README.rst

COBRA Tutorials

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

• analysis
• base
• dataIntegration
• design
• reconstruction
• 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.

There are two ways to contribute to the tutorials:

A) Contribute using the MATLAB.devTools

You can use the MATLAB.devTools to submit your tutorial.

B) 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:

   $ git clone git@github.com:<userName>/COBRA.tutorials.git fork-COBRA.tutorials.git

3. Change to the directory:

   $ cd fork-COBRA.tutorials.git/

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

   $ git remote add upstream git@github.com:opencobra/COBRA.tutorials.git

5. Fetch from the upstream repository

   $ git fetch upstream

6. Checkout a new branch from develop:

   $ 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.

   $ 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:

   $ git push origin <yourBranch>

10. Browse to your fork on https://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.