Archives des mots-clés : open science

Publishing computational research — A review of infrastructures for reproducible and transparent scholarly communication

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Authors : Markus Konkol, Daniel Nüst, Laura Goulier

Funding agencies increasingly ask applicants to include data and software management plans into proposals. In addition, the author guidelines of scientific journals and conferences more often include a statement on data availability, and some reviewers reject unreproducible submissions.

This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers.

Still, publishing reproducible articles is a demanding task and not achieved simply by providing access to code scripts and data files. Consequently, several projects develop solutions to support the publication of executable analyses alongside articles considering the needs of the aforementioned stakeholders.

The key contribution of this paper is a review of applications addressing the issue of publishing executable computational research results. We compare the approaches across properties relevant for the involved stakeholders, e.g., provided features and deployment options, and also critically discuss trends and limitations.

The review can support publishers to decide which system to integrate into their submission process, editors to recommend tools for researchers, and authors of scientific papers to adhere to reproducibility principles.

URL : https://arxiv.org/abs/2001.00484

Open forensic science

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Authors : Jason M Chin, Gianni Ribeiro, Alicia Rairden

The mainstream sciences are experiencing a revolution of methodology. This revolution was inspired, in part, by the realization that a surprising number of findings in the bioscientific literature could not be replicated or reproduced by independent laboratories.

In response, scientific norms and practices are rapidly moving towards openness. These reforms promise many enhancements to the scientific process, notably improved efficiency and reliability of findings. Changes are also underway in the forensic.

After years of legal-scientific criticism and several reports from peak scientific bodies, efforts are underway to establish the validity of several forensic practices and ensure forensic scientists perform and present their work in a scientifically valid way.

In this article, the authors suggest that open science reforms are distinctively suited to addressing the problems faced by forensic science. Openness comports with legal and criminal justice values, helping ensure expert forensic evidence is more reliable and susceptible to rational evaluation by the trier of fact.

In short, open forensic science allows parties in legal proceedings to understand and assess the strength of the case against them, resulting in fairer outcomes. Moreover, several emerging open science initiatives allow for speedier and more collaborative research.

URL : Open forensic science

DOI : https://doi.org/10.1093/jlb/lsz009

Thought Experiment on the Impact of Plan S on non-Plan S countries and Japan

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Author : Miho Funamori

In September 2018, a consortium of eleven European research funding agencies known as cOAlition S announced “Plan S,” which requires full and immediate Open Access to all research publications stemming from projects funded by the agencies.

The goal of making research output openly available to all has been generally welcomed; however, the strict requirements of Plan S, which take effect on January 1, 2020, have drawn criticisms from various stakeholders. Researchers from affected countries considered it a violation of their academic freedom, as they will be forced to publish only in conforming journals.

Publishers, especially those publishing high profile journals, claim that it will be impossible to sustain their business if forced to convert to Open Access journals and to rely solely on article processing charges. Institutions operating their own Open Access platforms or Open Access repositories view the requirements as well-intended but difficult to meet.

Despite the turmoil, little has been heard from non-Plan S countries, especially from non-English speaking countries outside Europe. There have been scarcely any comments or analyses relating to the impact of Plan S on these non-Plan S countries.

This paper aims to fill the gap with a thought experiment on the impact of Plan S requirements on various stakeholders in these non-Plan S countries. The analysis concludes that non-Plan S countries are indirectly affected by Plan S by being forced to adapt to the world standard that Plan S sets forth.

As many non-Plan S countries lack support for this transition from their respective funding agencies, they will be seriously disadvantaged to adapt to the new standards. The article processing charge for publishing in Open Access journals and the strict requirements for Open Access platforms could suppress research output from non-Plan S countries and reduce their research competitiveness.

Local publishers, whose financial position in many cases is already precarious, may be forced to shut down or merge with larger commercial publishers. As scholarly communication is globally interconnected, the author argues the need to consider the impact of Plan S on non-Plan S countries and explore alternative ways for realizing full and immediate OA by learning from local practices.

This analysis uses Japan as an exemplar of non-Plan S countries. Its distinctiveness is specified where applicable.

URL : https://www.semanticscholar.org/paper/Thought-Experiment-on-the-Impact-of-Plan-S-on-S-and-Funamori/f5c702b7f98ceec54f9409a693802c9c0a971ef2

Transparent, Reproducible, and Open Science Practices of Published Literature in Dermatology Journals: Cross-Sectional Analysis

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Authors : J Michael Anderson, Andrew Niemann, Austin L Johnson, Courtney Cook, Daniel Tritz, Matt Vassar

Background

Reproducible research is a foundational component for scientific advancements, yet little is known regarding the extent of reproducible research within the dermatology literature.

Objective

This study aimed to determine the quality and transparency of the literature in dermatology journals by evaluating for the presence of 8 indicators of reproducible and transparent research practices.

Methods

By implementing a cross-sectional study design, we conducted an advanced search of publications in dermatology journals from the National Library of Medicine catalog. Our search included articles published between January 1, 2014, and December 31, 2018.

After generating a list of eligible dermatology publications, we then searched for full text PDF versions by using Open Access Button, Google Scholar, and PubMed. Publications were analyzed for 8 indicators of reproducibility and transparency—availability of materials, data, analysis scripts, protocol, preregistration, conflict of interest statement, funding statement, and open access—using a pilot-tested Google Form.

Results

After exclusion, 127 studies with empirical data were included in our analysis. Certain indicators were more poorly reported than others. We found that most publications (113, 88.9%) did not provide unmodified, raw data used to make computations, 124 (97.6%) failed to make the complete protocol available, and 126 (99.2%) did not include step-by-step analysis scripts.

Conclusions

Our sample of studies published in dermatology journals do not appear to include sufficient detail to be accurately and successfully reproduced in their entirety. Solutions to increase the quality, reproducibility, and transparency of dermatology research are warranted.

More robust reporting of key methodological details, open data sharing, and stricter standards journals impose on authors regarding disclosure of study materials might help to better the climate of reproducible research in dermatology.

URL : Transparent, Reproducible, and Open Science Practices of Published Literature in Dermatology Journals: Cross-Sectional Analysis

DOI : https://doi.org/10.2196/16078

Open Science in the Humanities, or: Open Humanities?

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Author : Marcel Knöchelmann

Open science refers to both the practices and norms of more open and transparent communication and research in scientific disciplines and the discourse on these practices and norms.

There is no such discourse dedicated to the humanities. Though the humanities appear to be less coherent as a cluster of scholarship than the sciences are, they do share unique characteristics which lead to distinct scholarly communication and research practices.

A discourse on making these practices more open and transparent needs to take account of these characteristics. The prevalent scientific perspective in the discourse on more open practices does not do so, which confirms that the discourse’s name, open science, indeed excludes the humanities so that talking about open science in the humanities is incoherent.

In this paper, I argue that there needs to be a dedicated discourse for more open research and communication practices in the humanities, one that integrates several elements currently fragmented into smaller, unconnected discourses (such as on open access, preprints, or peer review).

I discuss three essential elements of open science—preprints, open peer review practices, and liberal open licences—in the realm of the humanities to demonstrate why a dedicated open humanities discourse is required.

URL : Open Science in the Humanities, or: Open Humanities?

DOI : https://doi.org/10.3390/publications7040065

Does the use of open, non-anonymous peer review in scholarly publishing introduce bias? Evidence from the F1000 post-publication open peer review publishing model

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Authors : Mike Thelwall, Verena Weigert, Liz Allen, Zena Nyakoojo, Eleanor-Rose Papas

This study examines whether there is any evidence of bias in two areas of common critique of open, non-anonymous peer review – and used in the post-publication, peer review system operated by the open-access scholarly publishing platform F1000Research.

First, is there evidence of bias where a reviewer based in a specific country assesses the work of an author also based in the same country? Second, are reviewers influenced by being able to see the comments and know the origins of previous reviewer?

Scrutinising the open peer review comments published on F1000Research, we assess the extent of two frequently cited potential influences on reviewers that may be the result of the transparency offered by a fully attributable, open peer review publishing model: the national affiliations of authors and reviewers, and the ability of reviewers to view previously-published reviewer reports before submitting their own.

The effects of these potential influences were investigated for all first versions of articles published by 8 July 2019 to F1000Research. In 16 out of the 20 countries with the most articles, there was a tendency for reviewers based in the same country to give a more positive review.

The difference was statistically significant in one. Only 3 countries had the reverse tendency. Second, there is no evidence of a conformity bias. When reviewers mentioned a previous review in their peer review report, they were not more likely to give the same overall judgement.

Although reviewers who had longer to potentially read a previously published reviewer reports were slightly less likely to agree with previous reviewer judgements, this could be due to these articles being difficult to judge rather than deliberate non-conformity.

URL : https://arxiv.org/abs/1911.03379

Open Systems Pharmacology community – an open access, open source, open science approach to modeling and simulation in pharmaceutical sciences

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Authors : Jörg Lippert, Rolf Burghaus, Andrea Edginton, Sebastian Frechen, Mats Karlsson, Andreas Kovar, Thorsten Lehr, Peter Milligan, Valerie Nock, Sergej Ramusovic, Matthew Riggs, Stephan Schaller, Jan Schlender, Stephan Schmidt, Michaël Sevestre, Erik Sjögren, Juri Solodenko, Alexander Staab, Donato Teutonico

Systems Pharmacology integrates structural biological and pharmacological knowledge and experimental data enabling dissection of organism and drug properties and providing excellent predictivity.

The development of systems pharmacology models is a significant task requiring massive amounts of background information beyond individual trial data. Qualification of models needs repetitive demonstration of successful predictions.

Open Systems Pharmacology is a community that develops, qualifies and shares professional open source software tools and models in a collaborative open science way.

DOI : https://doi.org/10.1002/psp4.12473