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

Adam Rule; Amanda Birmingham; Cristal Zuniga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight; Niema Moshiri; Mai H Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W Rose

doi:10.1371/journal.pcbi.1007007

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

PLoS Comput Biol. 2019 Jul 25;15(7):e1007007. doi: 10.1371/journal.pcbi.1007007. eCollection 2019 Jul.

Authors

Adam Rule¹, Amanda Birmingham², Cristal Zuniga³, Ilkay Altintas⁴, Shih-Cheng Huang⁴, Rob Knight^{3

5}, Niema Moshiri⁶, Mai H Nguyen⁴, Sara Brin Rosenthal², Fernando Pérez⁷, Peter W Rose⁴

Affiliations

¹ Design Lab, UC San Diego, La Jolla, California, United States of America.
² Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, California, United States of America.
³ Department of Pediatrics, UC San Diego, La Jolla, California, United States of America.
⁴ Data Science Hub, San Diego Supercomputer Center, UC San Diego, La Jolla, California, United States of America.
⁵ Departments of Bioengineering, and Computer Science and Engineering, and Center for Microbiome Innovation, UC San Diego, La Jolla, California, United States of America.
⁶ Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, California, United States of America.
⁷ Department of Statistics and Berkeley Institute for Data Science, UC Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

No abstract available

Publication types

Editorial
Research Support, Non-U.S. Gov't

MeSH terms

Authorship
Computational Biology*
Documentation
Guidelines as Topic*
Humans
Writing*

Grants and funding

The authors received no specific funding for writing this article. Funding for the “Reproducible Research and Interactive Education - Application of Jupyter Notebooks” workshop was provided by the San Diego Supercomputer Center at UC San Diego.