iPlant Genomics in Education Workshop - Santa Fe - May 21-22, 2015
Organizers: | Uwe Hilgert |
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Local Point of Contact: |
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Trainers: | Uwe Hilgert, Jason Williams |
Date: | May 21-22, 2015 |
Location: | Santa Fe Community College |
Directions: | |
Map: | |
Parking: | North parking lot, free of charge |
Meeting point: | Room #490, Biology Lab, Health and Sciences Center |
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: //.
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:
http://gfx.dnalc.org
http://dnasubway.iplantcollaborative.org
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: |
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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 | Structure and function of untranslated regions (UTRs) in mRNAs (Links) | |
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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Friday | 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) |
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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 | ||
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
Instructors
Name | Contact | Institution |
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Uwe Hilgert | hilgert at email.arizona.edu | iPlant Collaborative, BIO5 Institute, U of Arizona |
Jason William | williams at cshl.edu | iPlant Collaborative, DNA Learning Center, Cold Spring Harbor Laboratory |
DNA Barcoding Experiment
Name | Contact | Institution | DNA Barcoding Sample | Experimentor/Sample No. | Sequence IDs | Family/Species by DNA | |
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Nadja M&M | SFCC/LANL | Orchid sp. | 01 | 01 | Student-01-M13F(-21)_A09 Student-01-M13R_E10 |
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Adam Kleinschmit | Adams State U | Eudicot sp. | 02 | 02 | Student-02-M13F(-21)_B09 Student-02-M13R_F10 |
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Pat Hilleren | Skidmore C | Eudicot sp. | 03 | 03 | Student-03-M13F(-21)_C09 Student-03-M13R_G10 |
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Kevin Divine | SFCC | Nanochloropsis | 04 | 04 | Student-04-M13F(-21)_D09 Student-04-M13R_H10 |
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Travis Robbins | NNMC | Spider plant | 05 | 05 | Student-05-M13F(-21)_E09 Student-05-M13R_A11 |
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Lenny Gannes | SFCC | Chocolate flower (Berlandiera lyrata) | 06 | 06 | Student-06-M13F(-21)_F09 Student-06-M13R_B11 |
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Paul Laur | Eldorado Biofuels | Rose | 07 | 07 | Student-07-M13F(-21)_G09 Student-07-M13R_C11 |
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Matt Green | SFCC | Spider plant | 08 | 08 | Student-08-M13F(-21)_H09 Student-08-M13R_D11 |
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Creighton Robinson | NNMC | Cycad sp. | 09 | 09 | Student-09-M13F(-21)_A10 Student-09-M13R_E11 |
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Donovan | NMSU | Chenopodium sp. | 10 | 10 | Student-10-M13F(-21)_B10 Student-10-M13R_F11 |
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Diana Melin |