Please bring a laptop computer to class. By using Linux on your own computer you can more quickly incorporate what you learn into your own research. Before the first class, please…
You will need to bring either a MAC laptop or a laptop running Windows 10 (Anniversary update or higher) or a linux laptop. We will no longer be supporting PC laptops running Windows versions less than 10. If you don't have a Mac, Windows10, or linux laptop, please contact Erin Nishimura. We have Mac OS laptops you can borrow for part or all of the course, available for use during the class time. You will still need to make your own arrangements to perform Assignments outside of class in some other way.
The computer should be a laptop. A tablet-only or iPad is not going to cut it.
Summit is a high performance computing cluster (a.k.a. supercomputer) that is housed at the University of Colorado Boulder and available for us to use. Please request access to Summit by starting on Step 3 under HPC Summit: Get Started.
To do Step 3 you will need a DUO app on your phone. Many CSU students already have this, but in case you don't, go here for instructions to download: DUO
You will need…
MAC people: you are all good. Nothing to download. You can use the terminal.
PC people: Please download and install PuTTy PuTTy
Everyone will need to install a text editor for writing and modifying plain text files. We recommend BBEdit for Mac and Notepad++ for windows. We DO NOT recommend TextEdit, Wordpad, Notebook, or Microsoft Word. You are free to use vim or emacs if you are already familiar with those interfaces, but they are beyond the scope of this course.
We will use an interactive ftp client to transfer and edit files on remote servers. We recommend Cyberduck . Cyberduck is available on MacOS and PC. The Cyberduck in the Apple Store costs money, and we don't recommend it. Just obtain the free version from the cyberduck website.
MAC: To Install R
MAC: To Install RStudio
PC: To Install R:
PC: To Install RStudio
Download and install IGV. You may need to update java: