<h1 id="cookie-cutter"><a aria-hidden="true" class="anchor-heading icon-link" href="#cookie-cutter"></a>Cookie Cutter</h1>
Tired of having non consistent folder for MAPP Metabolomics reports.
Looking into cookie cutter (for data science) as a possible template to start with and have more consistency across these repos.
<a href="https://towardsdatascience.com/automate-the-structure-of-your-data-science-projects-with-cookiecutter-937b244114d8">https://towardsdatascience.com/automate-the-structure-of-your-data-science-projects-with-cookiecutter-937b244114d8</a>
Using the github template is allready a good start maybe <a href="https://levelup.gitconnected.com/quick-setup-of-data-science-github-repositories-647b111b3c5f">https://levelup.gitconnected.com/quick-setup-of-data-science-github-repositories-647b111b3c5f</a>
Having a look at <a href="https://www.youtube.com/watch?v=HM56wCNxCnQ">https://www.youtube.com/watch?v=HM56wCNxCnQ</a>
Stop at 1:04:00 and workinh here /Users/pma/Dropbox/git_repos/mapp-metabolomics-unit/cookie_cut_project
<a href="https://cruft.github.io/cruft/">https://cruft.github.io/cruft/</a>
cruft create <a href="https://github.com/mapp-metabolomics-unit/mapp-repo-cookiecutter.git">https://github.com/mapp-metabolomics-unit/mapp-repo-cookiecutter.git</a> --overwrite-if-existscruft create <a href="https://github.com/mapp-metabolomics-unit/mapp-repo-cookiecutter.git">https://github.com/mapp-metabolomics-unit/mapp-repo-cookiecutter.git</a> --overwrite-if-exists
You can check a project 
cruft check

Cookie Cutter

Concrete steps to access and contribute to the DBGI Dendron


![](/assets/images/allard-lab.jpg)

Welcome the the COMMONS Lab Open Dendron !

In the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.

For this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.

## What is this note

This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.

## Tutorial

### Dendron. 

#### What is Dendron ?

> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
> 
> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.

#### Where to get more info on Dendron ?

- You can get more information in the Dendron system at the official website www.dendron.so
- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.

#### Concrete steps to access and contribute to the DBGI Dendron

1. Install [VSCode](https://code.visualstudio.com/download)
2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace 
3. Clone the COMMONS Dendron repo

    In your terminal
    ```
    git clone https://github.com/commons-research/commons-dws-public.git
    ```
4. In VSCode open (File/Open) the cloned repository.
5. Voila ! You should now be in the COMMONS Lab Open Dendron.

Feel free to explore and contribute.
A first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]


## Questions, comments, suggestions ?

Feel free to contribute here https://github.com/orgs/commons-research/discussions

