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 U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1828227
- Alternate Identifier(s):
- OSTI ID: 1856707
- Grant/Contract Number:
- AC02-05CH11231 DE-AC02-06CH11357 DE-AC05-00OR22725 DE-AC02-98CH10886; AC05-00OR22725
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Education
- Additional Journal Information:
- Journal Name: Frontiers in Education Journal Volume: 6; Journal ID: ISSN 2504-284X
- Publisher:
- Frontiers Media S.A.
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; computational biology; bioinformatics; data science; STEM education and learning; undergraduate education
Citation Formats
Dow, Ellen G., Wood-Charlson, Elisha M., Biller, Steven J., Paustian, Timothy, Schirmer, Aaron, Sheik, Cody S., Whitham, Jason M., Krebs, Rose, Goller, Carlos C., Allen, Benjamin, Crockett, Zachary, and Arkin, Adam P. Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform. Switzerland: N. p., 2021.
Web. doi:10.3389/feduc.2021.711535.
Dow, Ellen G., Wood-Charlson, Elisha M., Biller, Steven J., Paustian, Timothy, Schirmer, Aaron, Sheik, Cody S., Whitham, Jason M., Krebs, Rose, Goller, Carlos C., Allen, Benjamin, Crockett, Zachary, & Arkin, Adam P. Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform. Switzerland. https://doi.org/10.3389/feduc.2021.711535
Dow, Ellen G., Wood-Charlson, Elisha M., Biller, Steven J., Paustian, Timothy, Schirmer, Aaron, Sheik, Cody S., Whitham, Jason M., Krebs, Rose, Goller, Carlos C., Allen, Benjamin, Crockett, Zachary, and Arkin, Adam P. Fri .
"Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform". Switzerland. https://doi.org/10.3389/feduc.2021.711535.
@article{osti_1828227,
title = {Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform},
author = {Dow, Ellen G. and Wood-Charlson, Elisha M. and Biller, Steven J. and Paustian, Timothy and Schirmer, Aaron and Sheik, Cody S. and Whitham, Jason M. and Krebs, Rose and Goller, Carlos C. and Allen, Benjamin and Crockett, Zachary and Arkin, Adam P.},
abstractNote = {Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.},
doi = {10.3389/feduc.2021.711535},
journal = {Frontiers in Education},
number = ,
volume = 6,
place = {Switzerland},
year = {Fri Oct 29 00:00:00 EDT 2021},
month = {Fri Oct 29 00:00:00 EDT 2021}
}
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https://doi.org/10.3389/feduc.2021.711535
https://doi.org/10.3389/feduc.2021.711535
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