Multi-agent systems have proven to be a powerful technology for building distributed applications. However, the process of designing, configuring and deploying agent-based applications is still primarily a manual one. There is a need for mechanisms and tools to help automate the many development steps required when building these applications. Using the Semantic Web ontology language OWL and the JADE platform we have developed a number of models and software tools that provide an end-to-end solution for designing and deploying agent-based systems. This solution supports the construction of detailed models of agent behavior and the automatic deployment of agents from those models. We illustrate its use in the construction of a multi-agent system that supports the configuration, deployment, and evaluation of analytic methods for detecting disease outbreaks.