AWS setup for QIIME Workshops
This document describes how to set up AWS instances for use in a QIIME workshop. These instructions are written for QIIME 1.9.1, and assume that users will be working through the Illumina Overview Tutorial using a Jupyter (IPython) Notebook server running on AWS. Other analyses are possible using this setup, so these instructions are a good starting point whenever you want to teach QIIME 1.9.1.
Students don't need to install QIIME on their laptops, the workshop will use AWS. Students should use Google Chrome during the workshop, which should be installed before they arrive.
Before the workshop begins you'll want to boot up all of the AWS instances that you'll use, and test the full tutorial using the same network that the students will be using. This will help you to identify any connectivity issues, etc. Conference and university "guest" networks often will not have port 22 open for ssh connections. If ssh connectivity is important for your workshop, be sure to figure out if this will be an issue. If you're only using the IPython notebook, ssh is not necessary.
You should start one m2.4xlarge instance per ~15 workshop participants to avoid having connections to the notebook be rejected. We also recommend starting a dedicated instance for the instructor - that way if connections get rejected for some users it doesn’t affect the instructors presentation.
Start your instances via the AWS interface, following the instructions in QIIME's Working with AWS documentation. Be sure to configure the security group to allow for use of the IPython Notebook, as described here. Once the instances are running, you'll need to follow the instructions for connecting to the EC2 instances using the IPython Notebook.
TODO: Determine if ~/temp is sufficient, or if the default should be changed.
You should now be able to access the IPython Notebook servers on the AWS instances. Confirm this by opening each via its URL.
You'll want to make the following information available to all students in the class. I often do this by publishing a google doc, and creating a shortened bit.ly link which I write on the board. For example, see http://bit.ly/anl-soils-2013, which is a published Google Doc. This makes it easy to drop extra text in the document as necessary through-out the workshop.
Logging into QIIME's IPython notebook:
[Insert IPython Notebook URL(s) here]
Password:
qiime
We'll work through this tutorial:
http://qiime.org/tutorials/illumina_overview_tutorial.html
Getting help with QIIME scripts:
http://scripts.qiime.org
Other useful QIIME links:
http://www.qiime.org
http://help.qiime.org
http://qiime.org/tutorials/working_with_aws.html
Interested in using AWS for research or education? AWS grants are available:
http://aws.amazon.com/education/
Each student should open the illumina_overview_tutorial_workshop_template link in the IPython notebook. They should immediately go to File > Save a Copy and save with a descriptive name (e.g., including their name in the notebook name). They should then execute all cells in the notebook to configure their environment. At this point, they’re ready to begin working through the tutorial.
TODO: Develop standard feedback questionnaire to provide to students.
Students sometimes will need a completion certificate when they process their reimbursements. The text below has been adapted based on the information that students often need. You can adapt this text, or write your own to provide this documentation. You should send to students as a PDF on an as-needed basis.
[Letterhead from your primary affiliation]
[your name, title, and contact information]
Dear Participant,
Thank you for registering for the QIIME workshop in [location] on [date] (cost of $[cost] USD). This document confirms that you paid in full, attended the whole workshop, participated fully, and completed all the exercises satisfactorily. We hope the skills you learned are useful for your ongoing studies.
All the best, [Image of your signature] [your name] (on behalf of the organizers)
