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The new age of preprints: enhanced, reproducible, and reusable

Introduction

In the era of Covid-19, life science and medical preprint submission has been rapidly rising. At the same time, more preprint sites and related services are appearing that could help preprints quickly evolve to be the dynamic, evolving story of research that journal articles have failed to realize. Preprints communicate the work at an earlier stage and there is an expectation that the research will continue to evolve and the preprint will either be updated or revised as a journal submission. This acceptance of preprints as impermanent sets them apart from how journal articles are perceived, as a static and immovable record of the research. 

With this increased attention to the preprint landscape, there is an opportunity to invest in preprint workflow and technologies to help realize the longstanding vision that research can be communicated rapidly and openly, with all relevant outputs such as datasets and code integrated. And that the research can be updated with new versions as the research evolves.  

Early and open sharing of research in progress

Preprints allow researchers to share work as it emerges rather than saving it up for a large publication. Providing a flexible format for preprints means the potential for more frequent, shorter communications to be shared, such as micropublications, a single figure, and null results. Preprints are open access, allowing others to comment on the work or incorporate it into their own research well before it’s published in a journal. 

Increasing reproducibility

With preprints, there is an opportunity to achieve the ‘born digital’ state that journals haven’t achieved, even after more than twenty years online. With tools such as Stencila, the platform for embedding live code and datasets to the manuscript used to create eLife’s recently announced Executable Research Article, preprints can become ‘born reproducible’ with authors demonstrating how their data and code work through the preprint itself. Beyond just linking related datasets, code, protocols, and resources to a published article, Stencila allows authors to build these into the manuscript without having any additional technical expertise. 

Stencila offers the promise of a pre-submission workflow for preprints that can incorporate tools such as DataSeer, an AI that reads documents and identifies datasets referred to but perhaps not cited. 

This pre-submission pipeline would allow authors to upload their manuscripts for submission to a preprint and follow a set of easy steps to create a living open science publication that is: 

  • Born reproducible by embedding data and code directly into the article.
  • Open data compliant by identifying datasets mentioned but not cited and offering authors a path to sharing and quickly formatting a publishable package for submission to preprint and journal sites that includes the article and links to all related research outputs identified in a structured, machine-readable statement.

Building use and reuse: the role of funders and institutions

Preprint servers have the opportunity for wide adoption, particularly if they are recognized by funders and institutions as a publication event that can be used in grant applications and tenure or promotion processes. If preprints are a ‘certified’ step in communicating research, they will offer provenance to the work rather than opening up the fear of being scooped. Funders such as Aligning Science Across Parkinson’s (ASAP) are now mandating preprints prior to or concurrent with journal article submission and even requiring that datasets, protocols, software and resources be open available and attached to the preprint. ASAP also requires that preprints from its grantees are licensed CC-BY to maximize reuse. This licensing requirement will also help prevent subversion of preprint servers into commercially-run silos. With more open science-oriented policies and practices, preprinting will be more readily adopted by researchers. 

Preprint evolution

While today preprints are underfunded and almost exclusively offered as static PDFs, the tools, workflows, and attention are all there to turn preprints into the vehicles for dynamic, living, reproducible research communication that we need. With the efforts of organizations such as ASAPbio and the support from open science funders, the preprint trajectory can be more quickly course-corrected in this direction than the more entrenched and commercialized journal publishing world.