A system for designing a therapy for treating a condition associated with excess weight and including a therapy signal and an agent that alters the energy balance of a subject comprising: at least one electrode configured to be implanted within a body of the patient beneath a skin layer and placed at a vagus nerve, the electrode also configured to apply therapy to the vagus nerve upon application of a therapy signal to the electrode; an implantable impulse generator for placement in the body of the patient beneath the skin layer, the implantable impulse generator being configured to generate the therapy signal and to transmit the therapy signal to the electrode, the implantable impulse generator being coupled to an implanted antenna; an external component configured to couple to a first external antenna configured to be placed above the skin layer and adapted to communicate with the implanted antenna across the skin layer through radiofrequency communication, the external component including a plurality of selectable operating modules, each operating module being associated with a different set of operations available for selection by a user; an external programmer configured to communicatively couple to the external component via a second port, the external programmer being configured to provide therapy instructions comprising: a) parameters for each therapy cycle to the external component, wherein the external component is configured to send the therapy instructions to the implantable impulse generator via the external antenna and the implanted antenna, and the parameters comprise a therapy signal selected to downregulate activity on the vagus nerve having a frequency of at least 300 Hz with an on time period of at least 30 seconds; and off time period, the off time period selected to allow partial recovery of nerve function, wherein the off time is at least one minute; b) to deliver multiple therapy cycles in a treatment period; and the external programmer being configured to provide information to the user to select an agent that alters energy balance in the patient and to decrease the dosage of the agent based on the health profile of the patient and the side effects of the agent. at least one electrode configured to be implanted within a body of the patient beneath a skin layer and placed at a vagus nerve, the electrode also configured to apply therapy to the vagus nerve upon application of a therapy signal to the electrode; an implantable impulse generator for placement in the body of the patient beneath the skin layer, the implantable impulse generator being configured to generate the therapy signal and to transmit the therapy signal to the electrode, the implantable impulse generator being coupled to an implanted antenna; an external component configured to couple to a first external antenna configured to be placed above the skin layer and adapted to communicate with the implanted antenna across the skin layer through radiofrequency communication, the external component including a plurality of selectable operating modules, each operating module being associated with a different set of operations available for selection by a user; an external programmer configured to communicatively couple to the external component via a second port, the external programmer being configured to provide therapy instructions comprising: a) parameters for each therapy cycle to the external component, wherein the external component is configured to send the therapy instructions to the implantable impulse generator via the external antenna and the implanted antenna, and the parameters comprise a therapy signal selected to downregulate activity on the vagus nerve having a frequency of at least 300 Hz with an on time period of at least 30 seconds; and off time period, the off time period selected to allow partial recovery of nerve function, wherein the off time is at least one minute; b) to deliver multiple therapy cycles in a treatment period; a) parameters for each therapy cycle to the external component, wherein the external component is configured to send the therapy instructions to the implantable impulse generator via the external antenna and the implanted antenna, and the parameters comprise a therapy signal selected to downregulate activity on the vagus nerve having a frequency of at least 300 Hz with an on time period of at least 30 seconds; and off time period, the off time period selected to allow partial recovery of nerve function, wherein the off time is at least one minute; b) to deliver multiple therapy cycles in a treatment period; and the external programmer being configured to provide information to the user to select an agent that alters energy balance in the patient and to decrease the dosage of the agent based on the health profile of the patient and the side effects of the agent.