Learning Center Home

Welcome to the Learning Center

CyVerse Learning Center is a release of our learning materials in the popular "Read the Docs" formatting.

What is CyVerse?¶

CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Our extensible platforms provide data storage, bioinformatics tools, data visualization, interactive analyses, cloud services, APIs, and more.

CyVerse cyberinfrastructure includes:

• A data storage facility called the Data Store
• An interactive, web-based, analytical data science workbench called the Discovery Environment or DE for short.
• Cloud infrastructure to access remote servers for computation, analysis, and storage called Atmosphere and Jetstream
• Web authentication and security services via KeyCloak and OAuth
• Support for scaling computational algorithms to run on large, high-speed computers
• Education and training in how to use cyberinfrastructure (these pages!)
• People with expertise in all of the above to help you and your team

Account Creation¶

• Create a CyVerse account

Data Store¶

• Data Store Guide

Discovery Environment Workbench¶

• Find apps in the Discovery Environment Guide

VICE¶

• Visual Interactive Compute Environment (VICE) includes popular integrated development environments: JupyterLab, RStudio, and VSCode.
• Instant and on demand virtual machines running Ubuntu Linux command line interface.
• Remote Desktops for high quality visualizations in your browser
• GPU computing for machine learning and artificial intelligence.

Cloud¶

• CyVerse created Atmosphere, a browser interface for working with OpenStack Cloud virtual machines
• Partnered with NSF XSEDE/ACCESS Jetstream-2 for more and larger virtual machines.

Atmosphere¶

• Request access to Atmosphere
• Use Atmosphere

Jetstream-2¶

• Create an XSEDE/ACCESS user account
• Request a start-up allocation on Jetstream-2

Choosing a Platform¶

What to do first

• Upload your data
• Launch an analysis

Featured Tutorials

• RNA-Seq with Kallisto and Sleuth
• Genome Annotation with MAKER
• Filter, Trim, and Process High-throughput Sequencing Reads with Trimmomatic

• Condensed R: 240-minute tutorial

• Self Paced Tutorials

For Advanced Users

• Command Line Transfer with iCommands
• Integrating Tools and Apps

Bring your own tools

• Create and Run Docker Images

---

Funding and Citations:

CyVerse is funded entirely by the National Science Foundation under Award Numbers DBI-0735191, DBI-1265383, and DBI-1743442.

Please cite CyVerse appropriately when you make use of our resources, see CyVerse citation policy

---

Fix or improve this documentation

• Search for an answer: CyVerse Learning Center
• Ask us for help: click the Intercom icon on the lower right-hand side of the page
• Report an issue or submit a change: Github Repo Link
• Send feedback: Tutorials@CyVerse.org

---

Learning Center Home