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
This Page Contains:
This Space Contains:
General learning materials
Name | Description | Source |
|---|---|---|
| Tutorials and workflows | See Tutorials List. | |
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 | |
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 | |
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 | |
Overview and New Release Updates | CyVerse YouTube video (Pub. 11/2013) |
Atmosphere
CyVerse's cloud-computing platform
Name | Description | Source |
|---|---|---|
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. | |
Getting started | CyVerse YouTube video (Pub. 1/2013 | |
| CyVerse YouTube video (Pub. 2/2014) | |
Atmosphere: Launching, connecting, suspending, terminating instances |
| CyVerse YouTube video (Pub. 2/2014) |
| CyVerse YouTube video (Pub. 2/2014) | |
CyVerse YouTube video (Pub. 6/2011) | ||
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 | |
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 | |
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 |
|---|---|---|
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
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 |
|---|---|---|
| CyVerse website | |
Introduction to DNA Subway | CyVerse YouTube video | |
User Guide | CyVerse Wiki | |
Using the Red Line to predict/annotate genes in up to 150kb of DNA | CyVerse YouTube video (Pub. 2/2014) | |
June 2014 | PDF: CyVerse Wiki | |
Using the Yellow Line | CyVerse YouTube video | |
Using the Blue Line Refresher webinar | CyVerse YouTube video | |
Barcoding | CyVerse YouTube video | |
Barcoding | Urban Barcode Project website | |
Barcoding | DNA Barcoding website |
Agave API and TACC/XSEDE
Application programming interface for the CyVerse cyberinfrastructure
Name | Source |
|---|
CyVerse Wiki | |
TACC website | |
TACC website | |
iPlant website |
TNRS (Taxonomic Resolution Name Service)
Learning materials for TNRS are embedded in the TNRS app.