Copy of iPlant Genomics in Education Workshop - University of Nevada, Reno - May 21-22, 2013

Organizers:	Jason Williams
Local Point of Contact:	Christie Howard
Trainers:	David Micklos, Uwe Hilgert
Date:	May 21 - 22, 2014
Location:	Savitt Medical Sciences building University of Nevada, Reno 1664 North Virginia street Reno, NV 89557
Parking	Park at the Pennington Medical Sciences parking lot, follow the signs to the iPlant workshop/Rm 56 in the Savitt Medical Sciences Bldg., pick up a parking permit, then return to your car and park close by in a parking lot you'll be directed to when you pick up the permit. Directions to the Pennington Medical Science lot: Enter campus from North Virginia Street. Drive past Lawlor Event Center and continue until to the blue sign directing you to the UN School of Medicine (note post office at the corner). Turn right at the blue sign and continue straight to the round-about. Continue straight at the round-about and park outside the Savitt Medical Sciences Bldg. in Patient Parking to pick up your permit. Do not leave your car in Patient Parking for an extended time period as it will be ticketed/towed!

Pre-Workshop Homework

If you are bringing your own laptop:

Most laptops (<5 years old) updated with the latest web browser (we recommend FireFox:http://www.mozilla.org/en-US/firefox/fx/ ) will have no problem.

Here are some things to check:

If possible, make sure you have have administrative privileges on your computer (should it become necessary to install or update software during the workshop).
Ensure that your computer is running a current browser (Mozilla Firefox 13/ Internet Explorer 8 (IE 9 preferred) / Safari 4 or later).
Be aware, Java 7 has known issues that limit some functionality on DNA Subway. Get Java 6 @ this link: http://java.com/en/download/manual_v6.jsp
If you are a Windows user, ensure that your computer is running Java 6 Update 19 or later by going to http://java.com and click ‘Do I Have Java?’ Then click ‘Verify Java version’ and install.
If you are a Mac user, check that your computer has the latest Java installed (probably Java 6) and that it also is enabled. (Check it out at http://java.com or contact williams@cshl.edu for additional advice).
To test your Java installation, go to http://gfx.dnalc.org/files/apollo/test/ and follow the instructions at that site. The test is successful if an image opens up on your computer that looks like this screenshot: Java Screenshot

You should be able to log into the DNA subway at: http://dnasubway.iplantcollaborative.org/.
If you do not have an iPlant account, please get one at: http://user.iplantcollaborative.org/register.

ReviewDNA Subway manual (a printed copy will be presented at the workshop)
Review DNA Barcoding laboratory (a printed copy will be presented at the workshop)
Bring a small sample of plant tissue (a leaf/flower/etc.) or collect one on campus before the experiment.
If you wish to bring sequence data for the DNA barcoding or genome annotation experiments feel free to do so!
Check out the slides and papers mentioned in the agenda.

Wednesday

Wednesday
Time	Topic	Slides	Handouts/Notes/Links
09:00-09:15	Welcome/Logistics
09:15-10:00	Introductions
10:00-10:15	iPlant Collaborative Overview, Workshop Objectives		iPlant Homepage iPlant account portal
10:15-10:30	Break
10:30-10:45	DNA Subway Tour		DNA Subway Homepage
10:45-11:15	Using DNA Subway to Teach Concepts in Molecular Biology
11:15-12:00	Setting up projects for Annotation - Red Line		Gene Annotation Paper
12:00-01:00	Lunch
01:00-01:15	Mini Seminar: Evidence Based Gene Modeling
01:15-02:30	Gene Annotation I – BLAST		ENCODE Project ENCODE Nature
02:30-02:45	Break
02:45-03:00	Mini-Seminar: RNA Splicing		Alternative Splicing Paper
03:00-04:15	Gene Annotation II – User-BLAST		Addtl. Annotation Files
04:15-05:00	RNA-Seq and Green Line Demonstration

Thursday
Time	Topic	Slides	Notes/Links
09:00-09:30	Review
09:30-9:45	Mini Seminar: Transposons
09:45-10:45	Transposon Sleuthing: Yellow Line		TARGeT Paper
10:45-11:00	Break
11:00-12:00	DNA Barcoding - DNA Isolation & PCR
12:00-01:00	Lunch
01:00-01:30	Mini Seminar: DNA Barcoding and Student Projects		Urban Barcode Project
01:30-02:30	DNA Barcoding - Electrophoresis and Sequencing Prep
02:30-02:45	Break
02:45-03:30	Using Blue Line to Analyze DNA Barcodes
03:30-04:15	Explore DNA Subway Lines on your own
04:15-04:45	Using DNA Subway in the Classroom - Initial Thoughts
04:45-05:00	Evaluation, and Closure

Please complete this survey at the conclusion of the workshop:

Instructions on retrieving your results will be posted here after the workshop.

Gel Images

DNA Subway instructions:

2. Start a blue line project

3. Under 'Select Project Type' select the project type to be ‘rbcL’ barcoding

4. Under ‘Select Sequence Source’ choose ‘Import Sequence from DNALC’ Your sequences have a the tracking number: 10-240033358

Name	Institution
Grant Cramer	University of Nevada, Reno
Hanna Damke	University of Nevada, Reno
Julie Ellsworth	Truckee Meadows Community College
Kevin Facemyer	University of Nevada, Reno
Ruth Gault	University of Nevada, Reno
Deborah Harbour	College of Southern Nevada
Christie Howard	University of Nevada, Reno
Scott Johnson	Wake Technical Community College
Davis Jones	University of Nevada, Reno
Brandie Littlefield	Wake Technical Community College
Talline Martins	University of Nevada, Reno
Maryam Rahmati Ishka	University of Nevada, Reno
Karen Schlauch	University of Nevada, Reno
Julie Petereit	University of Nevada, Reno
Tina Slowan-Pomeroy	Truckee Meadows Community College
Jason Stubrich	University of Nevada, Reno
Chong Tang	University of Nevada, Reno
Richard Tillett	University of Nevada, Reno
Claus Tittiger	University of Nevada, Reno
Shayne Urrutia	University of Nevada, Reno
Veronica Zepeda	University of Nevada, Reno