Literature DB >> 33151926

Using interactive digital notebooks for bioscience and informatics education.

Alan Davies1, Frances Hooley1, Peter Causey-Freeman1, Iliada Eleftheriou1, Georgina Moulton1.   

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.

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Mesh:

Year:  2020        PMID: 33151926      PMCID: PMC7643937          DOI: 10.1371/journal.pcbi.1008326

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.475


  7 in total

1.  Scientific Notebook Software: Applications for Academic Radiology.

Authors:  Michael L Richardson; Behrang Amini
Journal:  Curr Probl Diagn Radiol       Date:  2017-09-18

2.  Raising research quality will require collective action.

Authors:  Marcus Munafò
Journal:  Nature       Date:  2019-12       Impact factor: 49.962

3.  Best practices for scientific computing.

Authors:  Greg Wilson; D A Aruliah; C Titus Brown; Neil P Chue Hong; Matt Davis; Richard T Guy; Steven H D Haddock; Kathryn D Huff; Ian M Mitchell; Mark D Plumbley; Ben Waugh; Ethan P White; Paul Wilson
Journal:  PLoS Biol       Date:  2014-01-07       Impact factor: 8.029

4.  A global perspective on evolving bioinformatics and data science training needs.

Authors:  Teresa K Attwood; Sarah Blackford; Michelle D Brazas; Angela Davies; Maria Victoria Schneider
Journal:  Brief Bioinform       Date:  2019-03-22       Impact factor: 11.622

5.  Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?

Authors:  Angela C Davies; Diane Harris; Amanda Banks-Gatenby; Andy Brass
Journal:  PLoS Comput Biol       Date:  2019-06-27       Impact factor: 4.475

6.  Data availability, reusability, and analytic reproducibility: evaluating the impact of a mandatory open data policy at the journal Cognition.

Authors:  Tom E Hardwicke; Maya B Mathur; Kyle MacDonald; Gustav Nilsonne; George C Banks; Mallory C Kidwell; Alicia Hofelich Mohr; Elizabeth Clayton; Erica J Yoon; Michael Henry Tessler; Richie L Lenne; Sara Altman; Bria Long; Michael C Frank
Journal:  R Soc Open Sci       Date:  2018-08-15       Impact factor: 2.963

7.  Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Authors:  J Kyle Medley; Kiri Choi; Matthias König; Lucian Smith; Stanley Gu; Joseph Hellerstein; Stuart C Sealfon; Herbert M Sauro
Journal:  PLoS Comput Biol       Date:  2018-06-15       Impact factor: 4.475

  7 in total
  1 in total

1.  BioUML-towards a universal research platform.

Authors:  Fedor Kolpakov; Ilya Akberdin; Ilya Kiselev; Semyon Kolmykov; Yury Kondrakhin; Mikhail Kulyashov; Elena Kutumova; Sergey Pintus; Anna Ryabova; Ruslan Sharipov; Ivan Yevshin; Sergey Zhatchenko; Alexander Kel
Journal:  Nucleic Acids Res       Date:  2022-05-10       Impact factor: 19.160

  1 in total

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