Using interactive digital notebooks for bioscience and informatics education

Abstract

Interactive digital notebooks provide an opportunity for researchers and educators to carry out data analysis and report the results in a single digital format. Further to just being digital, the format allows for rich content to be created in order to interact with the code and data contained in such a notebook to form an educational narrative. This primer introduces some of the fundamental aspects involved in using Jupyter notebooks in an educational setting for teaching in the bio/health informatics disciplines. We also provide 2 case studies that detail how we used Jupyter notebooks to teach non-coders programming skills on a blended Master’s degree module for a Health Informatics programme and a fully online distance learning unit on Programming for a postgraduate certificate (PG Cert) in Clinical Bioinformatics with a more technical audience.

A modular mathematical model of exercise-induced changes in metabolism, signaling, and gene expression in human skeletal muscle

“…-Jupyter notebook (Davies et al, 2020) that provides reproducibility of results presented in the article. The notebook can be started on the BioUML server as well as using Binder technology.…”

“…-GitLab project that contains all source code for the developed model and its modules; -project on BioUML server which displays the developed model and its modules in visual form as well as provides possibilities for editing and simulation; -Jupyter notebook (Davies et al, 2020) that provides reproducibility of results presented in the article. The notebook can be started on the BioUML server as well as using Binder technology.…”

Ten Simple Rules for Implementing a Flipped Classroom

“…In the field of computational biology, learning a programming language and performing research projects are typical examples of learning objectives that are difficult to reach via traditional lecturing but strongly benefit from active learning. Interactive material such as Jupyter notebooks [32,33] or the Rosalind auto-correcting exercise collection [34] are valuable resources for learning how to program and discovering bioinformatics algorithms. Engaging teams of students in open research challenges is also a unique opportunity for students to learn what a research project is about [35].…”

Ten simple rules for teaching applied programming in an authentic and immersive online environment

“…Students also installed git so that the course material could be downloaded from GitHub. Course material was taught using Jupyter Notebooks downloaded from GitHub [ 16 ]. The reason for this was to give the students an opportunity to get to grips with a commonly used version controlling tool they would encounter in practice.…”

“…These have been mainly used in research to support the reproducibility of code [ 18 ]; however, the ability to juxtapose practical and instructional content really lends itself to teaching. The format of the Notebooks allows for rich content to be created in order to interact with the code and data contained in such a notebook to form an educational narrative; we have integrated these throughout our health informatics teaching [ 16 ]. This is because the blend of activities can be mixed in a variety of ways to meet the learning objectives, for example, they can include relevant problems for students to solve interspersed with informative content and working examples all of which help to build learning incrementally.…”