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Representing DNA for Machine Learning Algorithms: A Primer on One-Hot, Binary, and Integer Encodings
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Yash Munnalal Gupta; Satwika Nindya Kirana; Somjit Homchan – Biochemistry and Molecular Biology Education, 2025
This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning intervention focuses on developing practical skills in implementing these essential techniques for…
Descriptors: Science Instruction, Teaching Methods, Genetics, Molecular Biology
Using ChatGPT as a Tool for Training Nonprogrammers to Generate Genomic Sequence Analysis Code
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Haley A. Delcher; Enas S. Alsatari; Adeyeye I. Haastrup; Sayema Naaz; Lydia A. Hayes-Guastella; Autumn M. McDaniel; Olivia G. Clark; Devin M. Katerski; Francois O. Prinsloo; Olivia R. Roberts; Meredith A. Shaddix; Bridgette N. Sullivan; Isabella M. Swan; Emily M. Hartsell; Jeffrey D. DeMeis; Sunita S. Paudel; Glen M. Borchert – Biochemistry and Molecular Biology Education, 2025
Today, due to the size of many genomes and the increasingly large sizes of sequencing files, independently analyzing sequencing data is largely impossible for a biologist with little to no programming expertise. As such, biologists are typically faced with the dilemma of either having to spend a significant amount of time and effort to learn how…
Descriptors: Artificial Intelligence, Technology Uses in Education, Training, Teaching Methods
Incorporating Coding into the Classroom: An Important Component of Modern Bioinformatics Instruction
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Nichole Orench-Rivera; April Bednarski; Paul Craig; Austin Talbot – Journal of College Science Teaching, 2025
Advancements in computation and machine learning have revolutionized science, enabling researchers to address once insurmountable challenges. Bioinformatics, a field that heavily relies on computer-driven analysis of biological data, has greatly benefited from these developments. However, traditional bioinformatics instruction frequently lacks the…
Descriptors: Coding, Computer Science Education, Integrated Curriculum, Programming
Teaching Python Programming for Bioinformatics with Jupyter Notebook in the Post-COVID-19 Era
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Gupta, Yash Munnalal; Kirana, Satwika Nindya; Homchan, Somjit; Tanasarnpaiboon, Supatcharee – Biochemistry and Molecular Biology Education, 2023
The COVID-19 pandemic has forced the Bioinformatics course to switch from on-site teaching to remote learning. This shift has prompted a change in teaching methods and laboratory activities. Students need to have a basic understanding of DNA sequences and how to analyze them using custom scripts. To facilitate learning, we have modified the course…
Descriptors: Programming Languages, Teaching Methods, Computer Software, Genetics
Climate Change and Plant Rhizosphere Microbiomes: An Experiential Course-Embedded Research Project
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James A. Parejko – Journal of Microbiology & Biology Education, 2024
The current and ongoing challenges brought on by climate change will require future scientists who have hands-on experience using advanced molecular techniques, can work with large data sets, and can make correlations between metadata and microbial diversity. A course-embedded research project can prepare students to answer complex research…
Descriptors: Plants (Botany), Microbiology, Science Instruction, Teaching Methods