iPlant Genomics in Education Workshop - Community College of Denver - June 27-28, 2014
Organizers: | Jason Williams |
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Local Point of Contact: | Heidi G. Loshbaugh |
Trainers: | Jason Williams, Uwe Hilgert |
Date: | June 27-28 |
Location: | Community College of Denver – Auraria Campus |
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 .
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: //. 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
Friday | Room SI 1117 |
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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 |
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04:15-05:00 | Demonstration: RNA-Seq and Green Lin |
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Saturday | Room SI 1117 & SI 1103 (Wet lab) |
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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) |
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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 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
Attendees
Name | Contact | Institution | DNA Barcoding Sample | Experimentor/Sample No. |
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James Beck | james.beck at wichita.edu | Wichita State U | Polymnia canadensis |
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Dan Bergey | dbergey at sheridan.edu | Sheridan College | Crabapple |
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Sandra Berry-Iowe | sberrylo at uccs.edu | U of Colorado, Colorado Springs | Penstemon |
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Ravendra Chauhan | ravendra.chauhan at okstate.edu | Oklahoma State U | ?? |
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Sadanand Dhekney | sdhekney at uwyo.edu | U of Wyoming | Crabapple |
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Gregory DiCenzo | gdicenzo at gmail.com | Industrial User | Spinach |
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Claudia Gentry-Weeks | Claudia.Gentry-Weeks at colostate.edu | Colorado State U |
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Susan Gibson | susan.gibson at sdstate.edu | South Dakota State U | Milkweed |
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George Gigiolio | urban603 at comcast.net | Denver School of Science and Technology |
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Judy Harrington | judy.harrington at colostate.edu | Colorado State U | Disticklis spigata (Saltgrass) |
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Raju Kandel | rkandel at uwyo.edu | U of Wyoming | Crabapple |
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Tai Montgomery | tai.montgomery at colostate.edu | Colorado State U |
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