Setting up your working environment
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There are many ways in which you can organise the environment that you will work on. Here we present a few suggestions.

1. Where to write (notes, scripts, metadata, thesis etc.)
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There are several text editors available that are useful to keep notes, write/edit programming scripts, document pipelines or even write your thesis (if writing in Latex for example).

`Visual Studio Code (VSCode) <https://code.visualstudio.com>`_ is widely used in the bioinformatics community. It has several extensions that will allow you to better visualise your content, for example by colouring code or showing a preview. It also has a built-in integration with git (a distributed version control system).  

`Atom <https://atom.io>`_ is a different editor that has very similar functions.

Both software are very similar and the choice of an editor is a matter of personal taste. Visual Studio Code has a built-in terminal, which means that you can work on the command line while inside VSCode. Atom does not seem to come with this feature (but check this `stackoverflow post <https://stackoverflow.com/questions/43013195/how-to-open-the-terminal-in-atom>`_ about possible solutions, including 2021 updates).

.. figure:: ../images/vscode_markdown_print.png
    :alt: This is an example of VSCode in action showing a template for wet lab notebook using markdown language

    This is an example of VSCode in action showing a template for wet lab notebook using markdown language (see :doc:`wet_labbook_template`). On the left you see the list of files in the folder where you are working on, in the middle your text/code (where you type) and on the right the preview.