Various embodiments of a biological interface system and related methods are disclosed. The system may comprise a sensor comprising a plurality of electrodes for detecting multicellular signals emanating from one or more living cells of a patient and a processing unit configured to receive the multicellular signals from the sensor and process the multicellular signals to produce a processed signal. The processing unit may be configured to transmit the processed signal to a controlled device that is configured to receive the processed signal. The system is configured to perform an integrated patient training routine to provide a time varying stimulus to the patient and to generate one or more system configuration parameters used by the processing unit to produce the processed signal.