Hierarchical Modeling for Computational Biology

Maus, Carsten and John, Mathias and Röhl, Mathias and Uhrmacher, Adelinde M. (2008) Hierarchical Modeling for Computational Biology. In: Formal Methods for Computational Systems Biology, 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, Advanced Lectures, June 2-7, Bertinoro, Italy. Proceedings,, pp. 81-124.

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Official URL: http://dx.doi.org/10.1007/978-3-540-68894-5_4


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.

Item Type: Conference or Workshop Item (Paper)
Projects: GRK dIEM oSiRiS, DiErMoSiS