COBRA.tutorials

Repository of tutorials for The COBRA Toolbox

6 months after

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>__.

Contribute using the MATLAB.devTools

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

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]:/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 upstream/develop

  7. 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.m $ git add tutorial.mlx $ git commit -m "Changes to tutorial_"

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

    .. code-block:: console

    $ git push origin

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

  4. Click on Compare & Pull Request.

  5. Change the target branch develop.

  6. Submit your pull request.

  7. 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

awesome-go

awesome-go

A curated list of awesome Go frameworks, libraries and software ...

cobratoolbox

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox ...

fucking-awesome-go

fucking-awesome-go

awesome-go with :octocat: :star: and :fork_and_knife: ...

awesome-go

awesome-go

A curated list of awesome Go frameworks, libraries and software ...

awesome-go

awesome-go

A curated list of awesome Go frameworks, libraries and software ...