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Often the best way of figuring out how to code is to use examples from already written scripts or functions. Many example scripts and functions can be found in the OpenSim 4.0 resources directory (Typically /Documents/OpenSim/4.0/Code/Matlab). You can also download some additional example scripts that use the current API;

plotMuscleFLCurves.mFunction to compute and plot the active and passive force-length muscle curves
createActuatorsFile.mFunction to generate a generic OpenSim Actuator File from a Model
build_and_simulate_simple_arm.mDemonstrates building and simulating a simple arm model
pendulum_marker_positions.mBuild, simulate, and generate outputs for a double-pendulum model. Writes the results to .sto and .trc files.

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