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

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 Pre-Workshop Homework

Laptop Compatibility

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

Make sure you have a valid iPlant account

• 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.

Additional Readings and Assignments

• 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.

Workshop Agenda and Resources

Other Websites and Links and Resources

• DNA Subway Manual
• Workshop handouts in WORD and PDF
• DNA Barcoding Manual 
• Barcoding lab planning and prep
• http://www.learnaboutsma.org/   - SMA website and splicing animation.
• http://www.urbanbarcodeproject.org - UBP website
• http://www.iBoL.org - International Barcode of Life Project

Attendees

Post Workshop Survey

Please complete this survey at the conclusion of the workshop:

• https://www.surveymonkey.com/s/GenomicsInEducation_post

Post Workshop DNA Sequencing Results

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

Gel Images 

DNA Subway instructions:

 

1.       Log into DNA Subway (dnasubway.iPlantcollaborative.org)

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

and are posted as the entry under Jermel Watkins on 10/13/13

5.       Select the sequences you want to include and run your project; each person should have two sequences, 1 forward, 1 reverse.

           For example, Student 1 will have a sequence called Student1-M13F(21).... and a sample called Student1-M13R....

Important Pre-Workshop Travel Info

Recommended Lodging

There is no reimbursement for lodging. These hotels include those recommended by our hosting institution, but no guarantees are offered about the availability or suitability of the hotels.

Check website like hotels.com and travelocity.com for additional hotels and rates. 

Designated Lodging: Holiday Inn Express, 2375 Market Street, Reno Nevada  89502

Silver Legacy, Circus Circus, and the El Dorado are other options, all just across the freeway from UNR and are classic casino hotels along Virginia Street.  The Siena is a little farther down Virginia Street with very nice accommodations.

Parking Information/Directions:

See above. Find directions to and a map of the UNR campus at the following links: http://www.unr.edu/about/visit-campus/driving-directions; http://www.unr.edu/around-campus/maps

Transport Info:

Reno-Tahoe airport is approximately 10 minutes from campus and nearby hotels. From the Sacramento or San Francisco area, Megabus gets you to Reno for about $15-$17 one-way. The average travel time from the SF Bay Area is about 4-5 hours. Megabus is a great alternative to flying or driving. The bus will drop you off at the Silver Legacy bus stop. Circus Circus and Eldorado hotels are close by and the Siena is a few blocks at the downtown Riverwalk area next to the Truckee river.

http://us.megabus.com/