Computational reproducibility of Jupyter notebooks from biomedical publications.

ABSTRACT:

Background

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications.

Approach

We address computational reproducibility at 2 levels: (i) using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks associated with publications indexed in the biomedical literature repository PubMed Central. We identified such notebooks by mining the article's ful

SUBMITTER: Samuel S 

PROVIDER: S-EPMC10783158 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature