Week 2: Project organization and Unix shell basics
Overview
This week, we will cover best practices for project file organization, documenting your project with Markdown files, and the basics of the Unix shell. You will also get to know VS Code, a text editor you’ll spend a lot of time in during this course.
Learning goals & lectures
During the week’s lecture, you will learn:
Project file organization (Tuesday)
A number of best practices for research project…
- file organization
- file management
- documentation.
Markdown & VS Code (Tuesday/Thursday)
- How to use Markdown for documentation (and beyond).
- Get to know VS Code, the text editor you’ll use throughout the course.
Unix shell basics (Thursday)
- What the Unix shell is and what you can do with it
- Why it can be beneficial to use a command-line interface in general, and the Unix shell specifically
- How Unix commands are stuctured
- How to navigate around your computer with Unix commands
Readings
No required readings, but see the “Further resources” section below for optional readings.
Assignments & exercises
- Graded assignment: Markdown and shell basics (due Sun 09/07)
Further resources
Official VS Code introductory video
If you watch this, keep in mind that there are slight differences between the stand-alone VS Code app demonstrated in the video, and the VS Code Server app that you run in your browser via OSC OnDemand. For example, there is no “Live Preview” extension for HTML files available for VS Code Server.Buffalo (2015) – Chapter 2: Setting up and Managing a Bioinformatics Project (OSU library link)
Allesina (2019) – Chapter 1: Unix (OSU library link)
Noble (2009): A quick guide to organizing computational biology projects
Wilson et al. (2017): Good enough practices in scientific computing