Week 1: Pre-lab software checklist

Rika Anderson, Carleton College

Unix boot camp

For those of you who have not worked with Unix on the command line before, please go through this Unix boot camp. For all of you (regardless of whether you have worked on the command line before or not), please fill out the quick Unix worksheet on Moodle and submit by Friday. If you aren’t familiar with Unix, then this will be a handy cheat sheet for you. If you are, well, it won’t take long to fill out and it will help me check on where everyone is at.

Carleton VPN

Whenever you are doing bioinformatics analyses for this class and you are off-campus, please log in to the Carleton VPN. The VPN effectively “wraps” your computational inputs and outputs in a nice soft blanket of Carleton protection. If you are connecting remotely from China and having trouble accessing the VPN, contact the Carleton Helpdesk– they have a VPN option that might work for you.

Installing software

This bioinformatics class will, obviously, require us to do some hands-on bioinformatics. Most of the software you need is already installed on the remote server (i.e. a giant computer) that we’ll learn how to log onto next week. However, you’ll also need other software for some analyses. Usually, this software is installed in the Carleton computer labs where we do our in-person labs, but this year is obviously a little different.

If you are at Carleton, this software is available on the lab computers in CMC110 and in the Hulings computer lab. If you don’t want to have to worry about software installation on your own computer, I recommend working in one of those two computer labs.

If you are working from home or working at Carleton with your own laptop, you will need to install software for this class using one of the two options below. Folks at ITS can help you with this if you run into problems.

Option 1: REMOTELAB. ITS has built a REMOTELAB environment for accessing lab software from personal computers. ITS Wiki

Option 2: Installation on your local computer. ITS has pulled together information on what software can be installed on personally owned computers. ITS Wiki

Software that you should have installed on your own computer:

Terminal to log on to a remote server

If you have a Mac, you should be all set.

If you have a PC or some other operating system, you should install a Ubuntu terminal if you can.

If that doesn’t work, you can use PuTTY.

Text editor

If you have a Mac, I recommend BBEdit’s free version.

If you have a PC, Microsoft Notepad works, and it should already be on your computer.

Seaview: alignment visualization

Available for Mac or PC. Link here

IGV Viewer: mapping and SNP visualization

Available for Mac or PC. There is also a web version that works similarly and may be fine for our purposes, but I haven’t thoroughly tested it. Link here