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

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, a...

Full description

Bibliographic Details
Main Authors: Ludmilla Figueiredo, Cédric Scherer, Juliano Sarmento Cabral
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2022-09-01
Series:PLoS Computational Biology
Online Access:https://doi.org/10.1371/journal.pcbi.1010356
_version_ 1828386142560452608
author Ludmilla Figueiredo
Cédric Scherer
Juliano Sarmento Cabral
author_facet Ludmilla Figueiredo
Cédric Scherer
Juliano Sarmento Cabral
author_sort Ludmilla Figueiredo
collection DOAJ
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.
first_indexed 2024-12-10T05:32:06Z
format Article
id doaj.art-be7b0589d543417f8469acf74fc118ff
institution Directory Open Access Journal
issn 1553-734X
1553-7358
language English
last_indexed 2024-12-10T05:32:06Z
publishDate 2022-09-01
publisher Public Library of Science (PLoS)
record_format Article
series PLoS Computational Biology
spelling doaj.art-be7b0589d543417f8469acf74fc118ff2022-12-22T02:00:30ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-09-01189e101035610.1371/journal.pcbi.1010356A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.Ludmilla FigueiredoCédric SchererJuliano Sarmento CabralThe 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.https://doi.org/10.1371/journal.pcbi.1010356
spellingShingle Ludmilla Figueiredo
Cédric Scherer
Juliano Sarmento Cabral
A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.
PLoS Computational Biology
title A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.
title_full A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.
title_fullStr A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.
title_full_unstemmed A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.
title_short A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research.
title_sort simple kit to use computational notebooks for more openness reproducibility and productivity in research
url https://doi.org/10.1371/journal.pcbi.1010356
work_keys_str_mv AT ludmillafigueiredo asimplekittousecomputationalnotebooksformoreopennessreproducibilityandproductivityinresearch
AT cedricscherer asimplekittousecomputationalnotebooksformoreopennessreproducibilityandproductivityinresearch
AT julianosarmentocabral asimplekittousecomputationalnotebooksformoreopennessreproducibilityandproductivityinresearch
AT ludmillafigueiredo simplekittousecomputationalnotebooksformoreopennessreproducibilityandproductivityinresearch
AT cedricscherer simplekittousecomputationalnotebooksformoreopennessreproducibilityandproductivityinresearch
AT julianosarmentocabral simplekittousecomputationalnotebooksformoreopennessreproducibilityandproductivityinresearch