Health care is a rapidly evolving field that is increasingly supported through clinical information systems (CIS) that integrate care providers, patients, and computer applications. Local and federal regulations require health care systems to define and enforce privacy and security policies to protect sensitive patient data within CIS. Service-oriented architectures (SOA) have been successfully applied to specific clinical services, such as decision support, but have yet to be adopted for large-scale CIS that need to account for diverse information technology architectures and complex person-computer interactions. In this work, we demonstrate that the incorporation of model-based design techniques and high-level modeling abstractions provide a framework to rapidly develop, simulate, and deploy CIS prototypes. This paper describes the implementation of a graphical design environment that allows CIS architects to develop formal system models and from these automatically generates executable code for deployment. The design tool leverages SOA to create reusable services that can be rapidly adapted. We illustrate the functionality of the tool by modeling a secure messaging service in the MyHealth@Vanderbilt patient portal, a portion of the Vanderbilt University Medical Center CIS.