2015 06 18 Genomics in Education Workshop - South Dakota State University/ University of South Dakota
Organizers: | S. Gibson, S. Subramanian, J. Williams |
|---|---|
Local Point of Contact: | |
Trainers: | Uwe Hilgert, Jason WIlliams |
Date: | June 18-19, 2015 |
Location: | South Dakota State University Brookings, SD Northern Plains Biostress Lab, SNP 67 |
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: //.
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:
If Java still does not open, enter 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
Thursday | Room tba | WiFi: | Pwd: |
|---|---|---|---|
Time | Topic | Slides | Notes/Links |
08:30-9:00 | Arrive / Set up Computers |
|
|
09:00-09:15 | Welcome/Logistics |
|
|
09:15-09:45 | Introductions |
|
|
09:45-10:00 | iPlant Collaborative & workshop objectives | ||
10:00-10:15 | DNA Subway tour |
| |
10:15-10:30 | Break |
|
|
10:30-12:00 | Using the Red Line & DNA Annotation to Teach Concepts in Molecular Biology | ||
12:00-01:00 | Lunch |
|
|
01:00-01:15 | Mini Seminar: Evidence Based Gene Modeling |
| |
01:15-02:30 | Annotate Genes I: On Your Own |
| |
02:30-02:45 | Break |
|
|
02:45-03:00 | Mini-Seminar: RNA Splicing | ||
03:00-04:00 | Annotate Genes II: User-BLAST |
| "User Evidence:" (save file to desktop, then upload to annotation project) |
04:00-05:00 | Demonstration: RNA-Seq and Green Line |
| |
|
|
|
|
Friday | Room tba |
|
|
Time | Topic | Slides | Notes/Links |
09:00-09:30 | Review, Open Questions From Day 1 |
|
|
09:30-9:45 | Mini Seminar: Transposons |
| |
09:45-10:30 | Find Transposons in a Genome (Yellow Line) |
|
Paper: Slides: |
10:30-10:45 | Break |
|
|
10:45-12:00 | DNA Barcoding - Isolate DNA & Prep PCR |
| |
12:00-01:00 | Lunch |
|
|
01:00-01:15 | Mini Seminar: DNA Barcoding and Student Projects | ||
01:15-02:15 | DNA Barcoding - Electrophorese and Prep DNA for Sequencing |
|
|
02:15-02:30 | Break |
|
|
02:30-03:30 | Analyze DNA Barcodes (Blue Line) |
| |
03:30-03:45 | Evaluation, and Closure |
| Survey Link: https://www.surveymonkey.com/s/GenomicsInEducation_post |
Other Websites and Links and Resources
Workshop "Walk-trhough" handout package 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
Instructors
Name | Contact | Institution |
|---|---|---|
Uwe Hilgert | hilgert at email.arizona.edu | iPlant Collaborative, BIO5 Institute, U of Arizona |
Jason Williams | williams at cshl.edu | iPlant Collaborative, DNA Learning Center, Cold Spring Harbor Laboratory |
Attendees
Name | Contact | Institution | DNA Barcoding Sample | Experimentor/Sample No. | No. on gel | Sequence IDs |
|---|---|---|---|---|---|---|
Brian Blais | brian.blais at yellowjackets.bhsu.edu | Black Hills State U | Angiosperm at 44*18' 35.49' 96*45'40.35" | 14 | Gel #2 14 | Experimentor14-F Experimentor14-R |
Elizabeth Bloomfield | bloomfieldl at divinechildhighschool.org | Divine Child HS | Tulip Tree | 17 | n/a | n/a |
Heike Bücking | heike.bucking at sdstate.edu | South Dakota State U | Oxytropio lambertii | 12 | Gel #1 12 | Experimentor12-F Experimentor12-R |
Catherine Chappell | cattchappell at gmail.com | Black Hills State U | Bass wood at 44*19' 14.65'"96*47'10.97" | 13 | Gel #2 13 | Experimentor13-F Experimentor13-R |
Serge Danielson-Francois | sdanielso at ltu.edu | Divine Child HS | Small herbaceous something; same as SG | 15 | n/a | n/a |
Anne Danielson-Francois | danfranc at umd.umich.edu | U Michigan - Dearborn | Blueberry | 16 | n/a | n/a |
Carla Delucchi | cdelucchi at mccneb.edu | Metropolitan CC, Omaha, NE | Purple locoweed; Oxytropis lambertii | 11 | Gel #1 11 | Experimentor11-F Experimentor11-R |
Gunbharpur Gill | Gunbharpur.Gill at yellowjackets.bhsu.edu | Black Hills State U | Purple loco weed | 9 | Gel #1 9 | Experimentor09-F Experimentor09-R |
Anna Hafele | anna.hafele at yellowjackets.bhsu.edu | Black Hills State U | American bass wood at 44*19' 14.65'"96*47'10.97" | 18 | Gel #2 18 | Experimentor18-F Experimentor18-R |
Ann Impullitti | impullit at augsburg.edu | Augsburg C | Soybean | 6 | Gel #1 6 | Experimentor06-F Experimentor06-R |
Raeann Mettler | raeann.mettler at bhsu.edu | Black Hills State U | Some tree outside of Biostress Lab at SDSU | 2 | Gel #1 2 | Experimento02-F Experimentor02-R |
Debra Mixon | debra.mixon at breckschool.org | Breck School | Daisy fleabane | 21 | Gel #2 21 | Experimentor21-F Experimentor21-R |
Fangping Mu | fangping.mu at sdstate.edu | South Dakota State U | Green tree | 10 | Gel #1 10 | Experimentor10-F Experimentor10-R |
Michael Oberle | michael.oberle at yellowjackets.bhsu.edu | Black Hills State U | Some weed at 44*19' 14.65'" 96*47'10.97" | 7 | Gel #1 7 | Experimentor07-F Experimentor07-R |