KBase in the Classroom - The tools and resources for using KBase in education, including labs and lectures from high school through graduate level courses.
Dec 4, 2020

KBase for Educators

Join the community of educators using KBase to teach bioinformatics and computational biology!

Why KBase?

While KBase is routinely used for advanced analysis by scientists around the world, the interface is adaptable to meet the needs of educators and students in the classroom. Learning bioinformatics and molecular biology analysis can often be a black box, unless you have extensive programming experience. Teaching these methods can be even harder, especially in this time of distance learning. To tackle these challenges, KBase collaborated with educators to create teaching resources based on the free, easily accessible and open source KBase Narrative user interface.

KBase is a robust data science platform that integrates many resources for bioinformatics analysis in one place. KBase also allows users to customize their data analysis and create reproducible workflows for research publications. These tools provide the resources to answer questions that guide the exploration of concepts: 

  • Determine which genes are responsible for antibiotic resistance in a bacterium using comparative genomics.
  • Develop hypotheses on gene evolution across species by building gene trees. 
  • Identify species and examine their roles in a microbial community from environmental samples with metagenomic tools.
  • Compare the genetics of single species or within a clade using pangenomic analysis. 

The Educator’s Group

Over the summer, KBase worked with a group of educators who teach at various levels from high school through graduate courses. These volunteers contributed their time and experience to develop workflows within KBase aimed at transferring analytical skills to students in a virtual (or in-person) classroom. The goal was to give students a realistic data science research and analysis experience. 

One result of this effort is a connected workflow that integrates genomics, metagenomics, phylogenetics, and pangenomic concepts in a “choose your own adventure” framework. Each concept is stand alone, while complementing one another as they flow from one topic to another across concepts. The pace of each workflow can be adjusted with the flexibility of modules that are shareable and allow students to copy and interact with data and analyses.

Concepts and Student Workflows On-Hand

This image illustrates the conceptual workflow of student modules divided into individual Narratives between genomics, metagenomics, phylogenetics and pangenomics.

The concept workflow of genomics includes genome analysis and comparison. The modules guide students through tools to assemble and annotate a genome. Steve Biller, Assistant Professor of Biological Sciences at Wellesley College, was a lead contributor and devised a branched path into optional modules to further analyze metabolism and compare two strains of a bacterium.  

Metagenomics focusing on community level of analyses, starts similarly to the genomics modules with assembly and annotation. Our lead contributor, Elisha Wood-Charlson, KBase User Engagement Lead, shaped the modules exploring a metagenomic workflow that builds in taxonomic analysis to have students compare methods and tools. Jon Benskin, Biology Teacher at Boca Raton Community High School, contributed further questions and tools that explore species relationships and abundance.

Phylogenetics investigates species evolution and taxonomic relationships. Aaron Schirmer, Associate Professor of Biology at Northeastern Illinois University, and Kathleen Morrow, Biology Teacher at Thomas Jefferson High School for Science & Technology contributed to development of a workflow in which students create a local database from a phylogenomic tree to explore gene evolution using tree building and analysis. 

The pangenome workflow builds upon the prior concepts and leads students to define and build a working pangenome, the set of genes for all strains within a clade. Ellen Dow, KBase User Engagement, developed these modules as a framework to analyze and compare pangenomic data with Carlos Goller, Associate Professor of Teaching at North Carolina State University, Biotechnology Program. The modules are adaptable and can be used to compare methods of analysis within a dataset. Optional pathways provide genome comparisons and phylogenomic analysis using pangenome data.

Using the KBase Narrative

The unique interactive KBase platform enables students to engage in active learning with real-world data. The Narrative User Interface works similar to a laboratory notebook. Instructors can provide background information, links to resources and videos, and embed written and image-based instructions and questions that guide students through analysis pipelines similar to the process of a researcher. Overall, modules are adaptable to a variety of baseline knowledge, ranging from high school to graduate students. Established workflows can be applied to variety datasets that are publicly available or even from student-collected data. 

Additionally KBase provides organizational tools for classes and courses through KBase Organizations (Orgs). Educators can create an Org within KBase to share workflows with their students. The Narrative is flexible and adaptable. Using Markdown, instructions meet student knowledge and provide structure and guidance, while supporting independent exploration and challenging critical thinking.

Get Involved

Educators can request to join the KBase Educators Org to access these resources, learn best practices, and take part in discussion among the community of peers using KBase in their curriculum. Send an email to engage@kbase.us and let us know your interest and what you teach!

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.