2012 08 22 Genomics in Education Workshop, UWisconsin-Madison

Section Navigation

• Pre-workshop Homework
• Workshop Agenda and Resources
• Travel Information

 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

• Review the DNA Subway Manual (a printed copy and some other handouts will be presented to you at the workshop).
• Review the DNA Barcoding wet-lab.
• 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

Wiki Short URL: http://www.iplantcollaborative.org/madwiki

Wedesday, August 22nd 

Thursday, August 23rd

Other Websites and Links and Resources

http://www.learnaboutsma.org/   - SMA website and splicing animation.

http://www.iBoL.org - International Barcode of Life Project

DNA Subway exercises and handouts in word andpdf format. 

DNA Barcoding planning and prep section. 

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

Gel Photo for samples 1-12

Gel Photo for samples 13-16

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: 10-204444324 on 8/29/12, (Its the second entry by Jermel Watkins)

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

Nearest Airports/ Rail

Shuttle Services from Airports and Buses

Call ahead of time to reserve/confirm

Parking Information:

On-Campus Directions:

See the Campus Map.