Bioinformatics Zen

Be more productive - throw away your mouse

// Wed August 22 2007

The mouse, or two dimensional motion pointing device, is undoubtedly useful, especially when you're new to computers. It lets you open windows, click around, and explore. However the more time you spend using a computer, and the more proficient you become, the more the mouse becomes a hindrance to how fast you can work.

In a simplistic sense, using the keyboard the majority of the time saves your elbow. Regular switching between the keyboard and the mouse will give you repetitive strain injury, I know because I get a dull ache in my right elbow and wrist when I'm doing it too much. Usually mice are not the best shape either, it rotates your wrist about 135 degrees wise to your elbow: put your hand on your mouse and have a look.

The real advantage from using the keyboard, is that it allows you to work much faster. If you know the keyboard shortcuts for the five top actions you usually use the mouse for, I think you'll be surprised at how much faster you can work. For example, in your code editor, useful keyboard commands to know could be: switch between files, compile and run the code, auto-complete, copy an entire line, and code reformat.

The Command Line

In my opinion, if you're a bioinformatician you need to know how to use command line. Powerful and versatile, this is the program I use most. Just about anything you do with your mouse, you can do a whole lot faster with the command line. Manipulating files, changing directories, and selectively performing actions based file type, the list is long. Getting used to the command line has a learning curve but the investment is very worthwhile, the returns in the speed at which you perform actions will mean you never look back. If you're using Linux, you're probably already familiar with using the console, on a Mac you'll need to look in /Applications/Utilities for terminal. Windows Vista users have something similar in Command Shell, or if you're an XP user I recommend downloading cygwin.


If you've ever given vim a try, you probably think that it makes no sense to anyone except Unix administrators, and it's true that the learning curve is steep. Vim is an entirely keyboard operated text editor. As with the command line, I would say that the investment is entirely worth it, once you understand how to use vim, you'll have an extremely useful tool at your disposal. What makes vim special for me is that all text editing actions can performed by chaining a series of single character commands together. For example typing "/vi" will take me to the next instance of the characters 'vi', then typing "2dw" will delete the next two words. Reading this, you might make it sound a bit of novelty, but imagine all the times you have to click around in Word, instead replaced with a few simple commands run from the keyboard. I do all my text editing in vim, including writing this blog post. To get started with vim have a look around on the web, or try the tutorial by typing "vimtutor" at the command line.

My message for this post is simple, keyboard good, mouse bad. Try to use the keyboard as much as possible, find the common keyboard shortcuts for your favourite programs, and use the command line. Hopefully you'll see the rewards in how you work.