2016 02 01 Genomics in Education Workshop - University of Delaware

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 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 Workshop Exchanges

• Summary of Faculty Challenges in Teaching Bioinformatics

• Notes from CURE discussion

Other Websites and Links and Resources

• DNA Subway Manual

• Workshop "Walk-trhough" 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

Attendees

Barcoding samples and Gel Images

Open