Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Editorial
. 2019 Jul 25;15(7):e1007007.
doi: 10.1371/journal.pcbi.1007007. eCollection 2019 Jul.

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

Adam Rule  1 , Amanda Birmingham  2 , Cristal Zuniga  3 , Ilkay Altintas  4 , Shih-Cheng Huang  4 , Rob Knight  3   5 , Niema Moshiri  6 , Mai H Nguyen  4 , Sara Brin Rosenthal  2 , Fernando Pérez  7 , Peter W Rose  4
Affiliations
Editorial

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

Adam Rule et al. PLoS Comput Biol. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Iterative workflow for applying the 10 simple rules to the creation of Jupyter Notebooks.
The cycle describes three overlapping phases of developing a well-documented and functional Jupyter Notebook. First, we organize and document the notebook (Rules 1–3). Second, the code is developed following the rules proposed here about quality standards (Rules 4–7). Finally, the notebook is made available, along with its data (Rule 8), in a manner encouraging public exploration and contribution (Rules 9–10).
See this image and copyright information in PMC

References

    1. Barba LA. The hard road to reproducibility. Science. 2016;354: 142 10.1126/science.354.6308.142 - DOI - PubMed
    1. Peng RD. Reproducible Research in Computational Science. Science. 2011;334: 1226–1227. 10.1126/science.1213847 - DOI - PMC - PubMed
    1. Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK. Good enough practices in scientific computing. PLoS Comput Biol. 2017;13(6):e1005510 10.1371/journal.pcbi.1005510 - DOI - PMC - PubMed
    1. Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013;9(10):e1003285 10.1371/journal.pcbi.1003285 - DOI - PMC - PubMed
    1. Taschuk M and Wilson G. Ten simple rules for making research software more robust. PLoS Comput. Biol. 2017;13(4):e1005412 10.1371/journal.pcbi.1005412 - DOI - PMC - PubMed

Publication types