Learning Materials Table of Contents
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 |