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Resources for learning to operate a computer from the command-line

Much of the work that we do in computational biology operates from what we call “the command-line” interface. The command-line allows us to carry out nearly all of the operations that you can with a graphical user interface (GUI), with its “point-and-click” interface. In many cases, (e.g., in launching large-scale computational processes, such as needed for genomic data analysis), it is much more efficient to do so from the command-line, especially if you are going to be using cloud-based or other remote computing resources.

That said, working at a computer from the command-line is unfamiliar, challenging, or even intimidating for many people. In our experience, ANYONE can learn to work at the command-line, but it takes time, practice, and just “making your own mistakes.” to get comfortable.

Here are a set of resources that should provide quite a bit of help for those who want to learn to “think in command line:”

Introductory videos from the Hubbard Center for Genome Studies, provided in association with the New Hampshire INBRE program. These are a wonderful set of short videos, typically running between 5 and 15 minutes in length, giving an introduction to various concepts in working at the unix command line. A complete list of videos can be found here.

Here are a few that we have found particularly helpful for getting started (though all are quite useful):

Also, as with our list of external R resources, we also recommend some of the courses set up by the folks at Data-Carpentry and Software-Carpentry.

Finally, for a much more in-depth but very useful and well-laid out tutorial, is the Introduction to Remote Computing, provided by the UC Davis Data Lab, run by Professor C. Titus Brown. The document is very comprehensive, so it is a very good resource, but it covers much more than we need for this week