A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research

PLoS Comput Biol. 2022 Sep 15;18(9):e1010356. doi: 10.1371/journal.pcbi.1010356. eCollection 2022 Sep.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Documentation*
  • Records*
  • Reproducibility of Results
  • Workflow

Grants and funding

Development and part of the publication fees of this work was supported by a grant from Wikimedia Deutschland’s Open Science Fellows program (2020/2021 edition, https://de.wikiversity.org/wiki/Wikiversity:Fellow-Programm_Freies_Wissen) granted to LF. This publication was also supported by the Open Access Publication Fund of the University of Würzburg granted to LF. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.