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This project aims to make the life of a researcher and end-user a bit easier in dealing with Neuro-Biomechanical models. If you are new to modelling, or even expert in computational and human/animal movement science, you may have to deal with installation of several packages. OpenColab (OpenSim + Google Colab) allows you to use ๐Ž๐ฉ๐ž๐ง๐’๐ข๐ฆ ๐จ๐ง ๐ญ๐ก๐ž ๐ฐ๐ž๐› (e.g. Google Colab) with "๐™๐ž๐ซ๐จ ๐œ๐จ๐ง๐Ÿ๐ข๐ ๐ฎ๐ซ๐š๐ญ๐ข๐จ๐ง ๐ซ๐ž๐ช๐ฎ๐ข๐ซ๐ž๐, ๐…๐ซ๐ž๐ž ๐š๐œ๐œ๐ž๐ฌ๐ฌ ๐ญ๐จ ๐†๐๐”๐ฌ ๐š๐ง๐ ๐„๐š๐ฌ๐ฒ ๐ฌ๐ก๐š๐ซ๐ข๐ง๐ ".

License: OpenColab Notebook v1

This project aims to make the life of a researcher a bit easier in dealing with Bio-mechanical models. OpenSim has got ๐š๐ฆ๐š๐ณ๐ข๐ง๐  ๐ˆ๐ง๐ญ๐ž๐ซ๐Ÿ๐š๐œ๐ž๐ฌ including C++, Python, and Matlab. Normally, the user installs them on their PC.

This project adds another interface where one can ๐ซ๐ฎ๐ง ๐ง๐ž๐ฎ๐ซ๐จ๐ฆ๐ฎ๐ฌ๐œ๐ฎ๐ฅ๐จ๐ฌ๐ค๐ž๐ฅ๐ž๐ญ๐š๐ฅ ๐ฆ๐จ๐๐ž๐ฅ๐ข๐ง๐  & ๐ฌ๐ข๐ฆ๐ฎ๐ฅ๐š๐ญ๐ข๐จ๐ง๐ฌ ๐จ๐ง ๐ญ๐ก๐ž ๐ฐ๐ž๐› (particularly on ๐†๐จ๐จ๐ ๐ฅ๐ž ๐‚๐จ๐ฅ๐š๐›). You can imagine ๐†๐จ๐จ๐ ๐ฅ๐ž ๐ƒ๐จ๐œ๐ฌ (๐จ๐ง ๐ญ๐ก๐ž ๐ฐ๐ž๐›) ๐ฏ๐ฌ. ๐Œ๐ข๐œ๐ซ๐จ๐ฌ๐จ๐Ÿ๐ญ ๐–๐จ๐ซ๐ (๐จ๐ง ๐š ๐๐‚).

๐†๐จ๐จ๐ ๐ฅ๐ž ๐‚๐จ๐ฅ๐š๐›:
"๐‚๐จ๐ฅ๐š๐›๐จ๐ซ๐š๐ญ๐จ๐ซ๐ฒ, ๐จ๐ซ "๐‚๐จ๐ฅ๐š๐›" for short, allows you to write and execute Python in your browser, ๐ฐ๐ข๐ญ๐ก ๐™๐ž๐ซ๐จ ๐œ๐จ๐ง๐Ÿ๐ข๐ ๐ฎ๐ซ๐š๐ญ๐ข๐จ๐ง ๐ซ๐ž๐ช๐ฎ๐ข๐ซ๐ž๐, ๐…๐ซ๐ž๐ž ๐š๐œ๐œ๐ž๐ฌ๐ฌ ๐ญ๐จ ๐†๐๐”๐ฌ, ๐„๐š๐ฌ๐ฒ ๐ฌ๐ก๐š๐ซ๐ข๐ง๐ . Whether you're a student, a data scientist, or an AI researcher, Colab can make your work easier. Watch Introduction to Colab to learn more, or just get started below! https://colab.research.google.com/ "

If you are new to modeling, or even an expert in computational and human/animal movement science, you may have to deal with the installation of several packages, set up a new environment on your computer which usually keeps you away from the actual research.


In this project, we use Google Cloud (esp. Google Colab notebooks) and ๐ข๐ง๐ฌ๐ญ๐š๐ฅ๐ฅ ๐Ž๐ฉ๐ž๐ง๐’๐ข๐ฆ via Anaconda Cloud easily (<๐Ÿ•๐ฆ๐ข๐ง) so that we can use it without any issue at any computer, collaborate with others and share models fast without even a need to install OpenSim on your computer. ๐’€๐’๐’– ๐’‹๐’–๐’”๐’• ๐’๐’†๐’†๐’… ๐’•๐’ ๐’‰๐’‚๐’—๐’† ๐’‚๐’„๐’„๐’†๐’”๐’” ๐’•๐’ ๐’•๐’‰๐’† ๐’Š๐’๐’•๐’†๐’“๐’๐’†๐’• ๐’‚๐’๐’… ๐‘ฎ๐’Ž๐’‚๐’Š๐’ ๐’‚๐’„๐’„๐’๐’–๐’๐’•. The ๐ข๐ง๐ข๐ญ๐ข๐š๐ฅ ๐ฌ๐ž๐ญ๐ฎ๐ฉ ๐ฐ๐จ๐ฎ๐ฅ๐ ๐ญ๐š๐ค๐ž <๐Ÿ ๐ฆ๐ข๐ง.

That is it! Enjoy OpenColabing!

We also created several ๐ฏ๐ข๐๐ž๐จ ๐ญ๐ฎ๐ญ๐จ๐ซ๐ข๐š๐ฅ๐ฌ (e.g. https://youtu.be/iEjd7OSOitg) to learn Google Colab (basic python programming on the web) and OpenColab (๐Ž๐ฉ๐ž๐ง๐’๐ข๐ฆ + ๐†๐จ๐จ๐ ๐ฅ๐ž ๐‚๐จ๐ฅ๐š๐›): https://tinyurl.com/xukhmnez



๐‡๐จ๐ฐ ๐Ž๐ฉ๐ž๐ง๐‚๐จ๐ฅ๐š๐› ๐ฐ๐จ๐ซ๐ค๐ฌ ๐š๐ง๐ ๐ก๐จ๐ฐ ๐๐จ ๐ฐ๐ž ๐ฏ๐š๐ฅ๐ข๐๐š๐ญ๐ž ๐ข๐ญ?

The image below shows how we developed and validated OpenColab. As mentioned, the Conda package was developed to install OpenSim on Colab. For validation, we compared the GUI results (for Scaling, IK, ID, RRA, SO, and CMC) with OpenColab results. The outcomes matched very well.

๐๐จ๐ญ๐ž๐›๐จ๐จ๐ค๐ฌ:
To download the latest Ipython notebook (OpenColab.ipynb), please visit Github:
https://github.com/hmok/OpenColab

๐‡๐จ๐ฐ ๐ญ๐จ ๐ฌ๐ž๐ญ ๐ฎ๐ฉ ๐ข๐ง <๐Ÿ๐ฆ๐ข๐ง ๐š๐ง๐ ๐ซ๐ฎ๐ง ๐ข๐ง๐ฏ๐ž๐ซ๐ฌ๐ž ๐ฉ๐ซ๐จ๐›๐ฅ๐ž๐ฆ ๐ข๐ง ๐Ž๐ฉ๐ž๐ง๐‚๐จ๐ฅ๐š๐›?
Please follow the following steps to start running OpenSim simulations in < 1 min.
Go to this website: https://colab.research.google.com/

a) Upload the following file from Supplementary Material 2: โ€œOpenColab.ipynbโ€œ or from this link https://github.com/hmok/OpenColab/blob/main/OpenColab.ipynb
b) Wait till the file is loaded.
c) Press Ctrl+F9 or Runtime ---> Run all (setup finished in < 1 min)
d) No action needed by the user: OpenSim will be installed (5-7 min)
e) The simulations will generate the results of this paper.

๐“๐ก๐ž ๐Ÿ๐จ๐ฅ๐ฅ๐จ๐ฐ๐ข๐ง๐  ๐ฏ๐ข๐๐ž๐จ ๐ฌ๐ก๐จ๐ฐ๐ฌ ๐ก๐จ๐ฐ ๐ญ๐จ ๐๐จ ๐ญ๐ก๐ข๐ฌ:


If you are interested in contributing, please feel free to reach out at ๐ฆ๐จ๐ค๐ก๐ญ๐š๐ซ๐ณ๐š๐๐ž๐ก ๐ƒ๐Ž๐“ ๐ก๐จ๐ฌ๐ฌ๐ž๐ข๐ง ๐€๐“ ๐†๐ฆ๐š๐ข๐ฅ ๐ƒ๐Ž๐“ ๐œ๐จ๐ฆ.

Please cite the following:
Mokhtarzadeh, Hossein, Fangwei Jiang, Shengzhe Zhao, and Fatemeh Malekipour. 2021. โ€œOpencolab Project: Opensim in Google Colaboratory to Explore Biomechanics on the Web.โ€ engrXiv. September 30. doi:10.31224/osf.io/f8a3h.






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