Interactive educational media for Food Biotechnology via Jupyter

This project aimed to update the Food Biotechnology curriculum to incorporate interactive learning elements and computational exercises based on Jupyter notebooks and deployed on LET’s JupyterHub. We developed interactive Jupyter notebooks for both active in-class exercises and self-guided learning activities to complement lectures, deepening student learning via interactive visualizations and exercises covering topics such as sequence alignment, genome assembly, metabolic modeling, and microbial growth modeling. This was done with the goal of increasing learning efficacy and practical training in computational competencies, motivated by the need for more visualization and modeling training in the Food Science bachelors and masters programs. This was also motivated by the desire to implement such competencies in the context of systems-oriented courses in which programming is not the explicit learning outcome. Hence, Jupyter notebooks were seen as an ideal medium for delivering this content to students, enabling interactive data visualization and bioinformatics training in non-methodological courses. We modified our previous JupyterHub environment to add additional tools for genome assembly and metabolic modeling; developed four new notebooks for use in active learning sequences in class; developed interactive visualizations in these notebooks; and implemented these already in 2023-2024 as a trial run for using these materials in class.

We developed interactive Jupyter notebooks on the topics of sequence alignment, genome assembly, metabolic modeling, and microbial growth modeling. Each of these was used as the focus of an active learning sequence in which students tested their knowledge ahead of the class, completed the notebook by working together in class, and discussed the outcomes, interpretation, and theory in class. Two of these notebooks were implemented in the bachelor-level course, «Food Biotechnology». Two were implemented in the masters-level course, «Functional Microorganisms in Foods and the Human Microbiome». In the bachelor-level course, these notebooks were revisited as a learning aid at other times during the course. The use of JupyterHub was successful in both courses, eliminating hardware and installation issues for the students, and in the bachelor level course in particular making it possible to interactively simulate and visualize data (e.g., bacterial growth curve modeling) without the need for data entry or programming, making it easier to scale to a large class size, including students with less programming background.

The project goals were achieved without any deviations. The students enjoyed the interactive sequences and felt that they were useful training, as measured via student evaluations and informal feedback. Use of Jupyter notebooks enabled efficient integration of training in practical computational competencies in a moderately large course (~60 students in the bachelor-level course), demonstrating promise for further scaling in other settings. In future years, more work is needed to better connect these practical exercises to other lectures in the same course, particularly in the master-level course. JupyterHub also presented a slight learning curve for students at the bachelor level who encountered this for the first time, so introductory materials may be needed to guide students who have not encountered JupyterHub before. Nevertheless, our impression is that JupyterHub could be successfully used for simulation, visualization, and entry-level bioinformatics analysis in a medium class size, which could probably be scaled to larger class sizes. Given the success in 2023-2024, we plan to further develop these materials for continued use in these courses.