On the open-source landscape of PLOS Computational Biology

Boudreau, Mathieu; Poline, Jean‐Baptiste; Bellec, Pierre; Stikov, Nikola

doi:10.1371/journal.pcbi.1008725

Cited by 10 publications

(6 citation statements)

References 4 publications

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“…Though currently in beta testing, with a view to open to public submissions in December 2023, NeuroLibre has already been featured in a few journal editorials [33][34][35][36]. Following the standards defined by NeuroLibre, executable notebooks for some of these journals were built by a small team of collaborators and have been featured in the recently announced MRPub [37], as well as in a survey on code sharing conducted by PLoS [38].…”

Section: Neurolibre Offers New Possibilities For Collaboration and Pa...mentioning

confidence: 99%

The Canadian Open Neuroscience Platform—An open science framework for the neuroscience community

et al. 2023

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The Canadian Open Neuroscience Platform (CONP) takes a multifaceted approach to enabling open neuroscience, aiming to make research, data, and tools accessible to everyone, with the ultimate objective of accelerating discovery. Its core infrastructure is the CONP Portal, a repository with a decentralized design, where datasets and analysis tools across disparate platforms can be browsed, searched, accessed, and shared in accordance with FAIR principles. Another key piece of CONP infrastructure is NeuroLibre, a preprint server capable of creating and hosting executable and fully reproducible scientific publications that embed text, figures, and code. As part of its holistic approach, the CONP has also constructed frameworks and guidance for ethics and data governance, provided support and developed resources to help train the next generation of neuroscientists, and has fostered and grown an engaged community through outreach and communications. In this manuscript, we provide a high-level overview of this multipronged platform and its vision of lowering the barriers to the practice of open neuroscience and yielding the associated benefits for both individual researchers and the wider community.

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Section: Neurolibre Offers New Possibilities For Collaboration and Pa...mentioning

confidence: 99%

The Canadian Open Neuroscience Platform—An open science framework for the neuroscience community

et al. 2023

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“…As scientists increasingly recognize the value in sharing their code and data [ 25 ], this approach could facilitate an important transition in scientific publishing. By leveraging MyST as an emerging standard for integrated research objects, alongside modular components for their hosting and reexecution through BinderHub and other open technologies, scientists will be better positioned to author articles that center all the research objects supporting a scientific result, in addition to the underlying narrative.…”

Section: Centering Complex Objects In Scientific Publishing With Cloud Infrastructurementioning

confidence: 99%

Beyond advertising: New infrastructures for publishing integrated research objects

et al. 2022

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“…An ongoing challenge is that most researchers are still not properly recognized by funding agencies for having developed reproducible research practices in their lab and for sharing it with the community. Nonetheless, there is growing recognition across journals 6,7 that reproducible research objects that incorporate code and data are important for their readership and communities. This is slowly also translating to a growing recognition among funding agencies that this activity is important.…”

Section: % Of Total Papers That Shared… 2019 2020 2021mentioning

confidence: 99%

On the open‐source landscape of Magnetic Resonance in Medicine

Boudreau

Stikov

Jezzard

2022

Magnetic Resonance in Med

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The tides of the open-source movement reached the coast of our journal just prior to the coronavirus disease 2019 (COVID-19) pandemic with an editorial 1 on reproducibility and the future of MRI research. In it the authors argued that, for improved reproducibility, the concept of a "paper" should be extended to encapsulate the entirety of the scholarly work done authors. These extensions should include data and analysis code, which may be as essential to papers as figures and tables. In the spring of 2020, the journal therefore added an optional (but strongly encouraged) Data Availability Statement section to articles, making it easier to access supplementary data and code from an author's linked repository. Also, the journal's outreach initiative, MRM Highlights,* transitioned from highlighting Editor's Picks, to focusing on articles that demonstrate exemplary reproducible research practices, such as sharing all the data/code needed to reproduce figures, the use of Jupyter/R Markdown notebooks, container technology (eg., Docker, Singularity), interactive figures, etc. In addition to the Highlights interviews that showcased the authors and their publication, each feature was accompanied by an additional written interview where those authors explicitly discussed their reproducible research practices.In this editorial, we explore the reproducible research practices of the community in the wake of these changes.It would be interesting to observe what effect these changes had on the reproducible research practices of Magn Reson Med authors. Fortunately, we have an earlier snapshot of the open-source landscape of Magn Reson Med before the changes, captured in a blog post from 2019. † For this blog post, all the articles published in Magn Reson Med in 2019 were analyzed with an automated script to find which of them contained at least one of a list of keywords related to data/code sharing or reproducible research practices. These were all entered in a spreadsheet, and then manually checked to see if a reproducible research object was really shared, or if it was a false positive. The identified articles were then evaluated based on what was shared (e.g., code, data, etc.

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On the open-source landscape of PLOS Computational Biology

Cited by 10 publications

References 4 publications

The Canadian Open Neuroscience Platform—An open science framework for the neuroscience community

The Canadian Open Neuroscience Platform—An open science framework for the neuroscience community

Beyond advertising: New infrastructures for publishing integrated research objects

On the open‐source landscape of Magnetic Resonance in Medicine

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