Abstract: A method for configuring a protocol for use in providing a medical treatment to a patient is provided. A protocol may be selected for configuration, the protocol being associated with a medical treatment having a process flow including multiple steps. A protocol template may be created for the protocol, including selecting and arranging flowchart components to create a graphical flowchart representation of the process flow, and defining one or more variables for one or more steps in the process flow. The one or more variables may be linked to one or more existing objects such that when the protocol is executed, the existing objects are automatically accessed to facilitate execution of the protocol.