This space is home to learning materials and tutorials created for CyVerse products and services. To search the entire CyVerse wiki, use the box at the upper right.

Maintenance: Tues, 28 Jan 2020


Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
User Portal                   8:00am to 5:00pm MST
The User Portal,, will be unavailable while we perform maintenance and updates.
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA 

Keep up to date with our maintenance schedules on the CyVerse public calendar
Check your local timezone here 
Please contact for any questions, or concerns.






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Welcome to the home of the CyVerse Learning Materials space. It is open to the public. If you're visiting here to see what's available, or if you want to learn more about how to do something, this is the place. This space contains tutorials and links to YouTube videos that instruct users how to use the CyVerse apps and platforms.

About tutorials

Tutorials in this space were created and are managed by the tutorial's author. For questions about a tutorial, please contact the person listed as Added by at the top of each tutorial page.

To view the full list of tutorials, see the Tutorials List.

For help on adding a tutorial or item to this space, please see Creating a Tutorial in the Learning Materials Space. This is the place to put your tutorials for use by others. Instructions are included for hiding the content until it's ready for prime time, as well as how to edit and use this wiki.

Feedback, questions, support

  • Ask CyVerse: Your go-to place for asking questions, viewing questions and answers submitted by other users, and providing feedback about CyVerse in order to enhance direct communication between CyVerse staff, collaborators, and the wider community. For information on using Ask, see Using Ask CyVerse. Access Ask CyVerse at
  • Submitting a Help Request and contacting Support: Help is available in each platform, but all the scoop is on the Get Help page on the website.
  • Using JIRA at CyVerse: Entering, editing, and tracking issues in JIRA, CyVerse's issue-tracking system.

Social media

Helpful Links

This Page Contains:

This Space Contains:

General learning materials




Tutorials and workflowsSee Tutorials List. 

CyVerse YouTube webinar

Variety of CyVerse tutorials ranging from overviews about the Discovery Environment to more in-depth videos about RNAseq, DNA Subway, Atmosphere, data management, workshop videos and webinars, and more.


Getting Started with CyVerse Home

Information about registering and managing your CyVerse account, CyVerse mailing lists, using the CyVerse Data Store, using the CyVerse bug-tracking system, FAQs, and more.

CyVerse Wiki

CyVerse Library

Repository for all types of media created within CyVerse, as well as for publications citing CyVerse, lists of software contributions made by CyVerse staff, and more.

CyVerse Wiki

Introduction to CyVerse

Overview and New Release Updates

CyVerse YouTube video (Pub. 11/2013)


CyVerse's cloud-computing platform




Atmosphere Manual

Help documentation for using Atmosphere

CyVerse Wiki

Atmosphere tutorialsTutorials used to help you learn how to use different Atmosphere images and apps on the images. 

Atmosphere Quick Start video

Getting started

CyVerse YouTube video (Pub. 1/2013

Atmosphere: Data transfer, Volumes, and Imaging


CyVerse YouTube video (Pub. 2/2014)

Atmosphere: Launching, connecting, suspending, terminating instances


CyVerse YouTube video (Pub. 2/2014)

Atmosphere: Minute Tour


CyVerse YouTube video (Pub. 2/2014)

Atmosphere: Using an EBS Volume

CyVerse YouTube video (Pub. 6/2011)

BATools 0.0.1

Atmosphere image that has R version 3.0.1 installed. BATools, an R package for Whole Genome Prediction, is also installed on this image.

CyVerse Wiki

Installing R packages on Atmosphere

Intended to teach users how to install R packages on Atmosphere. These packages could be publicly available on CRAN, or they could be packages developed for personal use. Although this tutorial is specific to R packages, many of the same principles also apply when installing other software on an Atmosphere instance.

CyVerse Wiki

ValidateToolkit-0.3 Tutorial

Intended to teach users how to validate GWAS applications on Atmosphere using Simulate and Validate. This Atmosphere image is publicly available as ValidateToolkit-dalanders-0.3.

CyVerse Wiki

BisQue Image Analysis System




Using the BisQue Image Analysis System

Advanced image database and analysis system for biological 5D images. Bisque supports large-scale image databases (TB to PB), flexible experimental data management, metadata- and content-based search, analysis integration, and knowledge discovery.

CyVerse Wiki

Overview of Bisque module integration

Key concepts involved in the process of integrating a new image analysis module into the BisQue platform.

CyVerse Wiki

Data Store

iPlant's data repository

DNA Subway

Scientific tools and data in interface to make high-level genome analysis broadly available to students and educators




DNA Subway login


CyVerse website

DNA Subway Introduction

Introduction to DNA Subway

CyVerse YouTube video

DNA Subway user guide (PDF)\

User Guide

CyVerse Wiki

DNA Subway: Red Line

Using the Red Line to predict/annotate genes in up to 150kb of DNA

CyVerse YouTube video (Pub. 2/2014)

DNA Subway: Red Line Walkthrough

June 2014

PDF: CyVerse Wiki

DNA Subway: Yellow Line

Using the Yellow Line

CyVerse YouTube video

DNA Subway: Blue Line Refresher webinar

Using the Blue Line Refresher webinar

CyVerse YouTube video

DNA Barcoding Techniques Refresher


CyVerse YouTube video

Urban Barcode Project website


Urban Barcode Project website

DNA Barcoding 101 website


DNA Barcoding website


Application programming interface for the CyVerse cyberinfrastructure



TNRS (Taxonomic Resolution Name Service)

Learning materials for TNRS are embedded in the TNRS app.