Model updating, which utilizes mathematical means to combine model simulations with physical observations for improving model predictions, has been viewed as an integral part of a model validation process. While calibration is often used to "tune" uncertain model parameters, bias-correction has been used to capture model inadequacy due to a lack of knowledge of the physics of a problem. While both sources of uncertainty co-exist, these two techniques are often implemented separately in model updating. This paper examines existing approaches to model updating and presents a modular Bayesian approach as a comprehensive framework that accounts for many sources of uncertainty in a typical model updating process and provides stochastic predictions for the purpose of design. In addition to the uncertainty in the computer model parameters and the computer model itself, this framework accounts for the experimental uncertainty and the uncertainty due to the lack of data in both computer simulations and physical experiments using the Gaussian process model. Several challenges are apparent in the implementation of the modular Bayesian approach. We argue that distinguishing between uncertain model parameters (calibration) and systematic inadequacies (bias correction) is often quite challenging due to an identifiability issue. We present several explanations and examples of this issue and bring up the needs of future research in distinguishing between the two sources of uncertainty.