This week, you will get an introduction to and overview of the course (Tuesday session) and will learn the basics of working in a Unix shell environment (Thursday session).
Some of the things you will learn this week:
What to expect from this course.
Which tools and languages we will use.
What is expected of you during this course.
Get up to speed on the infrastructure of the course.
Why using a command-line interface can be beneficial.
What the Unix shell is and what you can do with it.
Using the shell, learn how to:
The first few pages of our primary book, Computing Skills for Biologists by Allesina & Wilmes (CSB for short), should give you an introduction to the rationale behind the book, and behind this course, too. Try to read this before Tuesday’s class.
Our main text for this week will be Chapter 1 from CSB, which will introduce you to using the Unix shell. Please read this chapter before Thursday’s class when we will go through the chapter by means of “participatory live-coding” (code-along). Highlight sections that you find challenging and ask about these in class as needed. Because repetition is beneficial, you are welcome to actively work through the code in the chapter beforehand – this will be particularly useful for those who have never used a shell before.
(Side note: we will cover many of the commands from this week in more detail in weeks 4-6, using the Buffalo book.)
CSB Chapter 0: “Introduction Building a Computing Toolbox” – Introduction & Section 0.1 only
CSB Chapter 1: “Unix”
Buffalo Preface and Chapter 1: “How to Lean Bioinformatics”
A Software Carpentry shell tutorial – For another angle on similar material to what we cover this week.
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