Vega-Rodríguez, M. (eds) Theory and Practice of Natural Computing. TPNC 2016. Lecture Notes in Computer Science(), vol 10071. Springer, Cham. https://doi.org/10.1007/978-3-319-49001-4_12

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  • DOI: https://doi.org/10.1007/978-3-319-49001-4_12

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-49000-7

  • Online ISBN: 978-3-319-49001-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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