logo

 

CyVerse Wiki

Offers How-To instructions for using CyVerse platform, apps, and services.

learning center logo

 

Learning Center

Explore materials for learning about the major components of CyVerse infrastructure.

logo

 

Tutorials

Easily search and sort by tutorial name, title, author, platform, apps used, and more.

 

CyVerse Learning Institute

CyVerse Learning Institute (CLI) is a resource for researchers to actively explore and acquire skills, tools, and expertise needed for 21st century open science. Offering hands-on, intensive training as well as virtual events, CLI provides tried-and-true instructor-led, project-based learning in a welcoming, team-building environment. CLI will help you meet the challenges of using the growing array of computational tools and platforms that are essential for collaborative, trans-disciplinary open science.

There are also opportunities to work with the CyVerse team on location. Get one-on-one mentorship from our expert informaticians and educators to develop your data science skills and strengthen your labs. Contact info@cyverse.org for more information.

 

Focus Forum Webinars: Fall 2019

Join us this Fall for a series of free, half-hour long, focused webinars to help you do your science using CyVerse's open source resources.

Starting August 30, 2019, every other Friday at 10 am Pacific, 11 am Mountain, 12 pm Central, 1 pm Eastern

To see videos of past webinars, visit our YouTube channel.

Foundational Open Science Skills (FOSS)

February 17-21, 2020

University of Arizona, Tucson, AZ

This camp teaches foundational Open Science skills to early career researchers establishing a new team or seeking research funding, and to recently awarded first-time principal investigators wanting to utilize data science-based tools and platforms.

Not sure if Camp is for you?  Check out the syllabus for FOSS Camp 2019

CyVerse Container Camp

March 10-13, 2020

University of Arizona, Tucson, AZ

Back by popular demand! If reproducible science is important to you, then learning how to use container technology to do that will make your life easier. Join us for an intensive 3-day hands-on workshop to learn how to create, use, deploy, and share software containers (e.g., Docker, Singularity) across a variety of computational systems from your laptop to cloud and HPC.

Want to see what the buzz is about?  Check out the Agenda from Container Camp 2019

Core Education and Training Goals

We strive to achieve five objectives that we believe lower the barriers between CyVerse users and their educational and scientific objectives:

  • Give users a “Big Picture” understanding of the CyVerse cyberinfrastructure.

  • Help users identify components of our infrastructure to solve their problems.

  • Assist and motivate users to overcome technical and skill challenges that slow or prevent them from putting solutions into practice.

  • Illustrate how computational thinking can guide investigation design.

  • Gather user feedback and adapt to changing needs and opportunities.

Core Outreach Goals

Our EOT is committed to reaching scientists, developers, educators, and students who are underrepresented in the life sciences. Our EOT efforts focus on three key areas:

  • Educate and update community members on what CyVerse offers.

  • Reach and cater to new users.

  • Encourage users in diverse communities to adopt and adapt our infrastructure.

EOT Activities

Tools and Services Workshop (TSW):

This two-day workshop provides a comprehensive look at platforms, tools, and services for large-scale data analysis provided by CyVerse. Workshop topics build progressively to cater to the needs of general and advanced audiences, and are customized according to participant interests. Hands-on demos and guided exercises cover popular topics (e.g., genome assembly, genome annotation, RNA-Seq, GWAS, etc.). Workshop participants also are able to consult with instructors and bring their own data to get started with a project.

Genomes in Education Workshop (GinE):

This two-day workshop empowers college faculty to integrate modern methods for genome analysis into courses and student research projects. The content focuses on using DNA Subway, a website that introduces students to sophisticated bioinformatics through an easy-to-use interface. DNA Subway is used to analyze DNA sequences with a variety of outcomes, including determining the structure and function of genes and learning more about organisms’ genomes. A hands-on DNA extraction/PCR amplification lab and a DNA barcoding lab let students identify organisms by DNA sequencing. Participants conclude with discussion on implementation of these labs in undergraduate education settings.

Data-2-Publication Workshop:

This ad hoc program pairs faculty groups with CyVerse domain experts to move important datasets to publication readiness, and also serves as a focal point for solving cyberinfrastructure challenges (e.g., integrating new tools and workflows) that can be generalized into solutions to benefit the entire user community.

Seminars

What a Graduate Student Needs to Know about Cyberinfrastructure is presented (when possible) with the Tools and Services Workshop, and is offered to the larger group of graduate students who may not have attended the workshop. This seminar introduces life sciences students to key concepts in computational thinking and illustrates CyVerse’s role in these applications.

Click Here to Request/Host a Workshop.

Webinars and Online Learning

Get Started with CyVerse

This monthly, one-hour webinar welcomes new users with an orientation to various CyVerse services and serves as a forum for answering questions.

Update Webinars:

These webinars are scheduled after new releases of CyVerse products and serve to highlight new features and answer questions.

Follow-up Webinars

These webinars are scheduled after in-person Tools and Services/Genomics in Education workshops, and help users who may need time to develop datasets or implement the skills and lessons learned.

Learning Center: Through here, users can learn how to create and manage tutorials for the major components of the CyVerse cyberinfrastructure. In-depth tutorials cover popular science topics such as how to use RNA-Seq to study differential gene expression and how to use genome-wide association studies (GWAS) to identify genes and controlling elements associated with specific traits. Tutorials are focused not just on how to conduct analyses with CyVerse tools, but also on communicating best practices that help users apply computational thinking and avoid common bioinformatics pitfalls.

Wiki

The CyVerse wiki offers how-to instructions for using the CyVerse platforms, apps, and services. This is also the home of the tutorials; on the List of Tutorials page, you can easily search and sort by tutorial name, title, author, platform, apps used, and more.

 

Educational Cyberinfrastructure

DNA Subway bundles research-grade bioinformatics tools and databases into intuitive workflows, presenting them in an appealing interface modeled on the metaphor of a subway map. “Riding” on different DNA Subway lines, students can predict and annotate genes in up to 150 kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), and analyze DNA barcodes and construct phylogenetic trees (Blue Line). The Green Line provides an easy-to-use workflow to analyze RNA-Seq experiments, the most accessible whole genome datasets. Based on the popular Tuxedo Protocol, the RNA-Seq workflow uses high-performance compute resources of NSF’s Extreme Scientific and Engineering Discovery Environment (XSEDE), providing the first readily available “on ramp” to biological supercomputing.

You can reserve a portion of Atmosphere's cloud resources for classes or workshops. Have your students run identical analyses in identical environments. Instructors must request the reservation