Computing basics

Lab onboarding, training resources, and general reference.

• General advice
• Command Line and Bash Shell
• Git and GitHub
• Text Editor
• Markdown
• Python

General advice

Spend time everyday building and reinforcing computational skills. Like a foreign language, you need to use it to build mastery. Look for ways to use your new skills in various aspects of your work.

Command Line and Bash Shell

The command line allows you to run and automate commands on both a local computer and remote servers. While it may seem "dated" compared to our windows-oriented graphical desktops, it is incredibly powerful, and learning a few key commands will be critical for using git effectively (see below).

Installation:

• Mac: Use the Terminal app
• Windows: Use gitbash. See installation directions on this Software Carpentry page.

Reference:

• Mac Terminal Cheatsheet

Training:

• Software Carpentry's The Unix Shell Workshop

Git and GitHub

Git is powerful software to track changes and work collaboratively on code, while GitHub is a public git server. We use both the git program and the GitHub server for our laboratory notebooks.

Installation:

• Mac: Open the Terminal app and type git. If the software is not already installed follow the directions to install Command Line Tools.
• Windows: Use gitbash. See installation directions on this Software Carpentry page.

Reference:

• Git Cheatsheet
• Pro Git eBook
• Vince Buffalo's Bioinformatics Data Skills Book - Available in the lab

Training:

• Online git tutorial
• GitHub tutorial
• Write good commit messages or read a long version.
• Learn git branching - Advanced

Text Editor

Instructions are provided for Visual Studio Code (VS Code), but any text editor will work. Editors with git integration may be more useful.

Installation:

• Install VS Code

Setup:

• Basic set up
• Set up GitHub in VS Code
• Set VS Code to be your default editor for git

Markdown

Markdown is a simple way to format when writing in a plain text document. You gain the benefit of having the document stored in an archival format (plain text) but that can be compiled simply to a formatted document. For example, asterisks surrounding a word will make it italics. Here is a friendly article about markdown formatting.

Markdown documents typically have a .md file extension. The text you are reading is written in markdown.

It is important to note that there are different flavors of markdown that support different types of formatting: tables, etc. The basic syntax will work in (most) of the different flavors. When in doubt, keep the formatting simple.

Installation:

• None required! Try saving a document in your text editor with the .md extension.
• For fancier functions in your text editor, consider installing a Markdown extension.
• Can also experiment with Markdown format at the Dillinger.io online markdown editor.

Reference:

• Markdown cheatsheet
• Emoji cheat sheet
• The original markdown syntax from John Gruber

Python

Installation:

• Miniconda Python 3.x

Training:

• Data Science Hub Software Carpentry Course - Note that different courses cover different topics, so make sure the course is covering the language(s) of interest.
• Online Python course
• Python pandas tutorials

Becoming proficient:

• Exercism exercises