iPlant Genomics in Education Workshop - Hudson Alpha Institute - August 13-14, 2014

Pre-Workshop Homework

Laptop Compatibility

Preparing your laptop:

• Most laptops (<5 years old) updated with the latest web browser will have no problem. However, we do strongly recommend using the Firefox Browser (http://www.mozilla.org/en-US/firefox/fx/). Use of Internet Explorer will almost certainly cause problems, while Chrome has caused problems occasionally.Safari (Safari 4 or later) works well.
• If possible, make sure you have have administrative privileges on your computer (should it become necessary to install or update software during the workshop).
• Several workflows in the current version of DNA Subway require Java. Java 7 has had issues that limited some functionality in DNA Subway. Get Java 6 at 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 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: jpg/png/tif. Again, you may need to prime your Java installation as described above.

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

Instructors

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 #: 10-271794718

and are posted as the entry under Date: 8/16/14, Name: Jermel Watkins

5.       Select the sequences you want to include in your analysis 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 sequence called Student1-M13R.... (see table above for your sequence IDs)

Important Pre-Workshop Travel Info

Designated Lodging

Neither the iPlant Collaborative nor the HudsonAlpha Institute can reimburse lodging or other expenses associated with the attending the workshop.

Hotel Information:

• Towne Plaza Suites Huntsville, 125 McMurtrie Drive, Huntsville, AL 35806

Parking Information/Directions:

There is ample parking that will not require a fee or a parking permit. Don't park in guest parking spaces but follow the signs for “employee parking" and park in either of our large lots at the back of the building.

Meeting point

From the parking lot, enter the building through the back door, walk through the atrium to the front desk, where site coordinator Breanna Ruhlman will greet you and direct you to the Auditorium. We'll meet in the Auditorium and, once everybody arrived, will move to the instruction site.