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

Dow, Ellen; Wood-Charlson, Elisha; Biller, Steven; Paustian, Timothy; Schimer, Aaron; Sheik, Cody; Whitham, Jason; Krebs, Rose; Goller, Carlos; Allen, Benjamin; Crockett, Zachary; Arkin, Adam

doi:10.25982/90997.49/1783189

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

Abstract

Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. The KBase Educators Working Group developed modular, adaptable, and customizable instructional units. Each instructional module contains teaching resources, publicly available data, analysis tools, and markdown capability to tailor instructions and learning goals for each class. The online user interface enables students to conduct hands-on data science research and analyses without requiring programming skills or their own computational resources (these are provided by KBase). Alongside these resources, KBase continues to work with instructors, supporting the development of additional curriculum modules. For anyone new to the platform, KBase, and the growing KBase Educators Organization, provides a community network, accompaniedmore »« less

Authors:

;

; Krebs, Rose;

;

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

Publication Date:: 2021-05-17

Research Org.:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Subject:: 59 BASIC BIOLOGICAL SCIENCES

OSTI Identifier:: 1783189

DOI:: https://doi.org/10.25982/90997.49/1783189

Citation Formats


                    Dow, Ellen, Wood-Charlson, Elisha, Biller, Steven, Paustian, Timothy, Schimer, Aaron, Sheik, Cody, Whitham, Jason, Krebs, Rose, Goller, Carlos, Allen, Benjamin, Crockett, Zachary, and Arkin, Adam. Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform.  United States: N. p., 2021. 
        Web.  doi:10.25982/90997.49/1783189.

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                    Dow, Ellen, Wood-Charlson, Elisha, Biller, Steven, Paustian, Timothy, Schimer, Aaron, Sheik, Cody, Whitham, Jason, Krebs, Rose, Goller, Carlos, Allen, Benjamin, Crockett, Zachary, & Arkin, Adam. Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform.  United States.  doi:https://doi.org/10.25982/90997.49/1783189

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                    Dow, Ellen, Wood-Charlson, Elisha, Biller, Steven, Paustian, Timothy, Schimer, Aaron, Sheik, Cody, Whitham, Jason, Krebs, Rose, Goller, Carlos, Allen, Benjamin, Crockett, Zachary, and Arkin, Adam. 2021.  
"Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform".  United States.  doi:https://doi.org/10.25982/90997.49/1783189.  https://www.osti.gov/servlets/purl/1783189. Pub date:Mon May 17 00:00:00 EDT 2021

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@article{osti_1783189,

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

  author       = {Dow, Ellen and Wood-Charlson, Elisha and Biller, Steven and Paustian, Timothy and Schimer, Aaron and Sheik, Cody and Whitham, Jason and Krebs, Rose and Goller, Carlos and Allen, Benjamin and Crockett, Zachary and Arkin, Adam},

  abstractNote = {Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. The KBase Educators Working Group developed modular, adaptable, and customizable instructional units. Each instructional module contains teaching resources, publicly available data, analysis tools, and markdown capability to tailor instructions and learning goals for each class. The online user interface enables students to conduct hands-on data science research and analyses without requiring programming skills or their own computational resources (these are provided by KBase). Alongside these resources, KBase continues to work with instructors, supporting the development of additional curriculum modules. For anyone new to the platform, KBase, and the growing KBase Educators Organization, provides a community network, accompanied by community-sourced guidelines, instructional templates, and peer support to use KBase within a classroom whether virtual or in-person.},

  doi          = {10.25982/90997.49/1783189},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {2021},

  month        = {5}

}

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DOI: https://doi.org/10.25982/90997.49/1783189

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Works referenced in this record:

KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents
dataset, January 2021

Whitham, Jason
North Carolina State University
https://doi.org/10.25982/68579.143/1766297

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

Abstract

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