Week 1: Course Intro & Shell Basics

Author

Jelmer Poelstra

Published

February 25, 2024


2 Content overview

This week, you will get an overview of the course and a brief intro to the Ohio Supercomputer (OSC) during the Tuesday meeting, and will be taught the basics of working in a Unix shell environment during the Thursday meeting.

More specifically, some of the things you will learn this week:

Course intro & overview (Tuesday class)

  • 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.

OSC Intro (Tuesday class)

  • What is a supercomputer and why is it useful?
  • Overview of the resources the Ohio Supercomputer Center (OSC) provides.
  • How to use OSC OnDemand and access a Unix Shell in your browser.

Unix shell basics (Thursday class, Readings, and Exercises)

  • Why using a command-line interface can be beneficial.
  • What the Unix shell is and what you can do with it.
  • Using Unix commands, learn how to:
    • Navigate around your computer.
    • Create and manage directories and files.
    • View text files.
    • Search within, manipulate, and extract information from text files.

3 Readings

The first few pages of the book Computing Skills for Biologists by Allesina & Wilmes (CSB for short), should give you an introduction to the rationale behind the book as well as this course.

Our main text for this week will be Chapter 1 from CSB, which will introduce you to using the Unix shell.

I would recommend reading or at least skimming this before Thursday’s class, when we will go through much of the chapter’s content. That said, I will not assume you’ve read it during class, and you may prefer to focus your reading after the lectures. (We’ll discuss reading expectations and recommendations on Tuesday, too.)

You can access the books directly online through the links below, or download PDFs from the CarmenCanvas website. Consider buying a paper copy of one or both if you can afford it.

Required readings

  • CSB Chapter 0: “Introduction Building a Computing Toolbox” – Introduction & Section 0.1 only
  • CSB Chapter 1: “Unix”

Optional readings

  • Buffalo Preface and Chapter 1: “How to Learn Bioinformatics”
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