The immune system is an important area if study in basic biology, medicine and biotechnology. The vast amount of information about this system is unorganized and immunological databases would be of great benefit. In addition, to facts knowledge is needed about the operation of the immune system. We have approached this by building simulation models of the immune response. I will briefly discuss an agent based model of the humoral immune response and demonstrate its utility in the context of analyzing the immune response to annual influenza vaccination.