Generated July 26, 2021

Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform

Ellen G Dow1, Elisha M Wood-Charlson1, Steven J Biller2, Timothy Paustian3, Aaron Schirmer4, Cody S Sheik5, Jason M Whitham6, Rose Krebs7, Carlos C Goller7,8, Benjamin Allen9, Zachary Crockett9, and Adam P Arkin1,10

1Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 2Department of Biological Sciences, Wellesley College, Wellesley, MA, USA. 3Department of Bacteriology, University of Wisconsin, Madison, WI, USA. 4Department of Biology, Northeastern Illinois University, Chicago, IL, USA. 5Department of Biology and the Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, USA. 6Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA. 7Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA. 8Biotechnology Program (BIT), North Carolina State University, Raleigh, NC, USA. 9Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. 10Department of Bioengineering, University of California, Berkeley, CA, USA.

Concept Workflow

For the most up to date workflows and resources, see the KBase Educators Concept Overview. ConceptWorkflow_13Jul21_Workflow_Current-03.png

Concepts, Modules, and Learning Objectives


  • G1. Genome Assembly
    • G1.1 Explain how the 'shotgun' genome sequencing approach works
    • G1.2 Describe the basic process of how individual DNA sequences are generated
    • G1.3 Understand how to evaluate the output of a genome assembly run
  • G2. Genome Annotation
    • G2.1 Describe the steps required to annotate a genome
    • G2.2 Be able to interpret the output of a genome annotation and some associated terms
  • G3. Genome Analysis
    • G3.1 Learn how to interpret genomic annotation
    • G3.2 Understand how to summarize/abstract biological data
    • G3.3 Explore what a metabolic model can and can't tell you
    • G3.4 How to run a BLAST search and interpret the results
  • G4. Comparative Genomics

    • G4.1 Learn how to compare the overall structure and arrangement of two genomes
    • G4.2 Understand what different types of annotation comparisons can, and cannot, teach you about the organism
    • G4.3 Be able to explain the concept of a pangenome


  • M1. Data Input
    • M1.1 Evaluate read quality based on FastQC reports
    • M1.2 Perform read trimming with Trimmomatic
    • M1.3 Explain in your own words how adapter contamination can
      • M1.3a affect read quality
      • M1.3b be addressed with Trimmomatic
  • M2.Assembly
    • M2.1 Define assembly and contig
    • M2.2 Compare and contrast the output of different assemblers
  • M3. Read-based Taxonomy
    • M3.1 Understand the mechanisms behind taxonomic profiling
    • M3.2 Compare the outputs of two applications
  • M4. Binning
    • M4.1 Understand how binning works to group contigs of metagenomic assemblies
  • M5. Bin-based Taxonomy
    • M5.1 Explain another method of how to measure taxonomic diversity through binned assemblies
  • M6. Taxonomy and Evolution
    • M6.1 Understand how MAGs generated in a metagenomic study can be placed into a phylogenetic tree
    • M6.2 Understand how ANI can be used to determine relatedness
    • M6.3 Understand how to estimate relative abundance of a MAG within a metagenomic sample
    • M6.4 Learn how to use apps and tools within KBase to build upon foundational concepts and promote exploration


  • P1. Genome Species Tree
    • P1.1 Understand how bioinformatics can be used to understand and define species
    • P1.2 Understand how multiple genomes can be compared to identify patterns
    • P1.3 Understand how patterns may vary depending on gene choice
    • P1.4 Critically evaluate genome/pangenome and bioinformatic data
    • P1.5 Draw conclusions from data


  • PG1. Build and View a Pangenome
    • PG1.1 Explain annotation (which is also covered in Genome and Metagenome Modules)
    • PG1.2 Define the concept of pangenome
    • PG1.3 Explain why is visualizing a pangenome useful and interpret representative examples of pangenomes
    • PG1.4 List the main objects and main steps in the process of building a pangenome Advance
    • PG1.5 Identify quality control steps in the process of building pangenomes
    • PG1.6 Evaluate limitations of pangenome representations
  • PG2. Comparing Features
    • PG2.1 Evolutionary relationships
    • PG2.2 Define core and flexible genomes
    • PG2.3 Identify core functions
    • PG2.4 Identify variable functions across strains
    • PG2.5 Determine how pathogenesis is encoded and can be transferred
  • PG3. Phylogenomics
    • PG3.1 Explain the significance of an outgroup and how selection of an outgroup may change results.
    • PG3.2 Define outgroup in terms of phylogenies and evolutionary relationships
    • PG3.3 Identify and list differences between phylogenetic nodes of a pangenome

Metabolic Modeling

  • MM1. Drafting a metabolic model
    • A) Assembly
    • B) Annotation
      • MM1.1 Describe how sequencing data is generated for use in metabolic modeling
      • MM1.2 Explain why a metabolic model is created
      • MM1.3 Explain what a metabolic model creates
      • MM1.4 Predict the open reading frames of a new sequence
      • MM1.5 Determine which of the isolates should be able to grow on glucose
      • MM1.6 Determine which of the isolates are auxotrophs for histidine
  • MM2. Gapfilling and Flux Balance Analysis
    • MM2.1 Describe the steps required to run Flux Balance Analysis
    • MM2.2 Explain how a draft model differs from a gapfilled model.
    • MM2.3 Be able to interpret the output of a Flux Balance analysis to measure biomass
  • MM3. Manipulating Media
    • MM3.1 Demonstrate the effect of media on a metabolic model
    • MM3.2 Gain understanding of the predictions and parameters that go into model building
    • MM3.3 Consider how models compare to working in a lab
  • MM4. Model Comparison
    • MM4.1 Know how to read a metabolic model comparison.
    • MM4.2 Understand the basic steps of how to compare metabolic models
    • MM4.3 Compare metabolic models
  • MM5. Community Analysis
    • A) Mixed-Bag Community Modeling
    • B) Community Member Metabolite Exchange
      • MM5.1 Merge metabolic models into a community model
      • MM5.2 Identify metabolite exchange between interacting microbes
      • MM5.3 Use multiple media formulations and gapfilling to form microbial interactions
      • MM5.4 Create and alter microbial interactions through deleting, adding and constraining reactions
      • MM5.5 Compare the impact of alternate community members with similar functions on overall biomass

Case Study

North Carolina State University Biotechnology Course (BIT 477/577)

  • Gold: Krebs, Rose, and Goller, Carlos. Case Study: Can you find Delftia?. United States: N. p., 2020. Web. doi:10.25982/67335.259/1773074.

  • Silver: Whitham, Jason. KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents. United States: N. p., 2021. Web. doi:10.25982/68579.143/1766297.

Community Resources

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 (see above). From student and community feedback, resources including teaching Narratives, are improved and added to the KBase Educators Organization.

Join the KBase Educators Org