iPlant Genomics in Education Workshop - Santa Fe - May 21-22, 2015

Pre-Workshop Assignments

Confirm/Establish 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.
• Try to 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. Newer Java versions often limit some functionality in DNA Subway.
  • 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 a view of the Apollo annotation browser opens up that looks like this screenshot: jpg\/png\/tif\.
  • Ensure that your computer is running the latest Java by going to http://java.com and click ‘Do I Have Java?’ Then click ‘Verify Java version.’
  • If you are not running the latest Java, install or update it. (If you are a Mac user and experience trouble with this, contact williams@cshl.edu for additional advice).
  • Still having trouble opening Apollo? Open the Java settings (Control Panel or Systems Preferences), click Security tab. Add the following URLs to the Exception Site List:
    • http://gfx.dnalc.org
    • http://dnasubway.iplantcollaborative.org
  • If Java still does not open, enter these URLs into the Exception Site List as well. (One at a time.)
  • If none of the above worked, get Java 6 at this link:* http://java.com/en/download/manual_v6.jsp, and install it on your laptop.

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.

Go through these readings and other assignments:

• Review DNA 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 listed/linked in the agenda below.

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

DNA Barcoding Experiment

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 the Tracking # 10-298041655:

and are posted as the entry under Date: 5/27/2015, 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

Neither the iPlant Collaborative nor Santa Fe Community College can reimburse lodging or other expenses associated with attending the workshop.

Travel

Santa Fe is served by a municipal airport (SAF). Alternatively, travelers can fly into Albuquerque (ABQ) and either use train, shuttle or rental car to get to Santa Fe.

Lodging

Santa Fe has an ample number of accommodations. Excellent hotels that are located a few driving minutes from SFCC include:

• Holiday Inn Express, 3450 Cerrillos Rd, Santa Fe, NM 85701
• Best Western Plus Inn, 3650 Cerrillos Rd, Santa Fe, NM 8570