A muscle modelling framework is presented which relates the mechanical response of the rectus femoris muscle (at the organ level) to tissue level properties, with the capability of linking to the cellular level as part of the IUPS Physiome Project. This paper will outline our current approach to muscle modelling incorporating micro-structural passive and active properties including fibre orientations and nerve innervation. The technique is based on finite deformation (using FE analysis) coupled to electrical nerve initiated muscle activation, and we present the influence of active tension through an eccentric contraction at specific flexion angles. Finally we discuss the future goals of incorporating cell mechanics and validating at the organ level to provide a complete diagnostic tool with the ability to relate mechanisms of failure across spatial scales.