introphylogenomics/computingfundamentals

The fundamentals of command-line computing

Computing Fundamentals

This repository contains tutorials and associated files for learning about the fundamentals of computing and working at the command line. Primarily, we will talk about how to use commands and write scripts in Bash and Python. These two kinds of scripts are commonly used in bioinformatics and phylogenomics to manage large amounts of data and large numbers of files.

Select other markdown files (.md) to view tutorials specific to each topic:

• Practical Computing Advice and Plain Text Files
• Filesystems
• Command Line - Navigating
• Command Line - Editing
• Scripting

Here are some exercises to help practice the Bash skills we've covered:

• Changing File Extensions
• Extracting Lines
• Searching For a File
• Counting Lines in Files
• Calculator

Now that we've learned how to work at the command-line, here are some resources to learn a little about Python. We won't have time to cover Python together in this course, and it's not necessary for the later topics, but it will probably be useful to you at some point in your research so we encourage you to take a look:

• Python Basics
• More With Python

Here are some exercises to help practice the Python skills we've covered:

• Generating a Reverse Complement
• Rosalind Practice Problems