Many biological systems but also software systems (e.g. so called
multi-agent systems) are characterized by their complexity in terms of
number and heterogeneity of involved components and interaction
patterns.  To support an efficient and effective analysis of these
systems a flexible simulation system is needed.  Thereby flexibility
refers to the modeling and simulation layer alike. The modeling and
simulation system James II exploits reusable components for that
purpose. 

Whereas in the 90s simulation frameworks that were
aimed at supporting one formalism, one simulation algorithm, or
simulating one experiment still prevailed, slowly systems emerge that support
different modeling formalisms or simulation engines.  Into this
category also falls \textsc{James II}.  \textsc{James II} combines
ideas from software engineering with modeling and simulation
techniques. This facilitates the integration of different modeling
formalisms and their execution by different simulators. E.g., a PDEVS
model might be executed in paced, unpaced, sequential, parallel, or
flattened mode. Exploiting software patterns the changes and
refinements to realize a wide set of different simulators for a
formalism are nicely kept at bay. Selecting a simulator depending on
the model, the objective of the simulation experiments, and the
underlying infrastructure ensures an efficient execution of
simulation experiments. The flexibility has been put to test in
applying \textsc{James II} to simulate mobile agents, intelligent
agents, and cell biological applications. To the later belong
multi-level models of the Trytophan Synthase and Tryptophan Operon.
Currently, a multi-level model of the wnt-pathway is under way.