Hierarchical Modeling for Computational Biology
|Course type||Special Lecture|
|Instructor||Prof. Adelinde Uhrmacher|
|Time||Wednesday, 2008-05-21, 14:00–17:00|
|Language of instruction||English|
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 pi 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
pi 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.
Key words: hierarchical models, DEVS, pi calculus, model components