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.
In an ungraded assignment to get set up for upcoming modules, you will sign up for a GitHub account.
Like last week, there are exercises but no graded assignments (the first one will be issued next week).
Some of the things you will learn this week:
Some 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.
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.
While very useful for any biologist interested in computational skills, the Buffalo book is geared towards bioinformatics data, especially genomic data from Next-Generation Sequencing (NGS) experiments. If you don’t work with sequencing data, don’t fret about understanding the specifics of some of the examples and recommendations, and hopefully, the more general underlying ideas will still be helpful.
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.
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”
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