NeuroLibre is a preprint server for interactive research objects in neuroscience. It uses the Jupyter Book technology to convert static PDFs into living objects that incorporate data, code and interactive visualizations. Neurolibre is at a beta testing stage, and will be open for submission in winter 2022. Early versions of Neurolibre have already made important inroads in convincing publishers that they need to go beyond the PDF.
Below are six examples of collaborations with academic publishers that outline our vision for living research objects, enabling readers to engage with the content and encouraging scientists to reproduce each other’s work.
1. The very first NeuroLibre submission was a blog post on quantitative magnetic resonance imaging (qMRI), written by our software developer, Mathieu Boudreau. The blog post contained code examples and interactive visualizations powered by Plot.ly and won an award from the International Society for Magnetic Resonance in Medicine (ISMRM) for MRI education in the developing world. It was eventually picked up for publication by Elsevier as part of their book on qMRI. The book chapter is published under a creative commons license, making it possible to distribute the associated text, code, and data.
2. A NeuroLibre preprint published in eLife
In 2020 we submitted for publication to eLife a meta-analysis on myelin imaging with MRI. The meta-analysis was first available as a preprint on NeuroLibre, and the preprint is hyperlinked from the abstract of the eLife article. The eLife affiliate Stencila converted the preprint into an executable research article (ERA), and the article is available in both conventional and executable formats. The NeuroLibre article is one of only ten ERAs currently available in eLife. We are currently in communication with Stencila to ensure NeuroLibre is compatible with ERAs for smooth integration of future Neurolibre submissions. The meta-analysis template is freely available, and we expect other researchers to use this template to bring interactivity to systematic reviews.
3. A collaboration with PLoS that goes beyond neuroscience
In 2019 we published a post on the PLoS blog with the title ‘The Canadian Open Neuroscience Platform: Catching Up to Plan S and Going Further‘. This blog post led to a collaboration where a team of engineers in Macedonia (now dubbed the Notebook Factory) built two NeuroLibre research objects (Example 1 and Example 2) for the journal PLoS computational biology. The resulting Jupyter books motivated a survey conducted by PLoS to encourage code sharing, and a PLoS Computational Biology editorial authored by CONP developer Mathieu Boudreau. We are excited at the possibility of branching out beyond neuroscience to collaborate with other computationally intensive fields, growing the NeuroLibre community. Additionally, Notebook factory may be a viable model to support researchers adopting the Jupyter Book technology, and accelerating the transition towards reproducible articles.
4. MR Pub, a NeuroLibre style repository for magnetic resonance imaging
Encouraged by the enthusiastic PLoS response, we reached out to the journal Magnetic Resonance in Medicine (MRM, published by Wiley) and proposed building NeuroLibre style research objects from MRM articles that share code and data. The research objects were built by the Macedonian Notebook Factory team, and they were used to establish MR Pub, maintained by the reproducible research group of the International Society for Magnetic Resonance in Medicine (ISMRM). Following the successful launch of MR Pub, a competition was held where ISMRM researchers contributed other interactive research objects, many of them using the Jupyter Book format that is compatible NeuroLibre.
5. MRM Highlights, a blog for promoting reproducible research objects
The collaboration with the journal MRM continued with the blog MRM Highlights. The blog was initiated by NeuroLibre co-founder Nikola Stikov, and is more recently led by CONP developer Mathieu Boudreau, who selects MRM articles that promote reproducible research and publishes their insights. MRM Highlights is supported by CONP and the Quebec Bioimaging Network, and its content is published as a yearly magazine by Wiley. The Highlights content is produced by a team of volunteers coordinated by Mathieu Boudreau, and it engages with researchers on social media (Twitter, Facebook, YouTube) as well as in social events such as the yearly ISMRM Highlights party. Highlights is an important tool for community building and it shows the way toward broader adoption of NeuroLibre
6. A partnership with Aperture Neuro, an independent publishing platform supported by the Organization for Human Brain Mapping
Finally, NeuroLibre is partnering up with an independent journal (Aperture) published by the Organization for Human Brain Mapping (OHBM). Aperture plans to publish NeuroLibre articles in an overlay format (this blog post announces the partnership), reducing their costs by hosting the content directly on the NeuroLibre servers. As NeuroLibre resources are scarce, we envision that this format will bring funds to maintain our preprint servers, and will encourage journals to dedicate a portion of their article processing charges to supporting the NeuroLibre infrastructure. We are in the process of handling the first Aperture article and look forward to making NeuroLibre a native format for the Aperture interactive research objects.
In conclusion, NeuroLibre is showing the way forward to academic publishers, who need to go beyond the PDF to bring publishing into the 21st century. The NeuroLibre seeds have been planted in publishers as diverse as Elsevier, eLife, Wiley, PLoS and OHBM Aperture, and over the coming years we expect them to grow into a novel field of publishing, driven by interactivity, transparency and reproducibility.