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  (a printed copy and some other handouts will be presented to you at the workshop).

• Review the

• 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 and format. 

DNA Barcoding . 

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

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.