iPlant Genomics in Education Workshop - Hudson Alpha Institute - August 13-14, 2014
Organizers: | Jason Williams |
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Local Point of Contact: |
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Trainers: | Uwe Hilgert, David Micklos |
Date: | August 13-14 |
Location: | HudsonAlpha Institute |
Directions: | |
Map: |
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Parking: | Employee parking on west-side/back of building (see below) |
Meeting point: | Meet site coordinator Ms. Breanna Ruhlman at the front desk in the atrium (see below) |
Pre-Workshop Homework
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.
If possible, make sure you have 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. Java 7 has had issues that limited some functionality in DNA Subway. Get Java 6 at this link:* http://java.com/en/download/manual_v6.jsp
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 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: //. 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
ReviewDNA 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
Wednesday | Room tba | WiFi: HA-Public | Pwd: 601GenomeWay |
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Time | Topic | Slides | Notes/Links |
09:00-09:15 | Welcome/Logistics |
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09:15-10:00 | Introductions |
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10:00-10:15 | iPlant Collaborative & workshop objectives | ||
10:15-10:30 | DNA Subway tour |
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10:30-10:45 | Break |
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10:45-11:15 | Use DNA Subway to teach concepts in molecular biology |
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11:15-12:00 | Analyze a DNA contig (Red Line) |
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12:00-01:00 | Lunch |
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01:00-01:15 | Mini Seminar: Evidence Based Gene Modeling |
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01:15-02:30 | Annotate genes I – BLAST |
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02:30-02:45 | Break |
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02:45-03:00 | Mini-Seminar: RNA Splicing |
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03:00-04:15 | Annotate genes II – User-BLAST |
| "User Evidence:" (save file to desktop, then upload to annotation project) |
04:15-05:00 | Demonstration: RNA-Seq and Green Lin |
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Thursday | Room tba |
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Time | Topic | Slides | Notes/Links |
09:00-09:30 | Review |
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09:30-9:45 | Mini Seminar: Transposons |
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09:45-10:45 | Find transposons in a genome (Yellow Line) | | |
10:45-11:00 | Break |
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11:00-12:00 | DNA Barcoding - Isolate DNA & prep PCR |
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12:00-01:00 | Lunch |
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01:00-01:30 | Mini Seminar: DNA Barcoding and Student Projects |
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01:30-02:30 | DNA Barcoding - Electrophorese and prep DNA for sequencing |
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02:30-02:45 | Break |
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02:45-03:30 | Analyze DNA barcodes (Blue Line) |
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03:30-04:15 | Explore DNA Subway lines on your own |
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04:15-04:45 | Using DNA Subway in the Classroom - First Thoughts |
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04:45-05:00 | Evaluation, and Closure |
| Survey Link: https://www.surveymonkey.com/s/GenomicsInEducation_post |
Other Websites and Links and Resources
Workshop handouts in WORD and
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
Name | Contact | Institution |
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Uwe Hilgert | hilgert at email.arizona.edu | iPlant Collaborative, BIO5 Institute, U of Arizona |
Dave Micklos | micklos at cshl.edu | iPlant Collaborative, DNA Learning Center, Cold Spring Harbor Laboratory |
Attendees
Name | Contact | Institution | DNA Barcoding Sample | Experimentor/Sample No. |
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Chris Barton | chris.barton at belmont.edu | Belmont U | Not sure |
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Matthew Brewer | mbrewer at gsu.edu | Georgia State U | Rose, maybe |
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Jennifer Carden | jcarden at hudsonalpha.org | HudsonAlpha Institute for Biotechnology | Sumac, maybe |
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Andrea Cobb | adcobb at fcps.edu | Thomas Jefferson HS for Science and Technology | N. Virgina moss |
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Luis Cruz-Vera | Luis.Cruz-Vera at uah.edu | U Alabama in Huntsville | Grass |
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Roger Jackson | roger.jackson at belmont.edu | Belmont U | Rose |
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Ben Johnston | bjohnston at madisoncity.k12.al.us | Bob Jones HS | Northern Red Oak |
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Jeffrey Lehman | jlehman at otterbein.edu | Otterbein U | Highbush Blueberry (Vaccinium Corymbosum) |
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