A. Hlousek-Radojcic, J. Williams
Local Point of Contact:
Joslynn Lee, Jason Williams
Feb. 1-2, 2015
University of Delaware
Room: Interdisciplinary Science and Engineering Laboratory (ISE) - 410
221 Academy St. University of Delaware
- Pre-Workshop Assignments
- Workshop Agenda and Resources
- Other Workshop Exchanges
- Other Websites and Links and Resources
- Barcoding samples and Gel Images
- Post Workshop Survey
- Post Workshop DNA Sequencing Results
- Important Pre-Workshop Travel Info
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 firstname.lastname@example.org 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 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
|08:30-9:00||Arrive / Set up Computers|
iPlant Collaborative & workshop objectives
DNA Subway tour
Using the Red Line & DNA Annotation to Teach Concepts in Molecular Biology
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
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
Other Websites and Links and Resources
- DNA Subway Manual
- Workshop "Walk-trhough" 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
|First name||Last name||Research Area|
|Behnam||Abasht||Genetics and Nucleic Acids||abasht@UDel.edu|
|Jose Daniel||Chazi Capelo||Computer and Computation Researchemail@example.com|
|Weixuan||Fu||Systematic and Population Biologyfirstname.lastname@example.org|
|John R||Jungck||Molecular Biosciencesemail@example.com|
|Terry||Kamps||Genetics and Nucleic Acidsfirstname.lastname@example.org|
|Carl||Schmidt||Biochemistry and Molecular Structure and Functionemail@example.com|
|Armando||Solis||Biochemistry and Molecular Structure and Functionfirstname.lastname@example.org|
|Anne||Terrell||Science and Engineering Educationemail@example.com|
|Joseph||Tomlinson||Genetics and Nucleic Acidsfirstname.lastname@example.org|
Barcoding samples and Gel Images
|Name||Sample Number (for sequencing)||Bag Number||Species name (if known)|
|Seth Hunt||2||Tradescantia zebrina|
|Alenka Hlousek-Radojcic||5||2||ISE Lab|
|Alenka Hlousek-Radojcic||6||8||ISE Lab|
|Weixuan Fu||11||Aflican Violet|
|Jolie Wax||17||12||yellow flower|
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 #: 10-322601046
and are posted as the entry under Date: 2/4/16, Name: Jason Williams
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: www.udel.edu/transportation/parking/categories_vendor.html/
See the university website: http://www.udel.edu/visitus/