Journal:Using interactive digital notebooks for bioscience and informatics education
| Full article title | Using interactive digital notebooks for bioscience and informatics education |
|---|---|
| Journal | PLOS Computational Biology |
| Author(s) | Davies, Alan; Hooley, Frances; Causey-Freeman, Peter; Eleftheriou, Iliada; Moulton, Georgina |
| Author affiliation(s) | University of Manchester |
| Primary contact | Email: alan dot davies-2 at manchester dot ac dot uk |
| Editors | Ouellette, Francis |
| Year published | 2020 |
| Volume and issue | 16(11) |
| Article # | e1008326 |
| DOI | 10.1371/journal.pcbi.1008326 |
| ISSN | 1553-734X |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008326 |
| Download | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008326 (PDF) |
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Abstract
Interactive digital notebooks provide an opportunity for researchers and educators to carry out data analysis and report 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 Notebook in an educational setting for teaching in the bioinformatics and health informatics disciplines. We also provide two case studies that detail 1. how we used Jupyter Notebooks to teach non-coders programming skills on a blended master’s degree module for a health informatics program, and 2. a fully online distance learning unit on programming for a postgraduate certificate (PG Cert) in clinical bioinformatics, with a more technical audience.
Keywords: bioinformatics, health informatics, programming, data analysis, Jupyter Notebook, education
Introduction
Universities and other higher education institutions are now under increasing pressure to provide more online and distance learning courses and to deliver them cost effectively and rapidly. [1] This increase in demand is partly based on students wanting more flexible study options in comparison to traditional higher education course delivery to aid in study around employment and family commitments. This is also driven by financial considerations that allow higher education institutions to scale course delivery while managing infrastructural provision (e.g., access to rooms for teaching and limited capacity for face-to-face delivery). [2] To meet this challenge, we require tools that cater for students with varying levels of digital literacy and reduce the burden of them having to download and install software, all of which requires support, which is more difficult to provide at a distance. This can be further complicated when students use managed equipment (e.g., National Health Service [NHS] employees) and may not have administrator rights to install software.
References
Notes
This presentation attempts to remain faithful to the original, with only a few minor changes to presentation. Grammar and punctuation has been updated reasonably to improve readability. In some cases important information was missing from the references, and that information was added.
