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Organizers:

A. Hlousek-Radojcic, J. Williams

Local Point of Contact:

Alenka Hlousek-Radojcic

Trainers:

Joslynn Lee, Jason Williams

Date:

Feb. 1-2, 2015

Location:

University of Delaware

Newark, DE

Room: Interdisciplinary Science and Engineering Laboratory (ISE) - 410

221 Academy St. University of Delaware

Parking Information/Permits

https://udel.t2hosted.com/cmn/index.aspx.

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: 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 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 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:

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

Time

Topic

Slides

Notes/Links

08:30-9:00Arrive / Set up Computers  

09:00-09:15

Welcome/Logistics

 

 

09:15-09:45

Introductions

 

 

09:45-10:00

iPlant Collaborative & workshop objectives

iPlant & Workshop Overview

iPlant Homepage
iPlant Account Portal

10:00-10:15

DNA Subway tour

 

DNA Subway Homepage
DNA Subway Manual

10:15-10:30

Break

 

 

10:30-12:00

Using the Red Line & DNA Annotation to Teach Concepts in Molecular Biology

Red Line Annotation

Concepts and Links
Genomes as Information

Red Line Walk-through
Paper:
Gene Annotation

GFX DNALC Server

12:00-01:00

Lunch

 

 

01:00-01:15

Mini Seminar: Evidence Based Gene Modeling

Evidence

 

01:15-02:30

Annotate Genes I: On Your Own

 

ENCODE Project
ENCODE Nature

Ensembl video on genome patches and haplotypes

02:30-02:45

Break

 

 

02:45-03:00

Mini-Seminar: RNA Splicing

Splicing

Alternative Splicing Paper

03:00-04:00

Annotate Genes II: User-BLAST

 

"User Evidence:" EST data
Additional EST data: http://gfx.dnalc.org/files/evidence/Annotation/

04:00-05:00

Demonstration: RNA-Seq and Green Line

RNA-Seq

 

Friday

 

 

 

Time

Topic

Slides

Notes/Links

09:00-09:30

Review, Open Questions From Day 1

 

 

09:30-9:45

Mini Seminar: Transposons

Transposons

 

09:45-10:30

Find Transposons in a Genome (Yellow Line)

 

Yellow Line Walk-through
Paper: TARGeT
Paper: Ping Transposon Burst in Rice Tissue Culture

Paper: The Necessary Junk

Slides: Genome Evolution Propels Evolution of Function

10:30-10:45

Break

 

 

10:45-12:00

DNA Barcoding - Isolate DNA & Prep PCR

 

DNA Barcoding Protocol

12:00-01:00

Lunch

 

 

01:00-01:15

Mini Seminar: DNA Barcoding and Student Projects

DNA Barcoding

Urban Barcode Project

01:15-02:15

DNA Barcoding - Electrophoresis and Prep DNA for Sequencing

 

 

02:15-02:30

Break

 

 

02:30-03:30

Analyze DNA Barcodes (Blue Line)

 

Blue Line Walk-through

03:30-03:45

Evaluation, and Closure

 

Survey Link: https://www.surveymonkey.com/s/GenomicsInEducation_post

Other Workshop Exchanges

Other Websites and Links and Resources

Attendees

First nameLast nameResearch AreaEmail
BehnamAbashtGenetics and Nucleic Acidsabasht@UDel.edu
DylanAudetteDevelopmental Biologyaudetted@udel.edu
AmyBiddleOtherasbiddle@udel.edu
Jose DanielChazi CapeloComputer and Computation Researchjdchc@udel.edu
TrevorDalyChemistrytdaly@udel.edu
WeixuanFuSystematic and Population Biologywfu@udel.edu
JacquelineHilsenbeck-FajardoChemistryjfajardo@udel.edu
SethHuntEcological Studiessethhunt@udel.edu
John RJungckMolecular Biosciencesjungck@udel.edu
TerryKampsGenetics and Nucleic Acidstkamps@njcu.edu
SABARINATHNEERUKONDACell Biologynnvsnath@udel.edu
CarlSchmidtBiochemistry and Molecular Structure and Functionschmidtc@udel.edu
MarciaShofnerEcological Studiesmshofner@umd.edu
Juan PaoloSicatTrainingsicat.paolo20@gmail.com
ArmandoSolisBiochemistry and Molecular Structure and Functionasolis@citytech.cuny.edu
AnneTerrellScience and Engineering Educationaterrell@udel.edu
JosephTomlinsonGenetics and Nucleic Acidsmjtiv@udel.edu
JolieWaxOtherjwax@gmail.com
RandyWisserPlant Biologyrjw@udel.edu
RenateWuersig rwuersig@udel.edu

Barcoding samples and Gel Images

 

NameSample Number (for sequencing)Bag NumberSpecies name (if known)
Seth Hunt111Equisetum
Seth Hunt2 Tradescantia zebrina
Jacqueline Fajardo315Vinca
Jacqueline Fajardo417?
Alenka Hlousek-Radojcic52ISE Lab
Alenka Hlousek-Radojcic68ISE Lab
Terry Kamps77?
Terry Kamps8 Fern
Amy Biddle920berry
Amy Biddle10 grape
Weixuan Fu11 Aflican Violet
Weixuan Fu12 Bamboo
Joseph Tomlinson13 Pineapple
Joseph Tomlinson14 Amaryliss
Joslynn Lee154?
Joslynn Lee1619?
Jolie Wax1712yellow flower
Jolie Wax1814dandilion?
Michael Babak191?
Michael Babak2021?
Armando Solis21 orchid

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/

Travel/Lodging

See the university website: http://www.udel.edu/visitus/

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