Week 2: Project organization and Markdown
1 Links
Lecture pages
- Tue: Project organization
- Tue: Markdown & VS Code
- Thu: Managing files in the shell
Exercises & assignments
- Assignment: Create a GitHub account
- Week 2 exercises
2 Content overview
This week, we’ll talk about some best practices for project organization, managing your project’s files in the Unix shell, and documenting your project with Markdown files. We’ll also spend a bit of time getting to know VS Code, the text editor that you will spend a lot of time in during this course.
Some of the things you will learn this week:
- A number of best practices for project organization, documentation, and management.
- How to apply these best practices this in the shell.
- How to use Markdown for documentation (and beyond).
- Get to know our text editor for the course, VS Code, a bit better.
3 Readings
This week’s reading is Chapter 2 of our secondary book, “Bioinformatics Data Skills” (“Buffalo” for short – the author is Vince Buffalo), which deals with project organization and (file) management.
The chapter also contains several tips and tricks for using the shell for project organization, which we will work through in the Zoom sessions. For more material along these lines, optional reading is Buffalo Chapter 3.
Required readings
- Buffalo Chapter 2: “Setting up and Managing a Bioinformatics Project”
Optional readings
- Buffalo Chapter 3: “Remedial Unix Shell”
Further resources
- Wilson et al. 2017, PLOS Computational Biology: “Good enough practices in scientific computing”
- Kieran Healy: “The Plain Person’s Guide to Plain Text Social Science”