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Organizers:

R. Enke, J. Williams

Local Point of Contact:

Ray Enke

Trainers:

Jason WIlliams, Nirav Merchant

Workshop Prep

1. CyVerse Account

2. Atmosphere Access

3. Laptop

Please bring your own Wi-Fi enabled laptop to the workshop. Make sure your laptop has the following:


Etherpad Link: http://pad.software-carpentry.org/2017-07-10-jmu

Agenda


MONDAY

TimeTopic/ActivitySlidesGuidesNotes/Links
09:30-10:00 Setup, host-welcome, and participant introductionsslides  
10:00-10:30 DNA Subway Intro and Intro to DNA Barcoding

slides

guide 
10:30-10:45

Coffee Break

(last chance to get a barcoding sample)

   
10:45-12:30DNA Barcoding Lab – DNA Extraction and PCR 
12:30-01:30Lunch   
01:30-02:00Walkthrough of DNA Subway Blue Line Bioinformatics guide 
02:00-02:30On-your-own walkthrough of DNA Subway Barcoding Project   
02:30-02:45Coffee Break   
02:45-03:15 DNA Barcoding Lab - Electrophoresis   
03:15-03:45More on Bioinformatics: Reviewing BLAST and Phylogenetic Trees  
03:45-04:15Barcoding programs (Barcode LI, Urban Barcoding) and Instructor’s Questionsslides 
04:15-04:45Results review and annotation homework assignment (paper reading)  


TUESDAY

TimeTopic/ActivitySlidesGuidesNotes/Links
09:30-10:00Introduction to Genome Annotationslides paper
10:00-10:30Guided walkthrough of Red Line annotation pipeline guide 
10:30-10:45Break   
10:45-11:15Dynamic genome: Splicing, transposons, and other functional elementsslidesguidemPing paper
11:15-12:00Independent walkthrough of annotation projects   
12:00-01:00Lunch   
01:00-01:30Introduction to RNA-Seqslides 
01:30-02:00Walkthrough of DNA Subway Green Lineslidesguide 
02:00-02:30Enke Lab RNA-Seq CURE projectsslides  
02:30-02:45Coffee Break   
02:45-03:30Microbiome Demo and Jupyter Notebook Intro  


WEDNESDAY

TimeTopic/ActivitySlidesGuidesNotes/Links
09:30-10:00

Introduction to CyVerse

slides Pre-Survey
10:00-10:30

Data Management Basics and Data upload with Cyberduck

slidesguide 
10:30-10:45Break   
10:45-11:00

Data Sharing within CyVerse

   
11:00-12:00

CyVerse Discovery Environment walkthrough and exercises

(FastQC and Trimmomatic)

 
12:00-01:00Break   
01:00-01:45Cloud Computing with CyVerse Atmosphereslidesguide
01:45-02:15

Introduction to RNA-Seq with / New methods including Kallisto and Sleuth

  
02:15-02:45Kallisto tutorial guide 
02:45-03:00Break   
03:00-03:30Intro to R and RStudio  
03:30-04:30Guided Sleuth tutorial   
04:30-05:00Wrap-up and conclusion  Post-Survey

Other Important Info

Wireless Access for Non-JMU attendees (case sensitive):

  • Username: festivalsummer

  • Password: 322554

  • Network: JMU Visitors

 

Visitor Parking: JMU Lot D2 directly across from the Biosciences bldg at 951 Carrier Drive has been designated as the visitor parking lot for the workshop. Despite the signage, no permit will be required for visitor parking in this lot on the workshop dates. Please note: All regulations for JMU students, faculty and staff will remain in effect, and students attending the event are required to park in appropriate student parking lots with a JMU parking permit.

Workshop location: The Biosciences Bldg is located at 951 Carrier Drive Harrisonburg VA, 22807. The workshop will be held in room #2009. From the bldg entrance directly across from parking lot D2, proceed up to the 2nd floor and to the end of the hallway furthest from the parking lot. Room #2009 is on the left at the end of the hallway across from the stairwell.


 




 

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