Tools of the trade: The Up and Atom Edition

June 01, 2017 | 3 Minute Read

Given the amount of brain-space that I reserve to remembering all of the players from the 1992 West Coast Eagles premiership team and obscure Simpsons references, from the title of this post I think I’m forgiven from sharing this classic:

But I digress….

If you’re working in Bioinformatics you need to really love your text editor, because its a tool that you use every day to write scripts, research papers and notes. Because I’m a dinosaur and primarily use bash for most of my work, I have traditionally used Vim for most of my programming. However, considering I often find myself working away from the command-line, I have started to use an actual editor.

One such editor, the hackable text editor “Atom”, is a massive favourite my mine and my MSc student Ning “Lucas” Liu. It’s very customisable, is developed/maintained by the github guys and is free! So in this post, we’re going to review our top 5 favourite packages for Atom

Jimmy’s Top 5

1. Spell-check

Ok it’s a standard across most word processing software, but it’s crucial for my ridiculously poor spelling. Also allows you to easily switch locale’s instead of editing Australian/UK english to US e.g. “colour” to “color” (shudder)

2. Beautify

Was late to the party on this one, but can make your boring looking code look colourful

3. Markdown Plus

I write a lot of my notes and documents in either markdown to latex, and so having WYSISYG style rendering within the window is always a handy feature.

4. Git integration

While I’ve always coded in isolation, recently I have starting using github and bitbucket to collaborate more with other Bioinformaticians. Atom has a few cool packages that make working with github easier, such as git-plus with git-multi and git-recent functions and key-binding options. The git-diff options with split-diff is super handy too

5. To Do Lists with todo-show

I’ve got a shocking memory and so I’ve got to be extremely vigilate with note writing and comments in my code. I generally like using Things on mac but if I’m doing things in Atom I can now get all my to-dos in one place.

Ning’s Top 5

1. Programming language auto-detected

It’s inevitable that the perfect tools for your work just need slight lil changes. Atom is really handy for its auto-detect-language ability no matter the scripts are in Python, R, bash (shell), C++, Java, GO or other any other programming languages.

2. Autocomplete with autocomplete-python

As a pre-Sublime user and because I mostly handle data using Python, I wasn’t able to use Atom until I installed this package. And I believe no one can resist a “TAB complete” function.

3. File icons with file-icon

This hack give distinct icons to files so that you can clearly recognize the files you want to edit. I usually have tons of files with similar names ( in a single directory and they can be super confusing.

4. Highlight with highlight-selected

One of the most lovable features of Sublime, which I thought would be lost when moving to Atom. It is just so important when changing variable names in multiple places.

5. Ask questions with ask-stack

As a noob in Bioinformatics, I need to ask questions constantly. This hack allows you to easily ask questions in Stack Overflow with a simple Ctrl + Alt + A, and browse the questions and answers without open your web browsers (Firefox is seriously eating my RAM)!