eLife launches Executable Research Articles for publishing computationally reproducible results

Authors with a published eLife paper can now enrich their work with embedded code blocks and computed outputs to make their results more transparent, interactive and reproducible.
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eLife is pleased to announce today the launch of Executable Research Articles (ERAs), allowing authors to post a computationally reproducible version of their published paper in the open-access journal.

eLife invests in open-source technology innovation to improve online tools for sharing, using and interacting with new results. The organisation has been working on the concept of computationally reproducible papers since 2017, first in partnership with Substance and later with Stencila. The open-source suite of tools that started life as the Reproducible Document Stack is now live on eLife as ERA, delivering a web-native format for making published research more transparent, interactive and reproducible.

From today, authors with a published eLife paper can register their interest to enrich their work with the addition of live code blocks and computed outputs, such as statistical results, tables and graphs. The resulting new ERA publication will be presented as a complement to their original paper.

Readers can then inspect, modify and re-execute the code directly in their browser, enabling them to better understand how figures have been generated, change a plot from one format to another, alter the data range of a specific analysis, and more. Any changes made to the ERA will be limited to the reader’s browsing session and will not affect the published article, ensuring that anyone can experiment with the results safely. Readers can also download the ERA publication, with all the embedded code and data preserved, and use it as a basis for further study or derivative works.

“The reproducibility and transparency of published research are fundamental to science,” says Giuliano Maciocci, eLife Head of Product and Experience. “For example, to develop new medical treatments, such as for COVID-19 and other emerging and infectious diseases, scientists need to be able to validate and build on preclinical data. To help improve the replication and reuse of new results, we set out to create an article type that would treat live code and data as first-class citizens, and in a way that others could easily access it. After releasing the first demo of our computationally reproducible manuscript last year, we’re now pleased to make ERA more widely available for authors at a time when it is perhaps needed the most.”

eLife authors are already taking advantage of the new ERA, with articles published by Tim Errington, Director of Research at the Center for Open Science, US, and Matthew Nolan, Professor of Neural Circuits and Computation at the University of Edinburgh, UK.

Nolan says: “In addition to promoting reproducibility, we were motivated by making it easier to link analyses to descriptions of their results. As readers, we're often frustrated by how difficult it is to figure out details of analyses in published papers, including our own. This is largely a result of the standard format of journal papers. We're excited that, by solving this problem, ERAs should also make it easier for readers to ask new questions of published data and to apply published analyses to their own data. Stencila and eLife have done impressive work to make this feasible and, if widely adopted, then I think we can look forward to more efficient, as well as more transparent, communication of research outputs.”

ERA has been developed by eLife and Stencila as open-source software to allow other publishers to offer this format to their authors and readers. “The ERA technology stack is designed specifically with preprint and journal publishing in mind,” Maciocci explains. “Features including a versatile theming solution mean that ERA can be adapted to the visual style of virtually any online publication. We hope that other publishers will take advantage of this software so their own readers can have access to more interactive and reproducible research.”

Nokome Bentley, Founder and CEO of Stencila, adds: “Open-source languages like Python and R have become an important part of the modern research workflow, and Jupyter Notebooks and R Markdown are an increasingly common part of researchers’ toolboxes. By bridging the gap between those tools and published journal articles, ERA enables continuous reproducibility from the start to end of the project lifecycle and fosters rapid reuse of research methods and results.”

More information about ERA, including FAQs for publishers, authors and developers, is available in our latest blog post.

To view Tim Errington’s ERA, visit https://elifesciences.org/articles/30274/executable.

And Matthew Nolan’s ERA is available to view at https://elifesciences.org/articles/52258/executable.

Authors who are interested in composing an ERA complement to their published eLife article can register their interest here.

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eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. eLife invests heavily in software development, experience design, collaboration and outreach to help realise the full potential of the digital communication of new research. We support the development of open-source tools that can be used, adopted and extended by any interested party to help move towards an ecosystem that serves research as efficiently and as cost-effectively as possible. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about/technology.