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Carsten Maus, Stefan Rybacki, and Adelinde M Uhrmacher (2011)

Formal Rule-based Multi-Level Modeling

Poster, Heidelberg/Mannheim, Germany, 12th International Conference on Systems Biology (ICSB).

Biological systems comprise different levels of organization, e.g. proteins, compartments, individual cells, and cell populations. In order to capture the relevant dynamics, one might need to accordingly structure and to combine different levels in modeling a biological system. Formal modeling languages with explicit means for multi-level descriptions facilitate this endeavor. Rule-based modeling has gained increasingly attention in the past years. Due to specifying reaction patterns instead of defined reactions, rule-based modeling allows to effectively handle the combinatorial complexity of large systems. The presented approach (ML-Rules) shows how rule-based modeling can be extended in order to describe formal multi-level models. The approach allows to structure models in a nested hierarchical manner and to let the different levels influence each other via upward and downward causation, while its modeling metaphor close to the notation of chemical reaction equations facilitates understanding of models by non-experts and keeps the models small and readable.

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