Repository of tutorials for The COBRA Toolbox

COBRA Tutorials

Tutorials are here to get you started with using The COBRA Toolbox <>__. The tutorials are grouped according to the src/ folder structure:

  • |icon_analysis| analysis <>__
  • |icon_base| base <>__
  • |icon_dataIntegration| dataIntegration <>__
  • |icon_design| design <>__
  • |icon_reconstruction| reconstruction <>__
  • |icon_visualization| visualization <>__

All tutorials are provided in 4 formats: .mlx, .m, .pdf, and .html.

  • The interactive version .mlx is a MATLAB Live-script format and can be run using the MATLAB Live-script editor <>__.
  • The static version .html can be visualized on the tutorial section of the COBRA Toolbox documentation <>__.
  • For your reference, the .pdf version can be downloaded from the tutorial section <>__. The .m version of the tutorial can be opened and run directly in MATLAB. This is particularly useful to build new analysis scripts based on an existing tutorial.

Contribute a new tutorial or modify an existing tutorial

A template for generating a new tutorial is provided here <>__.

Contribute using the MATLAB.devTools

You can use the MATLAB.devTools <>__ to submit your tutorial.

Contribute using git (via command line)

Fork and checkout your branch ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  1. Fork the COBRA.tutorials repository <>__ on Github.

  2. Clone the forked repository to a directory of your choice:

.. code-block:: console

  $ git clone [email protected]:<userName>/COBRA.tutorials.git fork-COBRA.tutorials.git
  1. Change to the directory:

.. code-block:: console

  $ cd fork-COBRA.tutorials.git/
  1. Set the upstream to the opencobra/COBRA.tutorials repository:

.. code-block:: console

  $ git remote add upstream [email protected]:opencobra/COBRA.tutorials.git
  1. Fetch from the upstream repository

.. code-block:: console

  $ git fetch upstream
  1. Checkout a new branch from develop:

.. code-block:: console

  $ git checkout -b <yourBranch> upstream/develop
  1. Now, make your changes in the tutorial in MATLAB.

Submit your changes and open a pull request ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  1. Once you are done making changes, add the files to your branch, where tutorial_<yourFile> is the name of the tutorial. Make sure to add the .m and the .mlx files.

.. code-block:: console

  $ git add tutorial_<yourFile>.m
  $ git add tutorial_<yourFile>.mlx
  $ git commit -m "Changes to tutorial_<yourFile>"
  1. Push your commits on <yourBranch> to your fork:

.. code-block:: console

  $ git push origin <yourBranch>
  1. Browse to your fork on<yourUserName>/COBRA.tutorials, where <yourUserName> is your Github username.

  2. Click on Compare & Pull Request.

  3. Change the target branch develop.

  4. Submit your pull request.

  5. Wait until your pull request is accepted.

.. |icon_analysis| raw:: html

.. |icon_base| raw:: html

.. |icon_dataIntegration| raw:: html

.. |icon_design| raw:: html

.. |icon_reconstruction| raw:: html

.. |icon_visualization| raw:: html

Related Repositories



Repository of tutorials for The COBRA Toolbox ...