2017 07 06 Tools and Services Workshop - University of Arkansas
Organizers: | D. Rhodes, J. Williams |
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Local Point of Contact: | Douglas Rhoads |
Trainers: | John Fonner, Jason WIlliams |
Required Workshop Prep
1. CyVerse Account
- Get your free account at http://user.iplantcollaborative.org/ . (Make sure to REMEMBER your username and password.) Please register with an institutional email account as only this will give you access to the CyVerse cloud service Atmosphere (see next bullet). Please avoid gmail, yahoo, hotmail and the like for your CyVerse registration as you would not be able to register for Atmosphere with those.
2. Atmosphere Access
- Once you have your account, go to http://user.iplantcollaborative.org/ and log in. Under "Apps and Services," scroll down to "Available Services" and request access to Atmosphere and DNA Subway. Indicate that you are attending a workshop when you are asked for justification. (This will only be granted if you registered for CyVerse using an institutional account; see above.)
3. Laptop
Please bring your own WiFi 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 or Safari; Internet Explorer, Chrome and others have significant issues.)
- Java: Have JAVA installed, enabled and working with Firefox or Safari. (Help)
- Data Store: Download and install iDrop (iDrop for your OS) and iCommands (iCommands for your OS)
- VNC Viewer: Download the DMG (for MAC) or exe (for PC) (http://www.realvnc.com/download/viewer/)
- Windows Users: Download and install PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
- Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store#InstallingandconfiguringCyberduck
4. Pre-Workshop Guide and Homework
- Download and complete the exercises in the PRE-WORKSHOP PACKET to get the most out of the workshop.
- Complete this Pre-Workshop Survey
Instructional Materials
You can download a copy of the workshop packet (CyVerse Toolkit) to follow along:
Morning
Description | Slides | Guide | Links |
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Arrive / Sign-in / Setup Troubleshooting |
| ||
Welcome - Presenter/Participant Self-Introductions | slides | ||
Overview of the CyVerse | Getting Started with CyVerse | ||
Managing "Big Data" using the CyVerse Data Store | slides | guide | Data Store Overview |
Navigate the CyVerse Discovery Environment (DE) | slides | guide | |
Atmosphere Cloud Computing | slides | guide |
Afternoon Guided Tutorials
Description | Slides | Links |
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RNA-Seq in CyVerse | slides |
|
Overview and demo of CyVerse GWAS / Transcriptome assembly | ||
Getting started with Annotation: MAKER | ||
Visualization of RNA-Seq results in Atmosphere | slides | |
iCommands and other Data Store applications: |
| |
Survey |