We are developing a thermosphere-ionosphere-plasmasphere data assimilation model that will be used as an upper atmospheric component for a seamless ocean-atmosphere model. The ionosphere-plasmasphere data assimilation model was developed as part of an effort called the Global Assimilation of Ionosphere Measurements (GAIM). This data assimilation model is based on a physics-based model of the ionosphere-plasmasphere system that covers the E-region, F-region, topside ionosphere, and plasmasphere (an altitude range that extends from 90–30,000 km). This model is capable of assimilating real-time (or near real -time) data from a variety of sources, including bottomside N_e profiles from ionosondes, slant GPS/TEC from a network of stations, in situ N_e from DMSP satellites, line-of-sight UV emissions measured by satellites, and occultation data. The data are assimilated via an ensemble Kalman filter technique. In addition to the global N_e distribution, the data assimilation model also provides global distributions of the self-consistent drivers (neutral winds and composition, electric fields, and particle precipitation). The thermosphere data assimilation model has been constructed from a physics-based, global, thermosphere model using an ensemble Kalman filter technique. This model will eventually be able to assimilate UV radiances from the SSUSI and SSULI instruments, is situ winds and densities along satellite tracks, satellite drag data, and inferred neutral parameters from incoherent scatter radars. The goal is to couple the thermosphere-ionosphere-plasmasphere data assimilation model to the Navy's troposphere weather model (NOGAPS-ALPHA) at 90 km, and this will yield a seamless ocean-atmosphere model. This will allow for rigorous studies of the effect that tropospheric weather disturbances have on the upper atmosphere. The status of this modeling effort will be reviewed, with the emphasis on the effect that upward propagating tides and gravity waves have on the thermosphere-ionosphere system. The wave effects will also be compared with thermospheric disturbances generated by the ionosphere.