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Transcranial magnetic stimulation (TMS) is the most important technique currently available to study cortical excitability. Additionally, TMS can be used for therapeutic and rehabilitation purposes, replacing the more painful transcranial electric stimulation (TES). In this paper we present an innovative and easy-to-use tool that enables neuroscientists to design, carry out and analyze scientific studies based on TMS experiments for both diagnostic and research purposes, assisting them not only in the practicalities of administering the TMS but also in each step of the entire study's workflow. One important aspect of this tool is that it allows neuroscientists to specify research designs at will, enabling them to define any parameter of a TMS study starting from data acquisition and sample group definition to automated statistical data analysis and RDF data storage. It also supports the diagnosing process by using on-line support vector machines able to learn incrementally from the diseases instances that are continuously added into the system. The proposed system is a neuroscientist-centred tool where the protocols being followed in TMS studies are made explicit, leaving to the users flexibility in exploring and sharing the results, and providing assistance in managing the complexity of the final diagnosis. This type of tool can make the results of medical experiments more easily exploitable, thus accelerating scientific progress.