2012 05 17 QIIME Workshop

Organizers	Naim Matasci, iPlant Collaborative, and Julia Neilson, Director, Research Lab, Department of Soil Water and Environmental Science, UA
Date	May 17 @ 9 AM to 5 PM, 2012
Location	McClelland Park 102, University of Arizona (UITS Confirmation #20644, 25 seats avail )
Registration Link	http://www.iplantcollaborative.org/qiime2012
Other Links	www.qiime.org
Flyer	QIIME Flyer

Workshop Description

This hands-on workshop is sponsored by the iPlant Collaborative and is taught by lead developer/co-creator Greg Caporaso and TA'd by NAU PhD student Andy Krohn. It will cover using the QIIME software package to analyze microbial marker gene survey data (e.g., 16S rRNA) generated on "next generation" sequencing instruments. Participants will connect to the Amazon Web Services EC2 or iPlant's Atmosphere compute cloud to perform their analyses from Mac OS computers. If you have your own Mac laptop, please bring it along; otherwise lab computers will be available. Topics covered will include preparing your sample metadata, assigning operational taxonomic units and taxonomy to sequence reads, computing UniFrac distances between samples, and generating publication-quality graphical and statistical results. We will additionally cover basic techniques for interacting with remote unix systems via a command line to support your future analyses on the Cloud. This workshop will introduce you to QIIME, and provide the basis on which you can begin to perform your own QIIME analyses.

Preparing for the Workshop

If you'd like to study a little ahead of time, please check out these links:
http://qiime.org/tutorials/tutorial.html
http://qiime.org/tutorials/working_with_aws.html
http://qiime.org/tutorials/unix_commands.html

Agenda

Times may vary a little depending on the interest/issues we may encounter with different sections.

Time	Topic
9:00 AM - 10:00 AM	Background: high-throughput microbial ecology (lecture)
10:00 AM - 12:30 AM	Cloud computing and using QIIME in the cloud (lecture + hands-on)
12:30 AM - 1:30 PM	Lunch - delivered; you may use the foyer of McClelland Park
1:30 PM - 4:30 PM	QIIME analysis of a (relatively) small test data set (hands-on)
4:30 PM - 5:00 PM	Future directions with QIIME: What you can expect to see in the next few months to year (lecture)

Attendee List

Name	Email	Research Area	User Acct?
Kayla Arendt	krarendt@email.arizona.edu	Ecological Studies	X
Roger Barthelson	rogerab@email.arizona.edu	Cell Biology	X
Marco Coolen	mcoolen@whoi.edu	Biological Oceanography/Paleoecology	X
Jeff Eble	eble@email.arizona.edu	Ecological Studies	X
Juliana Gil-Loaiza	juligil@email.arizona.edu	Environmental Biology	X, no atmo
Steve Goff	sgoff@iplantcollaborative.org	Plant Biology	X
Michele Hoffman	mhoffman.az@gmail.com	Plant Biology	X
Parris Humphrey	pth@email.arizona.edu	Ecological Studies	X, no atmo
Julio Ignacio-Espinoza	ignacioe@email.arizona.edu	Environ. Microbiology	X, no atmo
Brandon Iker	ikerb3@gmail.com	Soil, Water, Env studies	X
Laurel Johnstone	laureljo@email.arizona.edu	Genetics and Nucleic Acids	X
Won Jong Kim	wjk@email.arizona.edu	Immunobiology	X
Eun-Hae Kim	eunhaek@email.arizona.edu	Environmental Biology	X, no atmo
Raina Maier	rmaier@ag.arizona.edu	Environmental Microbiology	X
Naim Matasci	nmatasci@iplantcollaborative.org	Genetics and Nucleic Acids	X
Nirav Merchant	nirav@email.arizona.edu	Information, Robotics, Intelligent Systems	X
Susan Miller	sjmiller@email.arizona.edu	Training	X
Julie Neilson	jneilson@email.arizona.edu	Other	X
Marianyoly Ortiz	moo@email.arizona.edu	Env Biology	X
Virginia Rich-CANCELLED	vrich@email.arizona.edu	Microbial Biology	X, no atmo
Brian Roxas	baproxas@email.arizona.edu	Microbiology	X
Kristina Solheim	kasolheim@gmail.com	Environmental Biology	X
Sergei Solonenko	ssolonen@email.arizona.edu	Ecological Studies	X
Jana U'Ren - NO SHOW	juren@email.arizona.edu	Ecological Studies	X
Dragos Zaharescu	zaharescu@email.arizona.edu	Geobiology	X

Other Information

UA Folks: At the workshop, to connect to UA WiFi using Windows 7:

Click the Network Connection icon located in the Taskbar in the bottom, right corner of your screen and select Connect to a Network.
Select UA WiFi from your list of available networks.
Click the Connect button or double-click on the network name.
Before connecting you to the network, Windows 7 will prompt you for additional information. Select Enter/select additional log on information.
Enter your UA NetID in the User Name field
Enter your UA NetID password in the Password field.
Leave the Login Domain field blank.
Click the OK button.
Next, Windows 7 will prompt you to verify the security certificate for UA WiFi. If the certificate listed is GeoTrust Global CA you may click the OK button to continue.
NOTE: If the certificate listed is NOT GeoTrust Global CA you may be connecting to an unsecured network posing as UA WiFi. If you are unsure, click the Cancel button to drop the connection.
After acquiring a network address, your computer will be connected to the network.

Those that are not UA employees will need to connect their wireless to UAPublic. I've included the link that discusses connecting to UAPublic.

http://uits.arizona.edu/services/uawifi

There is a separate VGA connection in the lab for external devices and you will have access to switch between inputs.