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Hierarchical Modeling for Computational Biology

  • Conference paper
Formal Methods for Computational Systems Biology (SFM 2008)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 5016))

Abstract

Diverse hierarchies play a role in modeling and simulation for computational biology, e.g. categories, abstraction hierarchies, and composition hierarchies. Composition hierarchies seem a natural and straightforward focus for our exploration. What are model components and the requirements for a composite approach? How far do they support the quest for building blocks in computational biology? Modeling formalisms provide different means for composing a model. We will illuminate this with Devs (Discrete event systems specification) and the π calculus. Whereas in Devs distinctions are emphasized, e.g. between a system and its environment, between properties attributed to a system and the system itself, these distinctions become fluent in the compact description of the π calculus. However, both share the problem that in order to support a comfortable modeling, a series of extensions have been developed which also influence their possibility to support a hierarchical modeling. Thus, not individual formalisms but two families of formalisms and how they support a composite modeling will be presented. In computational biology one type of composite model deserves a closer inspection, as it brings together the wish to compose models and the need to describe a system at different levels in a unique manner, i.e. multi-level models.

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  1. University of Rostock, Albert-Einstein-Str. 21, D-18059, Rostock, Germany

    Carsten Maus, Mathias John, Mathias Röhl & Adelinde M. Uhrmacher

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  1. Carsten Maus
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  2. Mathias John
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  3. Mathias Röhl
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  4. Adelinde M. Uhrmacher
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Marco Bernardo Pierpaolo Degano Gianluigi Zavattaro

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Maus, C., John, M., Röhl, M., Uhrmacher, A.M. (2008). Hierarchical Modeling for Computational Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds) Formal Methods for Computational Systems Biology. SFM 2008. Lecture Notes in Computer Science, vol 5016. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68894-5_4

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  • DOI: https://doi.org/10.1007/978-3-540-68894-5_4

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