Welcome to this course. Your enrolling to this course means your are other simply curious to see what the big deal is with the using Linux as a bioinformatic tool, or already a bit about it and want to expand your skill set.
The course is organized to be useful to beginners as well as those who may have a bit more experience.
You will learn by reading articles, doing exercises, checking your understanding in the quizzes and the final test, and through discussion with other learners.
Please also note that you might be required to access websites to use freely available bioinformatics tools.
Almost every step encourages use of the comments area, where everyone can comment and discuss the course material. We encourage you to use social learning: to share your thoughts and ideas. Some of the course’s Steps are Discussion Steps.
Write comments for sharing with others
Read your comments and responses through before posting
Make constructive comments - critique the idea, not the person
Write what you would also say face-to-face
For most learners English is their first language, so always try to write clearly
Remember that learners vary in age and experience
Explain any acronyms you use and avoid jargon if you can
What the next three weeks are about?
In Week 1 of the course, we will introduce you to Linux and explain why it is widely used in bioinformatics. We will talk about the Linux command line and explain the directory structure of the file system. Some essential Linux commands will demonstrate how to access, manipulate and edit text files. The concept of environment variables will be introduced, and we will also demonstrate how to install a piece of widely used bioinformatics software. In addition, we’re going to talk to a biologist who has found their work transformed by using command line Linux.
In Week 2, we’ll build on the commands you learnt in Week 1 and introduce you to bash scripting. As the week progresses, we’ll look at why using bash scripts is such a powerful means of automating repetitive commands. We’ll walk you through writing your very own first bash script and from there, you’ll learn about basic bash syntax in the form of variables, conditional logic and functions. And, most importantly, you’ll start to put your individual commands together to form simple bash scripts. You will also hear some advice from a professional bioinformatician. In the final exercise you will have an opportunity to write a script to parse biological data.
After you see how to handle and analyse your data using the command-line in Week 1, and how to write and run bash scripts to automate that handling during Week 2, in Week 3 you will see how you can analyse and visually represent your data using R and RStudio. We will first review together the key concepts and basics of using the R language. You will learn how to manipulate lists, vectors or dataframes, and how to read and interrogate data from files to create simple plots under R. We will then see how RStudio can simplify these processes, and you will learn how to work under RStudio to easily create simple or more complex plots using packages specifically designed for that purpose.