Computer-based simulation of influenza outbreaks in local communities can help researchers, epidemiologists, and decision makers better understand the impact of the community structure on the reproduction rate of disease, and the relative benefits of different types of prevention and interventions. The goal of scenario modeling is to develop a description of scenario components, such as the disease, the community, and interventions. An ontology-based representation of the scenario model together with a modeling tool, which is based on an extension to Protégé, assist scenario developers in formulating simulation specifications. This approach allows the exploration of new ideas by rapidly formulating and reconstructing scenarios from novel components.