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Captain is an automated workflow manager for research applications in proton therapy. It provides web interfaces to collect user inputs and display results, accessible from just about anywhere: the treatment room, a tablet or a smartphone. The Server for Calculation Automated for Proton Therapy advanced innovation (CAPTAin-server) triggers the automatic execution of REGGUI plugins in a Matlab environment when some pre-defined DICOM objects are received on the Orthanc DICOM server. The results are stored in a database on the server. The user can see the computation results through a Web interface provided by the CAPTAin server.