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An understanding of internal loading in the knee is important for improving treatments of soft tissues injuries and diseases such as osteoarthritis. Physics based simulation provides a non-invasive method for estimating these internal loads (i.e., joint contact forces/pressures, soft tissue tensions, and muscle forces) during a range of activities from passive flexion to walking to stair climbing. The loads determined in these simulations are useful for predicting the effects of surgical treatments (e.g., anterior cruciate ligament (ACL) reconstruction and total knee replacement). However, substantial parametric uncertainty exists in current models of the musculoskeletal system. We will demonstrate the use of High Throughput Computing (HTC) to account for parametric uncertainty in musculoskeletal simulations. We will also show the value of HTC for simulating surgical procedures and probing sensitivities of knee function to decisions made in the operating room.