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.

Apirhabdus apintestini gen. nov., sp. nov., a member of a novel genus of the family Enterobacteriaceae, isolated from the gut of the western honey bee Apis mellifera

“…Together, the conserved protein and whole genome phylogenies along with the OrthoANIu, AAI and dDDH results suggest that strain CA-0114 T represents a novel species belonging to a novel genus within the Enterobacteriaceae . The taxonomic novelty of strain CA-0114 T at the genus level within the Enterobacteriaceae was also confirmed using the GTDB taxonomic classifier version 1.7.0 software [ 65 ] (topology and ANI method) as implemented in the KBase server [ 66 ]. Interestingly, we found that the AAI, OrthoANIu, dDDH and 16S rRNA identity values between Tenebrionibacter intestinalis BIT-L3 T and Tenebrionicola larvae YMB-R21 T were alarmingly high (99.64, 99.83, 98.20 and 99.24 %, respectively) which suggests that these species are subjective synonyms [ 67 68 ].…”

Digital Literacy 5.0 to Enhance Multicultural Education

“…Furthermore, emphasis should be placed on cultivating students' abilities to manage and analyze large datasets, a pivotal competency in this field. Additionally, the curriculum must remain dynamic to adapt to the rapidly evolving nature of bioinformatics technologies and research methodologies (255,257,258).…”

Integrating computational skills in undergraduate Microbiology curricula in developing countries

“…Bioinformatics does not function in isolation; the effective processing of biological data is accomplished with a variety of programming languages. Many bioinformatics programs or pipelines are coded in languages such as R or rely heavily on Python programming language [ 79 ]. It has resulted in an increasing number of universities in the world including bioinformatics, programming or computer science in the curricula of undergraduate microbiology programmes as well as other life sciences, leading to students having understanding of the principal computational concepts underlying the tools they use on a regular basis in their research [ 80 ].…”