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+#+TITLE: Modeling musculoskeletal kinematic and dynamic redundancy using null space projection
+#+AUTHOR: Dimitar Stanev
+#+EMAIL: stanev@ece.upatras.gr
+#+OPTIONS: email:t date:nil toc:nil \n:nil num:nil
+#+LATEX_HEADER: \usepackage{fullpage}
+#+LATEX_HEADER: \usepackage{parskip}
+
+* Overview
+
+  This repository contains the setup scripts, documentation and source code
+  relevant to the publication "D. Stanev and Konstantinos Moustakas, Modeling
+  musculoskeletal kinematic and dynamic redundancy using null space projection,
+  PLoS ONE, 14(1): e0209171, Jan. 2019, DOI:
+  https://doi.org/10.1371/journal.pone.0209171".
+
+* How to run the Docker image
+
+  In order to provide a portable setup on which the published simulations and
+  analyses can be interactively reviewed, modified and executed, the provided
+  environment is built as a Docker image. Docker is available a multitude of
+  platforms and detailed installation instructions are provided as [[https://docs.docker.com/install/][part of the
+  project's online documentation]]. After installation, switch to the toplevel
+  directory of this repository and build the docker image:
+  #+BEGIN_SRC bash :exports code
+docker build -t ubuntu_opensim_stanev .
+  #+END_SRC
+  You can change the name of the image (here =ubuntu_opensim_stanev=) to your
+  liking. After building, which should take a few minutes, the image can be run
+  in a container with the following command:
+  #+BEGIN_SRC bash :exports code
+docker run -it -p 4000:80 ubuntu_opensim_stanev
+  #+END_SRC
+  The =-it= option instructs =docker= to run in interactive terminal mode, while
+  the =-p 4000:80= option bind the port 80 of the image to the port 4000 of the
+  localhost. Of course, the image name should match the one used in the build
+  command and the port 4000 can be substituted with any available port on the
+  localhost. After running the docker, open [[http://localhost:4000]] in your
+  browser and fill in the string 'stanev' (without the quotes) in the password
+  prompt.
+
+* Demos
+
+  The user can navigate into the corresponding folders and inspect the source
+  code. The following case studies are provided in the form of interactive
+  Jupyter notebooks:
+
+- *arm\under{}model/model.ipynb* presents a case study using muscle space
+  projection to study the response of segmental level reflexes
+
+- *arm\under{}model/muscle\under{}space\underprojection.ipynb* demonstrates
+  muscle space projection in the context of segmental level (reflex) modeling
+
+- *arm\under{}model/feasible\under{}muscle\under{}forces.ipynb* uses task space
+  projection to simulate a simple hand movement, where the feasible muscle
+  forces that satisfy this task are calculated and analyzed
+
+- *feasible\under{}joint\under{}reaction\under{}loads/python/feasible\under{}joint\under{}reaction\under{}loads.ipynb*
+  demonstrates the utilization of the feasible muscle forces to calculate the
+  bounds of the joint reaction loads during walking
+
+The .html files corresponding to the .ipynb notebooks included in the folders
+contain the pre-executed results of the demos.