Principal architecture of PAPAyA. User Interface combines elements of presentation and handles user actions. Presentation shows synchronously the present context(s), data, analysis results, output of tool executions, and visual elements for navigation and execution dynamically based on the current application context. Flow Control translates the context definitions into visualization components. Based on user's interaction, Action translates user requests into a change of display (and context) or requests a tool execution by the Tool Execution Engine. The latter component, based on the application context, user-provided input and the description of the tool handles the output. The execution instance of a Tool is controlled by the application to the extent that it provides parameters for its execution. Tools have access to the internal database, but given the loose coupling with PAPAyA, it is often the case that External Data is used by a tool. Such data comprise measurements, annotation, and results from the execution of other tools within PAPAyA.