Software Requirements & Setup Instructions

To fully participate in this course you will need access to the free open source software described below on your own laptop (N.B. You may need Administer privileges/permissions to install some of these).

Supported web browser We require an up-to-date web browser (current versions of Chrome, Firefox and Safari are preferred).

R and RStudio: Module 2 will use R in order to demonstrate data analyses. R can be downloaded and installed from CRAN (Comprehensive R Archive Network). If possible download the latest version of R. As of course launch (Jan 16) the latest release (2015-08-14, Fire Safety) is R-3.2.2.

We recommend using RStudio desktop, a slick visual interface for R.

Note that we use R in this course for several reasons:

  • R is open-source and freely available for Mac, PC, and Linux machines. This means that there is no restriction on having to license a particular software program, or have students work in a specific lab that has been outfitted with the technology of choice.
  • R is user-extensible and user extensions can easily be made available to others.
  • R is commercial quality. It is the package of choice for many statisticians and those who use statistics frequently.
  • R is very popular in the field of bioinformatics, especially in certain sub-disciplines, like genomics and structural bioinformatics.
  • R is very powerful. Furthermore, it is gaining new features every day. New statistical methods are often available first in R.

For motivated instructors only: Git and GitHub
Git is a version control system that lets you track who made changes to what and when. GitHub is a popular social code-hosting platform that greatly facilitates collaborative content development.

To learn more about the basics of Git and GitHub see Day4 of our Biocomputing Bootcamp course. For details on contributing to this course website via Git/GitHub please see this README.