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NeuroLibre Reproducible Preprints

https://github.com/neurolibre/brand/blob/main/png/card_tb.png?raw=true

As a registered preprint publisher, NeuroLibre goes beyond the traditional boundaries of research dissemination by offering NeuroLibre Reproducible Preprints (NRPs).

Code, data, and computational runtime are not supplementary but rather integral components of published research.

Embracing this principle, NRPs are built by seamlessly combining the outputs of your preprint’s executable content with the scientific prose, all within the same execution runtime required for your analyses.


Moving from static PDFs with code and data availability statements to NRPs is the quantum leap that modern research yearns for. With NeuroLibre, we are dedicated to make that leap as easy as it gets.

Explore a published NRP

https://doi.org/10.55458/neurolibre.00004

For further details on why moving beyond static text and illustrations is a central challenge for scientific publishing in the 21st century, see the following perspective article by the NeuroLibre team (DuPre et al. 2022):

https://doi.org/10.1371/journal.pcbi.1009651

Bird’s eye view of the NRP publication workflow

🚀 NRPs are dynamic

Enabling you not only to execute NRPs directly in your web browser and regenerate the figures from the preprint, but also providing support for interactive figures and even dashboards!

This interactivity allows for a more immersive exploration of the preprint, whether by reviewers upon peer-reviewed journal submission, or by researchers who are interested in your work.

To submit an NRP you need to provide the following:

  1. A public code repository that has a single or a collection of Jupyter Notebooks and/or MyST markdown files.
  2. A public data repository needed to generate the outputs (typically figures) from the executable part of your content.
  3. Reproducible runtime configurations recognized by BinderHub.
  4. A bibtex formatted bibliography (paper.bib) and author information (paper.md).

Using your ORCID, you can login to NeuroLibre’s submission portal and fill out a simple form. After content moderation, NeuroLibre starts a technical screening process, which takes place on GitHub using NeuroLibre’s one-of-a-kind editorial workflow, powered by the OpenJournals.

♻️ NRPs are FAIR

NeuroLibre archives all the necessary reproducibility assets required to successfully build an NRP at the time of submission.

NeuroLibre’s production BinderHub, container registry, data storage, and web servers are reserved for the published NRPs, ensuring the long-term functionality and accessibility.

This makes NRPs Findable, Accessible, Interoperable, and Reusable.

During the technical screening process, our editorial bot RoboNeuro and a screener works with you to ensure a successful build of your NRP on NeuroLibre test servers.

After a successful build, the following reproducibility assets are transferred from our preview server (public) to our production servers (reserved for published NRRs only) and archived individually on Zenodo:

  1. Docker image
  2. Dataset (unless already archived)
  3. Repository (version cut at the latest successful build)
  4. Built NRP (HTML pages of the executable book)

Each of these reproducibility assets is attributed to every author on the NRP, and they are assigned a DOI (Digital Object Identifier).

Once the archival process is complete, a summary PDF is generated. This PDF is necessary to officially register NRPs as preprints.

➕ More than another Binder/Jupyter instance

In addition to providing a seamless publication workflow for reproducible preprints and officially registering them for discoverability of scholarly content, NeuroLibre overcomes an important reproducibility roadblock. Because absent the bundling of reproducibility assets within a dedicated publication framework:

  • Public container registries wipe out images.
  • Future attempts to build the same images (like Binder) frequently stumble over version clashes, resulting in failures.
  • Unless cached on the same server where JupyterHub runs and archived, data often slips into the realm of inaccessibility.

As a next-generation publisher, NeuroLibre ensures that your preprint retains its reproducibility prowess. With our robust framework, we preserve and safeguard all necessary assets, leaving no room for disappearing images, version woes, or elusive data. Rest easy, knowing your preprint remains reproducible and readily available to all.

All the archived reproducibility assets, cited references, and the link to the reproducible preprint are resource linked to the DOI assigned by NeuroLibre upon publication (DOI: 10.55458/neurolibre).

Similar to that in traditional preprint repositories (e.g. arXiv), NeuroLibre updates metadata relationship to an Author Accepted Manuscript (AAM) or Version of Record (VoR) after your article has been accepted for publication by a journal, following the peer review process and any revisions requested by the reviewers or editors.

Contributions are welcome!

NeuroLibre is fully open-source and draws its strength from community-developed tools such as BinderHub and Open Journals. You can find more information under our github organization.

Author guidelines

Reader

Technical screening

Developer documentation

FAQ