Self learning
R
R is a common coding language used in bioinformatics. R for Data Science (2e) is an excellent place to start your journey into R.
If you prefer learning through self-paced courses: Dataquest has a free, self-paced course. CodeAcademy has a free course, but you will have to pay for the certificate.
And, of course, our 3 Bees workshop series!
Bash
Most servers run on a Unix build. It is intimidating to start with a new interface, but with these guides things will be a lot smoother!
Data Carpentry’s Intro to the shell is a great place to start when you are a new user of Linux. As is the The Unix Shell, a self paced introduction to the unix shell and command line operations, provided by the Software Carpentries.
If you don’t have access to a server yet, and would like to practice on your local Windows machine, download MobaXterm and run a shell session on your Windows machine. If you are using a Mac, you will be able to follow the tutorial from the terminal that comes with your operating system.
Visual Studio Code
Traditionally, Windows users had to connect to servers using PuTTy or a similar interface. We recommend making use of VSCode that comes with your Windows operating system (it can also be installed on machines that run Linux builds and MacOS).
With VSCode, you can connect to servers using ssh, install extensions supporting a variety of coding languages, write and render markdown documents, and more. VSCode makes working on servers much easier as you can have a text editor open to edit your scripts to save them directly on the server you are working on, have a file manager open for a more traditional view of the file tree, as well as having multiple terminals open simultaneously.
Connecting to Uppmax servers with VSCode
- Open VSCode
ctrl+shift+pRemote-SSH: Add new SSH Host- Follow login instructions on Uppmax support
- Add the info to the first .ssh file prompted
ctrl+shift+pRemote-SSH: Connect to Host