A system for treatment of a disorder in a gastrointestinal tract of a subject, the system comprising: at least one input module adapted to receive input from at least one of the subject, a medical practitioner treating the subject, and a care giver of the subject; a computer readable memory adapted to store a subject profile for the subject, said subject profile including subject data received as initial input by said at least one input module; a database including data relating to subjects treated for disorders in the gastrointestinal tract, to treatment protocols used for said subjects, and to the response to at least one specific subject to treatment of said at least one specific subject with a specific treatment protocol; a first vibrating ingestible capsule adapted to be activated to implement a first vibration protocol defined in a first treatment protocol, and adapted, in an operative mode, to deliver vibrations to a wall of the GI tract of the subject in accordance with said first vibration protocol, thereby to treat the subject; a second programmable vibrating ingestible capsule adapted to be programmed and activated to implement a second vibration protocol defined in a second treatment protocol, and adapted, in an operative mode, to deliver vibrations to a wall of the GI tract of the subject in accordance with said second vibration protocol, thereby to treat the subject; a processor, functionally associated with said at least one input module, said computer readable memory, and said database; and at least one sensor adapted to provide to said processor information regarding expelling of said first vibrating ingestible capsule from the body of the subject, wherein said at least one input module is adapted to receive feedback regarding a response of the subject to treatment in accordance with said first treatment protocol, wherein said processor is configured, based on at least one of said information regarding expelling and said feedback, to: automatically obtain an updated recommendation for an updated recommended treatment protocol based on said data included in said database, said data relating to at least one other subject of said subjects; and effect programming of said second programmable vibrating ingestible capsule to implement said second vibration protocol, said second treatment protocol including said second vibration protocol being based on said updated recommended treatment protocol. at least one input module adapted to receive input from at least one of the subject, a medical practitioner treating the subject, and a care giver of the subject; a computer readable memory adapted to store a subject profile for the subject, said subject profile including subject data received as initial input by said at least one input module; a database including data relating to subjects treated for disorders in the gastrointestinal tract, to treatment protocols used for said subjects, and to the response to at least one specific subject to treatment of said at least one specific subject with a specific treatment protocol; a first vibrating ingestible capsule adapted to be activated to implement a first vibration protocol defined in a first treatment protocol, and adapted, in an operative mode, to deliver vibrations to a wall of the GI tract of the subject in accordance with said first vibration protocol, thereby to treat the subject; a second programmable vibrating ingestible capsule adapted to be programmed and activated to implement a second vibration protocol defined in a second treatment protocol, and adapted, in an operative mode, to deliver vibrations to a wall of the GI tract of the subject in accordance with said second vibration protocol, thereby to treat the subject; a processor, functionally associated with said at least one input module, said computer readable memory, and said database; and at least one sensor adapted to provide to said processor information regarding expelling of said first vibrating ingestible capsule from the body of the subject, wherein said at least one input module is adapted to receive feedback regarding a response of the subject to treatment in accordance with said first treatment protocol, wherein said processor is configured, based on at least one of said information regarding expelling and said feedback, to: automatically obtain an updated recommendation for an updated recommended treatment protocol based on said data included in said database, said data relating to at least one other subject of said subjects; and effect programming of said second programmable vibrating ingestible capsule to implement said second vibration protocol, said second treatment protocol including said second vibration protocol being based on said updated recommended treatment protocol. automatically obtain an updated recommendation for an updated recommended treatment protocol based on said data included in said database, said data relating to at least one other subject of said subjects; and effect programming of said second programmable vibrating ingestible capsule to implement said second vibration protocol, said second treatment protocol including said second vibration protocol being based on said updated recommended treatment protocol.