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"Simulated muscle fiber lengths and velocities during walking and running"
URL: https://simtk.org/home/muscfib_walkrun
Publication: http://jeb.biologists.org/content/216/11/2150.abstract?
sid=28158300-d50b-4616-a145-8fca9537bd51

Authors: Edith M. Arnold, Samuel R. Hamner, Ajay Seth, Matthew Millard and 
Scott L. Delp
Contact: https://simtk.org/sendmessage.php?touser=451

This document describes what is included in the downloads section this project 
and how to use these files.

IMPORTANT NOTE ON MUSCLE MODELS:  A custom plug-in was written to use a 
two-state (length and activation) muscle model with the Zajac 1989 
formulation.  This included the ability to use two cubic splines to describe the 
force-length and force-velocity curves.  This model is, for legacy reasons and 
somewhat misleadingly, called "Thelen2003MuscleV1" in the .osim file.  The 
version of the scaled musculoskeletal model with this model is included for 
completeness, but is probably un-readable with most versions of OpenSim, so a 
version with the "Schutte1993Muscle" model is also included.  This one will 
enable the user to visualize the results states file in OpenSim, but this WAS NOT 
the one used to generate  the simulations. 

This complication was a necessary work-around when I was doing this work in 
2011, but has been made obsolete by improvements to the muscle models in 
more recent versions of OpenSim.  For an excellent discussion on the ins and 
outs of muscle models in OpenSim see the paper below by Matt Millard.

Millard, M., Uchida, T., Seth, A., Delp, S.L. Flexing Computational Muscle: 
Modeling and Simulation of Musculotendon Dynamics. Journal of Biomechanical 
Engineering, vol 135.

Zajac, F. E. (1989). Muscle and tendon: properties, models, scaling, and 
application to biomechanics and motor control. Crit. Rev. Biomed. Eng. 17, 
359-411.


This download includes:

1.  Arnoldetal2010_2Legs_v3_hplmuscles_240.osim
The generic musculoskeletal model used for this study.  This model is based on 
the model described by Arnold et al. 2010 (ref below).  It uses the 
Schutte1993Muscle model formulation.  Several changes were made to the 
original model to make it appropriate for the demands of this study.  See 
publication for description of these changes.  Please cite appropriately.

Arnold, E. M., Ward, S. R., Lieber, R. L. and Delp, S. L. (2010). A model of the 
lower limb for analysis of human movement. Ann. Biomed. Eng. 38, 269-279.
https://simtk.org/home/lowlimbmodel09


2.  A folder for each one of the five subjects in the affiliated publication.  In 
each folder you will find:

2.1 The generic OpenSim model described in (1) scaled to the subject.  
There are two versions one that was used for the actual simulation (naming 
convention below, this will not open in the OpenSim GUI) and a second that will 
open in the GUI and can be used with the states file to visualize the motion.
The naming convention is as follows: 
subjectNN_scaled_AHv3_FV1D_Vx15_ad0104_pf10_2F.osim
	AHv3 = This was version 3 of a hybrid model that (Edith) Arnold 
and (Sam) Hamner created for their PhD work.
	FV1D = A 1 dimensional force velocity curve was used (i.e. 
doesn't scale with activation)
	Vx15 = maximum fiber velocity set to 15 optimal fiber 
lengths/second
	ad0104 = activation and deactivation constants were 0.01 and 
0.04
	pf10 = plantarflexor tendon stiffness set to 10% strain at 
maximum isometric force
	2F = Force was multiplied by 2x from the generic model.  See 
discussion in publication for background and justification.

2.2 A folder with results for each speed studied.
The naming convention is gaittype_speedtrial_results.  eg.  
Run_20001_results was the subject running at 2.00 m/s, trial 01
Within each folder there are many files with results in tab delimited 
format.

2.2.1 *_states.sto: Forward simulation results with all states 
(generalized coordinates, muscle activations, and muscle fiber lengths)  angles 
are in radians.  If you want to visualize the simulation, load this file with the 
model in the OpsenSim application.

2.2.2 *_states_degrees.mot: same as above but with degrees instead 
of radians.  legacy OpenSim format.

2.2.3 *_Actuation_*:  Results from the actuation analysis package in 
OpenSim.  

2.2.4 *_MuscleAnalysis_*: Results from the muscle analysis package 
in OpenSim.  This is where the meat of the published results come from.