Join members of the OpenSim Team on Wednesday July 26th for an introduction to OpenSim and new tools for rapidly developing musculoskeletal simulations.

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Please follow the instructions below to prepare for the workshop. Note that there are separate software environments for each portion of the workshop.  

Part 1: OpenCap

1. Create account

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• Windows 10 or later (64-bit) or Mac (macOS 11 or later)
• Python via Anaconda
  • Python 3.10
  • NumPy
  • Matplotlib
• Matlab
  • Matlab 2016b or later (64-bit). Matlab 2018a or later is best.
• A text editor (e.g., Notepad++)

3.

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 OpenSim installation

OpenSim with Python (Windows only)

1. If you haven't already, download and install Anaconda.
2. Open the Anaconda Prompt (or, Powershell on Windows, Terminal on Mac, etc).

3. If not using the Anaconda Prompt, you may need to initialize conda for shell interaction by running

   Code Block
   > conda init <shell-name>

   where <shell-name> is one of the following: cmd.exe (Windows default), bash (macOS default), powershell, fish, zsh, tcsh, xonsh.

4. Create a new conda environment for Python 3.10.

   Code Block
   (base) C:\Users\me> conda create -n tgcs2023addbio-processing python=3.10 matplotlib

   
   

5. Activate the conda environment.

   Code Block
   (base) C:\>Users\me> conda activate tgcs2023

4. OpenSim installation

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1. 
   

2. If paths to previous OpenSim versions exist on your PYTHONPATH environment variable, remove them and restart the shell.

3. Install the OpenSim conda package. This installs a version of OpenSim including Moco that is compatible with Python 3.10 and includes NumPy 1.21. 

   Code Block
   (addbio-processing) C:\Users\

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1. me> conda install -c opensim-org opensim-moco=4.4.1=py310np121

   
   

2. Launch a Python interpreter from your conda environment.

   Code Block
   (addbio-processing) C:\

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1. Users\me> python

   
   

2. Test the OpenSim configuration by checking the timestamp from running 

   Code Block
   >>> import opensim >>> opensim.GetVersionAndDate()

   in the Python interpreter; the date should be in June 2023.

OpenSim with Matlab

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1. Download the OpenSim 4.4.1 software.
   1. Windows: 
   2. Mac: 
2. Install OpenSim to a location of your choice; perhaps C:\OpenSim opensim-core-4.4.1 (on Windows).
3. If you use Windows, edit your PATH environment variable to include OpenSim’s bin directory (e.g., C:\OpenSim opensim-core-4.4.1\bin). See here for instructions. Make sure to remove any previous OpenSim installations from your PATH.
4. Run the OpenSim application to open the GUI. If the instructions below do not work, go the OpenSim executable in the bin folder and launch it from there.  
   1. Windows: open the Start menu and click OpenSim 4.4
   2. Mac: go to Applications and click OpenSim 4.4
5. A prompt will appear to install the OpenSim resources to a location of your choice; perhaps C:\Users\<PROFILE_NAME_HERE>\Documents\OpenSim\4.4 (on Windows; replace <PROFILE_NAME_HERE> with your Windows profile name). We will refer to this directory as <RESOURCES_DIR> in the remaining instructions below.

6. Configure OpenSim with Matlab by starting Matlab and running configureOpenSim.m, located at <RESOURCES_DIR>at C:\opensim-core-4.4.1\Resources\Code\Matlab .

7. After the script completes, restart Matlab and test the configuration by checking the timestamp from running 

   Code Block
   >> org.opensim.modeling.opensimCommon.GetVersionAndDate()

    in the Matlab command window; the date should be in July 20222023.

8. Test that the visualizer is working by running the following:

   Code Block
   >> cd 'C:\Users\<profile>\Documents\OpenSim\opensim-core-4.4.1\Resources\Code\Matlab\Moco' >> exampleSlidingMass

   You should see a visualizer window appear with a sliding mass animation. Hit ESC twice to close the window.

9. Note for OpenSim 3.3 users: You cannot concurrently use OpenSim 3.3 and 4.4 in Matlab; to switch versions you must re-run configureOpenSim.m and edit your PATH environment variable.

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4. Download the example data

Download the example data: ExampleData.zip

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Visit the Moco website here.

Slides

TODO

Publications

Uhlrich SD, Falisse A, Kidzinski L, Muccini J, Ko M, Chaudhari AS, Hicks JL, Delp SL (2022) OpenCap: 3D human movement dynamics from smartphone videos. bioRxiv. https://doi.org/10.1101/2022.07.07.499061

Werling K, Bianco NA, Raitor M, Stingel J, Hicks JL, Collins SH, Delp SL, Liu CK (2023) AddBiomechanics: Automating model scaling, inverse kinematics, and inverse dynamics from human motion data through sequential optimization. bioRxiv. https://doi.org/10.1101/2023.06.15.545116

Dembia CL, Bianco NA, Falisse A, Hicks JL, Delp SL (2020) OpenSim Moco: Musculoskeletal optimal control. PLoS Comput Biol 16(12): e1008493. https://doi.org/10.1371/journal.pcbi.1008493

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