Local Point of Contact:
|Cheng-Li Jane Heisler-Lee|
Dave Micklos, Joslynn Lee, Pan Teng
March 29-30, 2016
Life Sciences Building II
Southern Illinois University Carbondale
Carbondale, IL 62901
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: jpg\/png\/tif\.
- 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 email@example.com 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 these URLs 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/CyVerse account:
- You should be able to log into the DNA subway at: http://dnasubway.iplantcollaborative.org/.
- If you do not have an iPlant/CyVerse 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
|08:30-9:00||Arrive / Set-up computers|
CyVerse & workshop objectives
DNA Subway tour
Using the Red Line & DNA Annotation to Teach Concepts in Molecular Biology
Red Line Annotation
Mini Seminar: Evidence Based Gene Modeling
Annotate Genes I: On Your Own
Mini-Seminar: RNA Splicing
Annotate Genes II: User-BLAST
Demonstration: RNA-Seq and Green Line
Green Line reads (.txt file)
Review, Open Questions From Day 1
Mini Seminar: Transposons
Find Transposons in a Genome (Yellow Line)
Paper: The Necessary Junk
DNA Barcoding - Isolate DNA & Prep PCR
Mini Seminar: DNA Barcoding and Student Projects
DNA Barcoding - Electrophoresis and Prep DNA for Sequencing
Analyze DNA Barcodes (Blue Line)
Evaluation, and Closure
Other Workshop Exchanges
- Summary of Faculty Challenges in Teaching Bioinformatics
- Notes from CURE discussion
Other Websites and Links and Resources
- DNA Subway Manual
- Workshop "Walk-through" handout package in WORD and PDF
- DNA Barcoding Manual
- Barcoding lab planning and prep
- http://www.learnaboutsma.org/ - SMA website and splicing animation
- http://www.urbanbarcodeproject.org - UBP website
- http://www.iBoL.org - International Barcode of Life Project
- http://www.dnabarcoding101.org/ - DNA Barcoding
Barcoding samples and Gel Images
|Name||Sample Number (for sequencing)||Species name (if known)|
Post Workshop Survey
Please complete this survey at the conclusion of the workshop:
Post Workshop DNA Sequencing Results
Instructions on retrieving your results will be posted here after the workshop.
DNA Subway instructions:
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 #: 10-328910033
and are posted as the entry under Date: 04/02/2016, Name: Joslynn Lee
5. Select the sequences you want to include in your analysis and run your project; each person should have two sequences, 1 forward, 1 reverse.
For example, Sample 1 will have a sequence called Sample01-F.... and a sequence called Sample01-R.... (see table above for your sequence IDs)
Important Pre-Workshop Travel Info
Neither CyVerse/iPlant Collaborative nor the local host can reimburse lodging or other expenses associated with attending the workshop.
Maps and parking information can be found here: http://parking.siu.edu/on-campus/index.html
Visitor Information: http://admissions.siu.edu/visit/visitor-information.php
See the city of Carbondale, IL website: http://www.carbondaletourism.org/categories/stay