Biotechnology data analysis training with Jupyter Notebooks

Biotechnology has experienced innovations in analytics and data processing. As the volume of data and its complexity grows, new computational procedures for extracting information are developed. However, the rate of change outpaces the adaptation of biotechnology curricula, necessitating new teaching methodologies to equip biotechnologists with data analysis abilities. To simulate experimental data, we created a virtual organism simulator (silvio) by combining diverse cellular and sub-cellular microbial models. With the silvio Python package, we constructed a computer-based instructional workflow to teach growth curve data analysis, promoter sequence design, and expression rate measurement. The instructional workflow is a Jupyter Notebook with background explanations and Python-based experiment simulations combined. The data analysis is either conducted within the Notebook in Python or externally with Excel. This instructional workflow was separately implemented in two distance courses for Master's students in biology and biotechnology with assessment of the pedagogic efficiency. The concept of using virtual organism simulations that generate coherent results across different experiments can be used to construct consistent and motivating case studies for biotechnological data literacy.

Here, the supplementary material is provided.

2207_BLS-RecExpSim.mbz
Moodle backup file for import as new moodle function.

BLS_RecExpSim_PerformanceEvaluation Rubric.docx
Expected learning outcomes with associated performance levels.

BLS_SurveryQuestions.docx
Survey questions to evaluate the educational approach.

RecExpSim.html
Html-Export of the Jupyter Notebook to teach biotechnology data analysis. This only serves as visual impression of the course because the dynamic Python-evaluations are not functioning.

RecExpSim_Lecture.pdf
Static pdf of preparatory lecture to cover the theoretical aspects in the simulations and to get student on comparable level.

RecExpSim_Lecture.pptx
Adjustable pptx of preparatory lecture to cover the theoretical aspects in the simulations and to get student on comparable level.