Conceptional modeling and analysis of spatio-temporal processes in biomolecular systems

  • Authors:

  • Andreas Schäfer;Mathias John

  • Affiliations:

  • University of Oldenburg, Oldenburg, Germany;University of Rostock, Rostock, Germany

  • Venue:
  • APCCM '09 Proceedings of the Sixth Asia-Pacific Conference on Conceptual Modeling - Volume 96
  • Year:
  • 2009

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Abstract

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 π-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 field 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.