2017 07 10 CGEMS Summer Training in Genomics
Organizers: | R. Enke, J. Williams |
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Local Point of Contact: | |
Trainers: | Jason WIlliams, Nirav Merchant |
Workshop Prep
1. CyVerse Account
Get your free account at http://user.cyverse.org/. Please register with an institutional email account.
2. Atmosphere Access
Go to http://user.cyverse.org/. In the Services Menu under ‘MY SERVICES’ you should see Atmosphere listed as an option you can launch. If not, look under the Available menu, and click the ‘REQUEST ACCESS’ link. You will receive an email requesting additional information. To qualify for an Atmosphere account, your CyVerse account must be associated with an institutional email address (e.g. .edu/.org/.gov).
3. Laptop
Please bring your own Wi-Fi enabled laptop to the workshop. Make sure your laptop has the following:
Internet Browser: Please have an up-to-date web browser (We strongly recommend Firefox, Safari, or Chrome and others have significant issues.)
VNC Viewer: Download the DMG (for MAC) or exe (for PC) (http://www.realvnc.com/download/viewer/)
Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store#
Etherpad Link: http://pad.software-carpentry.org/2017-07-10-jmu
Agenda
MONDAY
Time | Topic/Activity | Slides | Guides | Notes/Links |
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09:30-10:00 | Setup, host-welcome, and participant introductions |
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10:00-10:30 | DNA Subway Intro and Intro to DNA Barcoding |
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10:30-10:45 | Coffee Break (last chance to get a barcoding sample) |
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10:45-12:30 | DNA Barcoding Lab – DNA Extraction and PCR |
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12:30-01:30 | Lunch |
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01:30-02:00 | Walkthrough of DNA Subway Blue Line Bioinformatics |
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02:00-02:30 | On-your-own walkthrough of DNA Subway Barcoding Project |
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02:30-02:45 | Coffee Break |
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02:45-03:15 | DNA Barcoding Lab - Electrophoresis |
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03:15-03:45 | More on Bioinformatics: Reviewing BLAST and Phylogenetic Trees |
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03:45-04:15 | Barcoding programs (Barcode LI, Urban Barcoding) and Instructor’s Questions |
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04:15-04:45 | Results review and annotation homework assignment (paper reading) |
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TUESDAY
Time | Topic/Activity | Slides | Guides | Notes/Links |
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09:30-10:00 | Introduction to Genome Annotation |
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10:00-10:30 | Guided walkthrough of Red Line annotation pipeline |
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10:30-10:45 | Break |
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10:45-11:15 | Dynamic genome: Splicing, transposons, and other functional elements | |||
11:15-12:00 | Independent walkthrough of annotation projects |
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12:00-01:00 | Lunch |
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01:00-01:30 | Introduction to RNA-Seq |
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01:30-02:00 | Walkthrough of DNA Subway Green Line |
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02:00-02:30 | Enke Lab RNA-Seq CURE projects |
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02:30-02:45 | Coffee Break |
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02:45-03:30 | Microbiome Demo and Jupyter Notebook Intro |
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WEDNESDAY
Time | Topic/Activity | Slides | Guides | Notes/Links |
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09:30-10:00 | Introduction to CyVerse |
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10:00-10:30 | Data Management Basics and Data upload with Cyberduck |
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10:30-10:45 | Break |
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10:45-11:00 | Data Sharing within CyVerse |
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11:00-12:00 | CyVerse Discovery Environment walkthrough and exercises (FastQC and Trimmomatic) |
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12:00-01:00 | Break |
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01:00-01:45 | Cloud Computing with CyVerse Atmosphere | |||
01:45-02:15 | Introduction to RNA-Seq with / New methods including Kallisto and Sleuth |
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02:15-02:45 | Kallisto tutorial |
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02:45-03:00 | Break |
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03:00-03:30 | Intro to R and RStudio |
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03:30-04:30 | Guided Sleuth tutorial |
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04:30-05:00 | Wrap-up and conclusion |
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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.