Setting up your working environment ==================================== 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.) ---------------------------------------------------------- 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) `_ 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 `_ 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 `_ 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.