2012 04 26 Genomics in Education Workshop, Southern University at New Orleans
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Date: | April 26-27 |
Location: | Southern University at New Orleans, Park Campus, 6400 Press Drive, New Orleans, LA 70126 |
Section Navigation
Pre-Workshop Homework
Laptop Compatibility
If you are bringing your own laptop:
Most laptops (<5 years old) updated with the latest web browser (we recommend FireFox:http://www.mozilla.org/en-US/firefox/fx/ ) will have no problem.
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 3.6/ Internet Explorer 8 (IE 9 preferred) / Safari 4 or later).
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 the newest version.
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:
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 the (a printed copy and some other handouts will be presented to you at the workshop).
Review the
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
Thursday, April 26th
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09:00-09:15 | Welcome/Logistics |
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09:15-10:00 | Introductions |
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10:00-10:15 | Overview, Workshop Objectives, DNA Subway Tour |
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10:15-10:30 | iPlant Collaborative Overview |
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10:30-10:45 | Break |
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10:45-11:15 | Using DNA Subway to Teach Concepts in Molecular Biology |
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11:15-12:00 | Setting up projects for Annotation - Red Line |
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12:00-01:00 | Lunch |
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01:00-01:15 | DNA Barcoding setup |
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01:15-01:30 | Mini-Seminar: DNA Barcoding |
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01:30-02:45 | DNA Barcoding wet-lab cont'd |
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02:45-03:00 | Mini-Seminar: Evidence Based Gene Modeling |
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03:15-04:45 | Gene Annotation I |
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04:45-05:00 | Mini-Seminar: Alternative Splicing |
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Friday, April 27th
Time | Topic | Slides | Notes/Links |
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09:00-09:30 | Mini Seminar: Transposons |
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09:30-10:15 | Transposon Sleuthing: Yellow Line |
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10:15-10:30 | Break |
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10:30-11:30 | Gene Annotation II |
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11:30-12:00 | DNA Barcoding (PCR) |
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12:00-01:00 | Lunch |
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01:30-02:30 | DNA Barcoding - Blue Line |
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02:30-02:45 | Break |
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02:45-03:45 | Barcdoing electrophoresis and sequencing prep |
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03:45-04:30 | Implementation and Classroom Planning |
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04:30-05:00 | Summary, Evaluation, and Closure |
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Other Websites and Links and Resources
http://www.learnaboutsma.org/ - SMA website and splicing animation.
http://www.iBoL.org - International Barcode of Life Project
DNA Subway exercises and handouts in and format.
DNA Barcoding .
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
Your DNA Sequencing results are now (5/2/2012) available on DNA Subway!
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: 10-193907669 and are posted under Jermel Watkins on 5/2/12
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
Recommended Lodging
There is no reimbursement for lodging. These hotels include those recommended by our hosting institution,but no guarantees are offered about the availability or suitability of the hotels.
Check website like hotels.com and travelocity.com for additional hotels and rates.
Hotel | Website | Notes |
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Motel 6 | ~$50-$59 per night |
Nearest Airports/ Rail
Airport | Distance | Notes |
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Louis Armstrong International Airport | ~ 16 miles |
Shuttle Services from Airports and Buses
Call ahead of time to reserve/confirm
Service | Notes |
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New Orleans Mass Transit | |
Ground Transportation from MSY |
Parking Information:
Free parking is available on the campus street adjacent to the New Science Building. Walk along Emmet Bashful Blvd. and Campus Blvd. to reach the New Science Building. Alternatively, you can drive in through Gentilly/Press Drive, and make a left onto Emmet Bashful Blvd. Immediately you will see a large Education Building to your right with an adjoining parking lot. Park in that lot and walk up Campus Blvd. on the right; the next building is the New Science Building. In the NSB take the elevator to the 3rd floor, Room 313, where you will receive a temporary Parking Permit to be placed on the dashboard of your car. This is to avoid receiving a parking violation from the campus police.
On-Campus Directions:
See the campus map.