Multi-level modeling and simulation of cell biological systems with ML-Rules - A tutorial

Multi-level modeling is concerned with describing a system at different levels of organization and relating their dynamics. ML-Rules is a rule-based language developed for supporting the modeling of cell biological systems. It supports nested rule schemata, the hierarchical dynamic nesting of species, the assignment of attributes and solutions to species at each level, and a flexible definition of reaction rate kinetics. As ML-Rules allows the compact description of rather complex models, means for an efficient execution were developed, e.g., approximate and adaptive algorithms. Experimentation with ML-Rules models is further supported by domain-specific languages for instrumentation and experimentation which have been developed in the context of the modeling and simulation framework JAMES II. A signaling pathway example will illustrate modeling and simulation with ML-Rules.