2016 03 29 Genomics in Education Workshop - Southern Illinois University Carbondale

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\.
• Should you experience difficulties, follow these steps:
  • 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 jolee@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/CyVerse account:

• You should be able to log into the DNA subway at: http://dnasubway.iplantcollaborative.org/.
• If you do not have an iPlant/CyVerse 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 Workshop Exchanges

• Summary of Faculty Challenges in Teaching Bioinformatics
• Notes from CURE discussion

Other Websites and Links and Resources

• DNA Subway Manual
• Workshop "Walk-through" handout package 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
• http://www.dnabarcoding101.org/ - DNA Barcoding

Barcoding samples and Gel Images

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.

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 #: 10-328910033

and are posted as the entry under Date: 04/02/2016, Name: Joslynn Lee

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, Sample 1 will have a sequence called Sample01-F.... and a sequence called Sample01-R.... (see table above for your sequence IDs)

Important Pre-Workshop Travel Info 

Neither CyVerse/iPlant Collaborative nor the local host can reimburse lodging or other expenses associated with attending the workshop.

Maps and parking information can be found here: http://parking.siu.edu/on-campus/index.html

Visitor Information: http://admissions.siu.edu/visit/visitor-information.php

Travel/Lodging

See the city of Carbondale, IL website: http://www.carbondaletourism.org/categories/stay