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You are here: Home / BioFrontiers Workshops / Workshops in the Series / 2019 Short Read Workshop / 2019_Before_the_workshop


Class details


Times: 9 am – 12 am
Location: JSCBB E1B11
Days: M-F July 8-12 and July 15-19
Office hours: 1 pm -3 pm in E1B11.

More information about JSCBB and parking

 Contact Us

Do this NOW (must be done before class)

Below is your to-do list before class starts on Monday.  There are more instructions below for all of this if you don’t know how to do it.


If you are bringing a PC Install something that will allow you to connect to a cluster. I suggest you chose one of the options here.
      a. MobaXTerm
      b. Linux Bash Shell

No matter what kind of computer you are bringing (Mac, Linux, PC)

1)    Set up Github (link to more information on why we need git hub)

  • Get a github account and give information to IT. Your github user name will be used to login to the cluster.
  • Create a ssh key
  • Make the key public
  • Email IT your github username

2)    Install X2go


Class intro


This class is taught reverse class room. That means you will watch video lectures the day before class. In class, we will work through examples. Then you will be given homework for the next day. We will have open office hours from 1 pm to 3 pm each day.

We're looking forward to working with everyone this year! 




 I have a PC. Should I do something special?

Yes. Install Windows Subsystem for Linux  or Mobaxterm.

Windows Subsystem for Linux (pick Ubuntu)



Why are we using github user names instead of Fiji user names?

This year, the compute cluster for the workshop is going to be built in the Amazon cloud.  Part of this workshop has always been a small intro to cluster computing, so we're working hard to ensure that you won't even notice you aren't logging into our on-premise compute cluster.   Using the cloud has benefits and drawbacks, and one thing we like to tighten up on while using it is security. 

This year, instead of using passwords, we're going to be using SSH keys to allow access to the Amazon Machine Instances (AMIs) for the workshop. Ssh keys are like computer finger prints. If I am Mary Allen and I’m logging on from Mary Allen’s computer, I’m probably really Mary Allen. But if I’m Mary Allen logging on from Jon Demasis computer, I may not really be Mary Allen. Therefore, you are going to create a fingerprint for your computer before you come to class. All instructions are below, but if you're curious how SSH keys work for authentication purposes, have a look at this video:


How do I set up Github to create a username for class?

1)    Make a github account

  1. You will use your username a ton in this class… so you should be able to type it without misspelling it! (

2)    Check if you have a public ssh key.

  1. For example, you can see my public ssh key here
  2. Type<username.keys>
    1. Make sure you use your username instead of typing username.keys
    2. If you have a key (they look like a bunch of letters and numbers) then skip to step 3.
    3. If you get a blank page you don’t have a key. Make one.
      1. Make the key on the computer you are bringing to class
      2. Make that key public
      3. Then you need to check if you have one again<username.keys>

3)    Email BIT ( your github username. [They only need your username, not your key]. For example, my username is maallen3. Make the subject line of your email [sread2018].


How do I install x2go?

For all attendees, we will be using the X2Go Client for visualizing our read mapping data in IGV.  Please go to the X2Go Client Download Instructions and follow the links to directions for either PC or Mac users. Please have the client downloaded before the first day of class, we will perform a test run with everyone to log in and start IGV on the first day.



Can I skip some classes?

No, you cannot skip some classes. The classes build on each other, so you will have a hard time keeping up if you skip some days. Additional IT is only there the first and third day. So, if you don’t get the cluster set up the first day we probably can’t get you on the cluster.

Where do I park?



I can’t come any more. Can you take me off the list?

            Yes! We have 15 people on the waiting list. Email Mary.A.Allen@colorado. if you cannot make it.

Can I practice early?

Yes. We highly recommend all attendees go to Code Academy and take their free online course, Learn the Command Line. This course will teach you some of the basic Linux skills you will be using throughout this workshop and does not require a terminal or other programs (it uses an online simulator). The most common problem people run into in this workshop is learning to use the command line, this will give you a head start! (Note you will have to sign up for a free account)



Contact us for questions

1)    Computer related questions:

If you have any questions about the install processes above, please don't hesitate to reach out to our ticketing system by emailing - please include [sread2018] in your subject line.  Due to the sheer number of people receiving this message, BioFrontiers IT will ignore personal emails aside from those containing GitHub usernames. We will also be in the workshop room 30 minutes prior to the start on day 1 to help anyone who still needs to add keys. Please do not wait until then if you're having an issue, though - it will go much smoother if everyone is prepared ahead of time.

2)    All other questions:



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