institutions) is good for you to know about because Xsede also provides (assuming your application is accepted) these same cloud computing resources to researchers to facilitate research. The virtual computing environment you will be using is provided through a (U.S.) National Science Foundation funded program called Xsede, which (at least for those of you at U.S. This way of interacting with a computer may not be familiar to you, but you will get some practice during this lab. You will interact with your VM solely by typing or pasting commands into a terminal window. You will use Secure Shell (SSH) and sFTP to connect to your own personal virtual machine (VM). Feel free to download and use any and all software on your personal device as well, just know that not everything will necessarily finish running in the allotted time, depending on your device. We will be using more software throughout the workshop than what we’re asking you to download here, all of which should be accessible on the remote servers.

iTerm2 (optional, but many of us like this terminal program better than the one that comes with macOS).BBEdit (BBEdit is the 64 bit version of TextWrangler for contemporary macOS).Tracer (used for Bayesian divergence time analyses).FigTree (used to visualize phylogenetic trees).Seaview (used to visualize small alignments).Go to Settings, Preferences, New Document, and set the line endings to Unix. Git for Windows (This is a UNIX emulator for running command-line programs)Īfter you have installed Notepad++, open it.Please download and install the following programs if you haven’t already: Windows If you have trouble connecting to the internet, let one of the TAs or course directors know and we’ll help you get on the network. You should have received instructions for connecting to wifi with your room key. If you’ve lost your invitation to join this workspace, ask one of us and we’ll resend the invitation to your email address. You can use the Slack app on your laptop and your phone. There is a slack workspace set up for people to ask questions and to have discussions. Slack is a messaging/discussion program that allows for large groups to interact as needed. Create and edit files and directories on the cluster.Īsk for help if any of these things aren’t working by the end!.Navigate and understand the directory structure.(TRON, 1982) Goalsīy the end of this introduction, you should be able to: On the other side of the screen, it all looks so easy.

How to use notepad++ with cyberduck