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Published on Nov 29, 2022DOI

Computational notebooks for more openness, reproducibility, and productivity in research

A conversation with Ludmilla Figueiredo (part 2)

by Ludmilla Figueiredo, Ebuka Ezeike, and Jo Havemann
Published onNov 29, 2022
Computational notebooks for more openness, reproducibility, and productivity in research
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Ludmilla Figueiredo is a research data and code curator coming from a background in ecology and conservational biodiversity. In the first episode (part 1), she talks with Jo about the implementation of the open science principles within the fast-paced and heavy workload researchers must handle.
In the second episode (part 2), Ludmilla presents to you a simple yet effective computational workbook she developed with her colleagues, to make FAIR data sharing easy for anyone.

Computational Notebook (toolkit)

Ludmilla Figueiredo has completed a postdoc studying the payment of extinction debts at the Ecosystem modeling group of the University of Würzburg in Germany, and, since March 2022, works as a data and code curator at the Data and Code Unit of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. Among her duties, she has to support researchers in the application of Open Science and FAIR principles, sourcing from her participation in the “Freies Wissen” Open Science Fellows program (2020/2021, Wikimedia Deutschland).

References

Figueiredo L, Scherer C, Cabral JS (2022) A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research. PLoS Comput Biol 18(9): e1010356. https://doi.org/10.1371/journal.pcbi.1010356

Figueiredo, L., Krauss, J., Steffan-Dewenter, I. & Cabral, J. S. (2019). Understanding extinction debts: spatio–temporal scales, mechanisms and a roadmap for future research. Ecography 42, 1973– 1990.

Würzburg University press release (2019): Prize for Ludmilla Figueiredo. When ecosystems are disrupted, it can set species extinction in motion. For her research in this field, biologist Ludmilla Figueiredo receives a prize from the journal Ecography. https://www.uni-wuerzburg.de/aktuelles/pressemitteilungen/single/news/preis-fuer-ludmilla-figueiredo-1/ (german)

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A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research
by Ludmilla Figueiredo, Cédric Scherer, and Juliano Sarmento Cabral
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  • Published on Sep 15, 2022
  • dx.doi.org
Description

The ubiquitous use of computational work for data generation, processing, and modeling increased the importance of digital documentation in improving research quality and impact. Computational notebooks are files that contain descriptive text, as well as code and its outputs, in a single, dynamic, and visually appealing file that is easier to understand by nonspecialists. Traditionally used by data scientists when producing reports and informing decision-making, the use of this tool in research publication is not common, despite its potential to increase research impact and quality. For a single study, the content of such documentation partially overlaps with that of classical lab notebooks and that of the scientific manuscript reporting the study. Therefore, to minimize the amount of work required to manage all the files related to these contents and optimize their production, we present a starter kit to facilitate the implementation of computational notebooks in the research process, including publication. The kit contains the template of a computational notebook integrated into a research project that employs R, Python, or Julia. Using examples of ecological studies, we show how computational notebooks also foster the implementation of principles of Open Science, such as reproducibility and traceability. The kit is designed for beginners, but at the end we present practices that can be gradually implemented to develop a fully digital research workflow. Our hope is that such minimalist yet effective starter kit will encourage researchers to adopt this practice in their workflow, regardless of their computational background.

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Creative Commons Attribution 4.0 International License (CC-BY 4.0)
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