We present a novel pipeline for the construction of biomechanical simulations by combining generic anatomical knowledge with specic data. Based on functional descriptors supplied by the user, the list of the involved anatomical entities (currently bones and muscles) is generated using formal knowledge stored in ontologies, as well as a physical model based on reference geometry and mechanical parameters. This simulation-ready model can then be registered to subject-speci c geometry to perform customized simulations. The user can provide additional speci c geometry, such as a simulation mesh, to assemble with the reference geometry. Subject-specic information can also be used to individualize each functional model. The model can then be visualized and animated. This pipeline dramatically eases the creation of biomechanical models. We detail an example of a musculoskeletal simulation of knee flexion and extension and hip flexion and abduction, based on rigid bones and the Hill muscle model, with subject-specic 3D meshes non-rigidly attached to the simulated bones