COBRA Tutorials

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

• |icon_analysis| analysis <https://github.com/opencobra/COBRA.tutorials/tree/master/analysis>__
• |icon_base| base <https://github.com/opencobra/COBRA.tutorials/tree/master/base>__
• |icon_dataIntegration| dataIntegration <https://github.com/opencobra/COBRA.tutorials/tree/master/dataIntegration>__
• |icon_design| design <https://github.com/opencobra/COBRA.tutorials/tree/master/design>__
• |icon_reconstruction| reconstruction <https://github.com/opencobra/COBRA.tutorials/tree/master/reconstruction>__
• |icon_visualization| visualization <https://github.com/opencobra/COBRA.tutorials/tree/master/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 <https://nl.mathworks.com/help/matlab/matlab_prog/what-is-a-live-script.html>__.
• The static version .html can be visualized on the tutorial section of the COBRA Toolbox documentation <https://opencobra.github.io/COBRA.tutorials>__.
• For your reference, the .pdf version can be downloaded from the tutorial section <https://opencobra.github.io/COBRA.tutorials>__. 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 <https://github.com/opencobra/COBRA.tutorials/tree/master/.template/tutorial_template.mlx>__.

There are two ways to contribute to the tutorials:

A) Contribute using the MATLAB.devTools

You can use the MATLAB.devTools <https://github.com/opencobra/MATLAB.devTools>__ to submit your tutorial.

B) Contribute using git (via command line)

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

1. Fork the COBRA.tutorials repository <https://www.github.com/opencobra/COBRA.tutorials>__ 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

3. Change to the directory:

   .. code-block:: console

   $ cd fork-COBRA.tutorials.git/

4. Set the upstream to the opencobra/COBRA.tutorials repository:

   .. code-block:: console

   $ git remote add upstream [email protected]:opencobra/COBRA.tutorials.git

5. Fetch from the upstream repository

   .. code-block:: console

   $ git fetch upstream

6. Checkout a new branch from develop:

   .. code-block:: console

   $ git checkout -b <yourBranch> upstream/develop

7. Now, make your changes in the tutorial in MATLAB.

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

8. 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>"

9. Push your commits on <yourBranch> to your fork:

   .. code-block:: console

   $ git push origin <yourBranch>

10. Browse to your fork on https://www.github.com/<yourUserName>/COBRA.tutorials, where <yourUserName> is your Github username.

11. Click on Compare & Pull Request.

12. Change the target branch develop.

13. Submit your pull request.

14. 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