Rule-based multi-level modeling of cell biological systems
BMC Systems Biology, 5(166).
Background: Proteins, individual cells, and cell populations denote dierent levels of an organizational hierarchy, each of which with its own dynamics. Multi-level modeling is concerned with describing a system at these dierent levels and relating their dynamics. Rule-based modeling has increasingly attracted attention due to enabling a concise and compact description of biochemical systems. In addition, it allows dierent methods for model analysis, since more than one semantics can be dened for the same syntax.
Results: Multi-level modeling implies the hierarchical nesting of model entities and explicit support for downward and upward causation between dierent levels. Concepts to support multi-level modeling in a rule-based language are identied. To those belong rule schemata, hierarchical nesting of species, assigning attributes and solutions to species at each level and preserving content of nested species while applying rules. Further necessities are the ability to apply rules and exibly dene reaction rate kinetics and constraints on nested species as well as species that are nested within others. An example model is presented that analyses the interplay of an intracellular control circuit with states at cell level, its relation to cell division, and connections to intercellular communication within a population of cells. The example is described in ML-Rules - a rule-based multi-level approach that has been realized within the plug-in-based modeling and simulation framework JAMES II.
Conclusions: Rule-based languages are a suitable starting point for developing a concise and compact language for multi-level modeling of cell biological systems. The combination of nesting species, assigning attributes, and constraining reactions according to these attributes is crucial in achieving the desired expressiveness. Rule schemata allow a concise and compact description of complex models. As a result, the presented approach facilitates developing and maintaining multi-level models that, for instance, interrelate intracellular and intercellular dynamics.