Learning Center Home

Introduction to CyVerse Self-Guided Course: CyVerse USA

Goal

This is a short self-guided course that will take you through the basics of using CyVerse.

Tip

See other versions of this documentation (CyVerse UK and CyVerse Austria)

In the lower-left hand side of the screen, change the version of this documentation from cyverse-us to one of the other documentation sets developed for this online guide (cyverse-uk or cyverse-at) to see specifics for those installations.

---

Tutorial Maintainer(s)

Who to contact if this guide needs fixing. You can also email learning@CyVerse.org

Maintainer	Institution	Contact
Michael Culshaw-Maurer	CyVerse / University of Arizona	culshawmaurer@arizona.edu
Jason Williams	CyVerse / Cold Spring Harbor Laboratory	williams@cshl.edu
Tyson Lee Swetnam	CyVerse / University of Arizona	tswetnam@cyverse.org

---

• Tutorial home
• Course Overview
  • Create a CyVerse Account
  • Access and Search the CyVerse Learning Account
    • Self Assessment Questions
• CyVerse Background
  • CyVerse Background Videos and Slides
    • Self Assessment Questions
• Tour of the Discovery Environment
  • Self-guided Discovery Environment Tour
    • Self Assessment Questions
• Data Management I
  • Downloading data from the Discovery Environment
  • Uploading a File to the Discovery Environment
    • Self Assessment Questions
• Data Management II
  • Upload data with Cyberduck
    • Self Assessment Questions
• Data Management III
  • Editing Metadata on Single Files in the Discovery Environment
  • Apply metadata on multiple files in the Discovery Environment
  • Data Sharing in the Discovery Environment
    • Self Assessment Questions
• Analysis with the Discovery Environment
  • Find a Tool and Launch an Analysis
    • Self Assessment Questions
• Interactive Analyses
  • Getting VICE Access
  • Launching a VICE application
  • Completing our analysis in R
  • Terminating your VICE session and saving work to the Data Store
    • Self Assessment Questions
• Conclusion and Advanced Applications
  • Descriptive Steps
  • Additional information, help
• Delete this example guide page
  • Many of the examples Writing your documentation using sample data
  • Using in-line questions with tips
  • Other admonitions
  • Buttons and keyboard combinations
  • URLs/Links
  • Images

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite	Preparation/Notes	Link/Download
CyVerse account	You will need a CyVerse account to complete this exercise	CyVerse User Portal
VICE access	You must have permission to use Discovery Environment VICE applications; request access on the user portal (under ‘Services’)	CyVerse User Portal
Cyberduck	Standalone software for upload/download to Data Store	Download Cyberduck

Platform(s)

We will use the following CyVerse platform(s):

Platform	Interface	Link	Platform Tour
Data Store	GUI/Command line	Data Store	Data Store Guide
Discovery Environment	Web/Point-and-click	Discovery Environment	Discovery Environment Guide

Application(s) used

Discovery Environment App(s):

App name	Version	Description	App link	Notes/other links
Muscle	3.8.31	Multiple sequence aligner		Original App documentation muscle
Rocker	Latest	RStudio VICE application		Original App documentation rocker

---

Fix or improve this documentation

• Search for an answer: CyVerse Learning Center

• Ask us for help: click on the lower right-hand side of the page

• Report an issue or submit a change: Github Repo Link

• Send feedback: learning@CyVerse.org

---

Learning Center Home