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Organizers:

C.J. Geisler-Lee

Local Point of Contact:

Cheng-Li Jane Heisler-Lee

Trainers:

Dave Micklos, Joslynn Lee, Pan Teng

Date:

March 29-30, 2016

Location:

Life Sciences Building II
Room 404
Southern Illinois University Carbondale
Carbondale, IL 62901
Parking Information/Permits

Visitor Parking

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 jolee@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/CyVerse 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

Tuesday

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

CyVerse & workshop objectives

CyVerse 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

RNA Splicing 3D-Animation

SMA Therapy Animation

03:00-04:00

Annotate Genes II: User-BLAST

 

"User" Evidence: EST data (save file to desktop)
From Green Line (JB): additional EST data (save file to desktop)

04:00-05:00

Demonstration: RNA-Seq and Green Line

RNA-Seq

Green Line reads (.txt file)

Wednesday

 

 

 

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

  • Summary of Faculty Challenges in Teaching Bioinformatics
  • Notes from CURE discussion

Other Websites and Links and Resources

Barcoding samples and Gel Images

 

NameSample Number (for sequencing)Species name (if known)
JGLSample--01 
AASample--02 
JWSample--03 
JGSample--04 
CJSample--05IL plant
MSSample--06 
ATSample--07orchid
AJSample--08 
PTSample--09 
MVSSample--10 
ABSample--11 

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

Travel/Lodging

See the city of Carbondale, IL website: http://www.carbondaletourism.org/categories/stay

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