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Abstract The Iterative Driver Estimation and Assimilation (IDEA) data assimilation technique was used with the Whole Atmosphere Model (WAM) to improve neutral density specification in the upper thermosphere. Two different neutral density data sources were examined to enhance the capability of simulating the global thermospheric state. The first were accelerometer estimates of neutral density from the Challenging Mini‐Satellite Payload (CHAMP) satellite. The second were neutral density estimates from the Global Ultraviolet Imager (GUVI) limb‐scan airglow observations aboard the Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite. Due to the intensity of the November 2003 storm, two changes were necessary in WAM. The first was allowing the Kp geomagnetic index to exceed 9 and the second was changing the relationship between Kp and the solar wind parameters used to drive the model. With these changes, results show that IDEA effectively captures the thermospheric neutral density at the CHAMP satellite altitude and follows the time‐dependence through the November 2003 storm period. Furthermore, a cross‐comparison was conducted with the GUVI dayside limb scan measurements. GUVI neutral densities within 270–320 km show the closest agreement with WAM when CHAMP data was assimilated by IDEA. We speculate on the potential for observations from GUVI at 300 km to be used as a data source in the IDEA‐WAM simulations. These simulations demonstrate the utility of the IDEA data assimilation technique with physical models and that using either accelerometer observations or ultraviolet airglow limb measurement during extreme storm periods could be used.