Using interactive digital notebooks for bioscience and informatics education

In this 2020 paper published in PLOS Computational Biology, Davies et al. of the University of Manchester discuss their experiences implementing Jupyter Notebooks in bioinformatics and health informatics education. Through these digital notebooks, the researchers were able to help teach future laboratorians with little coding experience how to perform basic coding of health informatics applications, as well as more advanced postgraduates how to apply the notebook to bioinformatics activities. After discussing the inner working of the Jupyter Notebook, the authors explain how such notebooks are able to enhance collaboration and reproducibility in laboratories, as well as improve learning and student assessment in the classroom. They then describe two education-based case studies of using the notebooks, and they describe the end results. The authors conclude that, given their experience as well as their students’ experience, such notebooks can act “as a useful resource for learning to code and communicate research findings and analysis” in higher education, with the experience being transferrable to professional work in the future.

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