The journal eLife recently published a “computationally reproducible” article:
Today eLife, in collaboration with Substance, Stencila and Tim Errington, Director of Research ar the Center for Open Science, US, published its first reproducible article, based on one of Errington’s papers in the Reproducibility Project: Cancer Biology. This reproducible version of the article showcases some of what’s possible with the new RDS tools, and we invite researchers to explore the newly available opportunities to tell their story.
eLife’s reproducible format essentially gives readers functionality like you would find in a Jupyter notebook or RMarkdown document, but in the standard browser interface on eLife’s website. This lets you modify analysis code and re-generate tables/figures without having to download anything, or set up a local R or Python environment!
If you read their post about this, it’s clear that a lot of effort went into the technology stack making this possible. It’s an impressive effort, and sorely needed by the scientific community.
Hopefully other publishers will follow suit—but even if they don’t, eLife uses an industry-standard format called JATS (of course it’s XML-based), which should allow publishers to handle these sorts of documents even if they don’t support the full suite of in-browser code execution capabilities that eLife does.
eLife is also working on better support for converting from Jupyter and RMarkdown to DAR (their document archive format). Kudos to them for supporting the literate programming technology the community is already using, rather than trying to force authors to use something else.
