Learning Materials Table of Contents

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 http://ask.cyverse.org/questions/.
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

Name	Description	Source
Tutorials and workflows	See 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.	YouTube
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)

Atmosphere

CyVerse's cloud-computing platform

Name	Description	Source
Atmosphere Manual	Help documentation for using Atmosphere	CyVerse Wiki
Atmosphere tutorials	Tutorials 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

Name	Description	Source
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

Data Store Quick Start Manual

iPlant Wiki

DNA Subway

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

Name	Description	Source
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	Barcoding	CyVerse YouTube video
Urban Barcode Project website	Barcoding	Urban Barcode Project website
DNA Barcoding 101 website	Barcoding	DNA Barcoding website

Agave API and TACC/XSEDE

Application programming interface for the CyVerse cyberinfrastructure

Name	Source

Getting Started with iPlant and HPC	CyVerse Wiki
TACC user portal login and registration	TACC website
XSEDE user portal and online training materials	TACC website
iPlant-XSEDE users group mailing list	iPlant website

TNRS (Taxonomic Resolution Name Service)

Learning materials for TNRS are embedded in the TNRS app.