iPlant Genomics in Education Workshop - Community College of Denver - June 27-28, 2014

 Pre-Workshop Homework

Laptop Compatibility

If you are bringing your own 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.

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/ Safari 4 or later).
• Be aware, Java 7 has known issues that limit some functionality on DNA Subway. Get either Java 6 from this link: http://java.com/en/download/manual_v6.jsp, or prime your Java installation as described on Page 5 in the Red Line Walk-through document.
• 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: 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

• 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 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

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 number: 

and are posted as the entry under 

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

Designated Lodging

Hotel Information:

SpringHill Suites Denver Downtown
1190 Auraria Parkway
Denver, Colorado 80204 USA

http://www.springhillsuitesdenver.com/map-directions/

The SpringHill Suites is in walking-distance to campus, and actually run by hospitality students at Metro State.

Parking Information/Directions:

Below is the link to the maps and a mapquest site.

http://www.ahec.edu/departments/parking/maps-directions-2/

Directions to St. Francis Parking Lot

A = Saint Francis Way

 They are in the Science Building at the intersection of Speer and Arapahoe in suite 1006 (first floor). The parking lot can only be reached by southbound Speer. If you are coming north on Speer, go to Arapahoe St.  (Denver Center Performing Arts) and turn to southbound Speer Boulevard. You will turn right on St. Francis Way (“A”). There is a round-about at the end of St. Francis Way, with a parking kiosk to the north. They are in the 3 & 4 story brick building to the north of the parking kiosk (where CCD is written in purple on the map below).