This paper discusses a simulation theory with learning agents which is serving as a formal specification to guide the de-velopment of GALATEA, a multi-agent simulation platform. We have extended an existing simulation language: GLIDER, with abstractions to model systems where autonomous enti-ties (agents) perceive and act upon their environments. We are now applying it to the study of multi-agent systems. In particular, an implementation on Biocomplexity [1] is briefly discussed in the paper. We also show how an Inductive Logic Programming system can be used to learn rules in a repre-sentation very close to the one used to guide the simulation in the biocomplex system. This establishes the feasibility of em-bedding (resource-bounded) learne...