  We present a new approach to the simulation and analysis of immune system
behavior. The simulations that can be done with our software package called
SIMMUNE are based on immunological data that describe the behavior of immune
system agents (cells, molecules) on a microscopial (i.e. agent-agent
interaction) scale by defining cellular stimulus-response mechanisms. Since the
behavior of the agents in SIMMUNE can be very flexibly configured, its
application is not limited to immune system simulations. We outline the
principles of SIMMUNE's multiscale analysis of emergent structure within the
simulated immune system that allow the identification of immunological contexts
using minimal a priori assumptions about the higher level organization of the
immune system.
