The KBase Educators Organization provides freely accessible resources and tools built by the community’s Working Groups. Becoming a contributing member benefits both the individual and the community as a whole.
Nov 5, 2021

Educators Community Working Groups Highlight

The KBase Educators Organization provides freely accessible resources and tools built by the community’s Working Groups. Becoming a contributing member benefits both the individual and the community as a whole. Read the project publication

From computing platform to learning resource

Who are KBase Educators?

KBase Educators are instructors of any level that utilize KBase as a tool for exploratory and research-based biological analysis experiences in their course curriculum. Most educators in this KBase community teach bioinformatics or molecular biology to high school and college-level students. Many courses include a lab or hands-on portion in their curriculum that supports virtual learning. 

KBase Educators Community. The community includes instructors that teach at High School and college levels. Resources are developed by the community, including teaching Narratives using bioinformatics tools wrapped as KBase Apps and supporting documentation. Working groups have developed workflows across common topics. From student and community feedback, resources including teaching Narratives, are improved and added to the KBase Educators Organization.

How did the community get started?

The KBase Educators program started as an effort to gather information on how the KBase platform could support educators, with the pandemic shifting education to virtual classrooms. KBase advertised an open call to instructors, via our Newsletter and Twitter, for a discussion of their needs and visions around how the KBase platform could be applied to a classroom. During that discussion, several working groups were established to develop resources for a pilot, which have been refined and formally released to the Educators community (link to KBase Educators Webinar from December 2020).

Learn more about the development and resources available through the KBase Educators program.

KBase Educators Concept Workflows and their modules, including Genomics, Metagenomics, Phylogenetics, Pangenomes, and Metabolic Modeling

Community Goals 

The Working Group members had a variety of goals - from exploring how to use the platform to actually implementing KBase into a virtual classroom. KBase, and the KBase Educators community, supports and welcomes all!

The KBase Educators community provided a wonderful group of peers using KBase and sharing experiences. This allowed us to plan and learn how to best implement KBase in an online version of a metagenomics course. – Carlos Goller, PhD; North Carolina State University

Developing concept workflows

The KBase Educators Working Group included college professors and high school teachers, with classes at different levels, learning goals, and a variety of time allocations for these activities. The volunteers brought their unique perspectives and experiences, and were able to collaborate effectively to develop and test resources that were used in the classroom (in-person, virtually, and/or hybrid) during Fall 2020. The end results? A modular concept workflow that is adaptable and customizable to different classes.

KBase, a narrative-style platform for reproducible systems biology, has helped me teach metagenomics concepts in a very digestible way to undergraduate and graduate-level students. I plan to expand my use of the platform for other course topics, like transcriptomics. – Jason M. Whitham, PhD; North Carolina State University

Exploring KBase

Working Group members benefited from joining and becoming a part of the community. Together, the community learned that KBase is adaptive for teaching with different approaches — from demonstrations to in-depth student analyses — and the user interface is non-intimidating for students first learning bioinformatics. With many resources and tools necessary to explore data in multiple ways, there isn’t a requirement to learn command-line or become familiar with multiple platforms. This empowers educators and students to take different approaches on how to answer research questions and connect the materials learned to their own biology research questions.

I have been able to incorporate new methods of bioinformatic analysis directly into my class with the tools on KBase. There is not a steep learning curve, so many of the tools can be immediately implemented. – Jon Benskin; Boca Raton Community High School

Teaching strategies

Working Groups also provided the space to have conversations that revealed gaps and important considerations for those transitioning teaching strategies and adapting between virtual and hybrid classes. Taking part in sharing and open resources allowed for members to consider alternative viewpoints to the challenges faced when teaching virtually and assessing student learning. 

I’ve learned an enormous amount from interacting with a group of great, experienced educators who are teaching at all levels. Our discussions have provided me with a number of ideas on how to approach different topics in the classroom, inspiration for new ways of assessing student learning, and different ways for structuring my courses. – Steve Biller, PhD; Wellesley College

Community-developed resources

The KBase Educators Organization (“Org”) is a centralized resource of teaching material accessible through a free KBase account, after approval. The Org houses KBase tutorial Narratives — shareable, reproducible workflows — for modularized concepts that are provided as a complete workflow, as well as other Narratives generated by community members. All members are welcome to contribute and use the resources and materials. We recommend starting with the KBase Educators Best Practices guide. 

The web-based nature of KBase significantly reduced the ‘barriers to entry’ for my students, allowing them to focus on what and why they were doing instead of how to make it work in the first place. Using the Narratives also eliminated the need for me as an instructor to spend time on complicated setup and maintenance of local or cloud-based computational resources. – Tim Paustian, PhD; University of Wisconsin – Madison

What is next and how to get involved?  

Latest From the Working Group

The KBase Educators Working Group has developed a metabolic modeling workflow and hosted discussions on developing consistency across evaluations and assessments. Read the publication from the KBase team and Working Group! 

Open call for Working Groups

If you’d like to start or join a working group, send an email to engage@kbase.us to tell us you are interested in co-creating a student workflows with fellow educators.

General information for joining

Educators can request to join the KBase Educators Org to access the KBase resources for educators, learn best practices, and take part in discussion among the community on Slack

To join, send an email to engage@kbase.us and let us know 1) what course you teach — topic and level, 2) when you are teaching the course, and 3) how KBase can help.

 

Ellen Dow
Ellen Dow
Lawrence Berkeley National Laboratory

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.

System Maintenance Oct 6

We will be performing system maintenance on Thursday, October 6, from 1-4pm PDT (3-6pm CDT).  Submitting and already running compute jobs for both narrative.kbase.us and appdev.kbase.us may be interrupted or nonfunctional for this time period.