Education, Outreach, Training
People are the principal component of cyberinfrastructure, and we consider everyone learning about or working within the life sciences our stakeholders. Since our stakeholders have a variety of personal objectives, CyVerse Education, Outreach, and Training (EOT) accomplishes its mission by offering targeted strategies that move each stakeholder group—especially those lacking the skills or access to best leverage bioinformatics—towards increasing knowledge, involvement, and use of cyberinfrastructure.
Core education and training goals
Our education and training objectives revolve around achieving five core objectives that we believe will lower the barriers between CyVerse users and their educational and scientific objectives:
- Give users a “Big Picture” understanding of the CyVerse computational infrastructure
- Help users identify applicable 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
- Use evaluation and assessment tools to gather user feedback and adapt to changing needs and opportunities
Core outreach goals
Our outreach objectives aim at “spreading the word” about CyVerse. This project has undergone several phases of growth: from gathering initial community input starting in 2008 to the successful grant renewal in 2013. This staggered development process necessitates tailoring EOT efforts to three key areas:
- Educate and update community members on what CyVerse is and what it offers
- Reach and cater to graduate students (new users) who tend to be early adopters
- Encourage users in diverse science communities to adopt and adapt our infrastructure
EOT is committed to reaching groups of scientists, developers, educators, and students who are underrepresented in the life sciences. We accomplish this by maintaining an EOT presence at conferences and meetings that serve these groups, and through targeted training locations.
EOT accomplishes its objectives through a variety of activities, summarized below. These activities, paired with our internal and external evaluation, help us meet the needs of our user community.
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.
Genomics 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 though 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 that will benefit the entire user community.
Graduate Student Seminar: “What a Graduate Student Needs to Know about Cyberinfrastructure” is a seminar that 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. The purpose of this seminar is to introduce life sciences students to key concepts in computational thinking and to illustrate CyVerse’s role in these applications.
Webinars and online learning
Get Started with CyVerse: This monthly, one-hour webinar welcomes new users with an orientation to various services CyVerse offers 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.
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.