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Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Systems
Schaefer, A. and John, M.
In life science, deeper understanding of biomolecular
systems is acquired by computational modeling and
analysis. For the modeling of several kinds of reaction
networks, e.g. signaling pathways, information
on intracellular space, like the locations and motions
of molecules, has to be taken into account. In this
paper, we introduce Labeled SpacePi, an extension
of the pi-calculus, in order to model spatio-temporal
processes in cells. The formalism is tailored to the
available data and knowledge about biomolecular systems.
For the analysis, we employ model checking
techniques known from the eld of safety-critical systems.
To this end, we develop a translation of Labeled
SpacePi models into hybrid automata. Two use cases
- one considering the activation of a signaling pathway
and the other one concerning active transport in
cells - demonstrate our concept by making use of the
established analysis tools HyTech and HySat.
Cite as: Schaefer, A. and John, M. (2009). Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Systems. In Proc. Sixth Asia-Pacific Conference on Conceptual Modelling (APCCM 2009), Wellington, New Zealand. CRPIT, 96. Kirchberg, M. and Link, S., Eds. ACS. 39-48.
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