Archives des mots-clés : open science

Low availability of code in ecology: A call for urgent action

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Authors : Antica Culina, Ilona van den Berg, Simon Evans, Alfredo Sánchez-Tójar

Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies.

Our results call for urgent action to increase code availability: only 27% of eligible articles were accompanied by code. In contrast, data were available for 79% of eligible articles, highlighting that code availability is an important limiting factor for computational reproducibility in ecology.

Although the percentage of ecological journals with mandatory or encouraged code-sharing policies has increased considerably, from 15% in 2015 to 75% in 2020, our results show that code-sharing policies are not adhered to by most authors.

We hope these results will encourage journals, institutions, funding agencies, and researchers to address this alarming situation.

URL : Low availability of code in ecology: A call for urgent action

DOI : https://doi.org/10.1371/journal.pbio.3000763

Transparency and open science principles in reporting guidelines in sleep research and chronobiology journals

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Authors : Manuel Spitschan, Marlene H. Schmidt, Christine Blume

Background

“Open science” is an umbrella term describing various aspects of transparent and open science practices. The adoption of practices at different levels of the scientific process (e.g., individual researchers, laboratories, institutions) has been rapidly changing the scientific research landscape in the past years, but their uptake differs from discipline to discipline.

Here, we asked to what extent journals in the field of sleep research and chronobiology encourage or even require following transparent and open science principles in their author guidelines.

Methods

We scored the author guidelines of a comprehensive set of 28 sleep and chronobiology journals, including the major outlets in the field, using the standardised Transparency and Openness (TOP) Factor.

This instrument rates the extent to which journals encourage or require following various aspects of open science, including data citation, data transparency, analysis code transparency, materials transparency, design and analysis guidelines, study pre-registration, analysis plan pre-registration, replication, registered reports, and the use of open science badges.

Results

Across the 28 journals, we find low values on the TOP Factor (median [25th, 75th percentile] 2.5 [1, 3], min. 0, max. 9, out of a total possible score of 28) in sleep research and chronobiology journals.

Conclusions

Our findings suggest an opportunity for sleep research and chronobiology journals to further support the recent developments in transparent and open science by implementing transparency and openness principles in their guidelines and making adherence to them mandatory.

URL : Transparency and open science principles in reporting guidelines in sleep research and chronobiology journals

DOI : https://doi.org/10.12688/wellcomeopenres.16111.1

Open Access uptake by universities worldwide

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Authors : Nicolas Robinson-Garcia​, Rodrigo Costas, Thed N. van Leeuwen

The implementation of policies promoting the adoption of an open science (OS) culture must be accompanied by indicators that allow monitoring the uptake of such policies and their potential effects on research publishing and sharing practices.

This study presents indicators of open access (OA) at the institutional level for universities worldwide. By combining data from Web of Science, Unpaywall and the Leiden Ranking disambiguation of institutions, we track OA coverage of universities’ output for 963 institutions.

This paper presents the methodological challenges, conceptual discrepancies and limitations and discusses further steps needed to move forward the discussion on fostering OA and OS practices and policies.

URL : Open Access uptake by universities worldwide

DOI : https://doi.org/10.7717/peerj.9410

 

Open peer review: promoting transparency in open science

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Authors : Dietmar Wolfram, Peiling Wang, Adam Hembree, Hyoungjoo Park

Open peer review (OPR), where review reports and reviewers’ identities are published alongside the articles, represents one of the last aspects of the open science movement to be widely embraced, although its adoption has been growing since the turn of the century.

This study provides the first comprehensive investigation of OPR adoption, its early adopters and the implementation approaches used. Current bibliographic databases do not systematically index OPR journals, nor do the OPR journals clearly state their policies on open identities and open reports.

Using various methods, we identified 617 OPR journals that published at least one article with open identities or open reports as of 2019 and analyzed their wide-ranging implementations to derive emerging OPR practices.

The findings suggest that: (1) there has been a steady growth in OPR adoption since 2001, when 38 journals initially adopted OPR, with more rapid growth since 2017; (2) OPR adoption is most prevalent in medical and scientific disciplines (79.9%); (3) five publishers are responsible for 81% of the identified OPR journals; (4) early adopter publishers have implemented OPR in different ways, resulting in different levels of transparency.

Across the variations in OPR implementations, two important factors define the degree of transparency: open identities and open reports. Open identities may include reviewer names and affiliation as well as credentials; open reports may include timestamped review histories consisting of referee reports and author rebuttals or a letter from the editor integrating reviewers’ comments.

When and where open reports can be accessed are also important factors indicating the OPR transparency level. Publishers of optional OPR journals should add metric data in their annual status reports.

URL : Open peer review: promoting transparency in open science

DOI : https://doi.org/10.1007/s11192-020-03488-4

University journals. Consolidating institutional repositories in a digital, free, open access publication platform for all scholarly output

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Authors : Saskia Woutersen-Windhouwer, Eva Méndez Rodríguez, Jeroen Sondervan, Frans J. Oort

Funders increasingly mandate researchers to publish their scientific articles in open access and to retain their copyright. Universities all over the world have set up institutional repositories and use repositories for the preservation and dissemination of academic production of their institutions, including scientific articles, reports, datasets, and other research outputs.

However, in general, authors do not find institutional repositories very attractive and accessible as an open access publication platform since repositories and open access are not part of the rewarding system.

We expect that researchers are more likely to publish and deposit their scientific papers in a repository, once they have the appearance, recognition and dissemination of a scientific journal.

That is why we took the initiative to set up a repository based journal ‘University Journals’ in which universities collaborate. The paper will explain the University Journals project and how the involved universities want to facilitate a valuable alternative publication platform that complies with Plan S principles and enables publication and dissemination of all research outcomes.

By establishing University Journals as a publication platform, university libraries are instrumental (and crucial) in achieving the ambitions of Open Science, and universities gain control over the publication process.

URL : University journals. Consolidating institutional repositories in a digital, free, open access publication platform for all scholarly output

DOI : http://doi.org/10.18352/lq.10323

The growth of open access publishing in geochemistry

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Authors : Olivier Pourret, Dasapta Erwin Irawan, Jonathan P. Tennant, Andrew Hursthouse, Eric D. van Hullebusch

In this communication, we look at Open Access (OA) publishing practices in geochemistry.

We examine a list of 56 journals and assess whether Article Processing Charges (APCs) and Journal Impact Factors (JIFs) appear to influence publication or not. More than 40% of articles in 2018-2019 were published OA, and about 70% of that portion in fully OA journals.

These had a mean APC of US$ 900, whereas the remaining were published in hybrid journals with a higher mean APC of more than $US 1,800. A moderate and positive correlation is found between the number of OA articles published in hybrids journals and their JIF, whereas there is a stronger positive relationship between the number of OA articles published in fully OA journals and the APC.

For OA articles published in hybrid journals, it seems that the proportion of OA articles tends to increase in journals with higher JIF.

DOI : https://doi.org/10.1016/j.ringeo.2020.100001

Where Does Open Science Lead Us During a Pandemic? A Public Good Argument to Prioritise Rights in The Open Commons

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Author : Benjamin Capps

During the 2020 COVID-19 pandemic, open science has become central to experimental, public health and clinical responses across the globe.

Open science is described as an open commons, in which a right to science avails all possible scientific data for everyone to access and use.

In this common space, capitalist platforms now provide many essential services and are taking the lead in public health activities.

These neoliberal businesses, however, have a central role in the capture of public goods. This paper argues that the open commons is a community of rights, consisting of people and institutions whose interests mutually support the public good.

If OS is a cornerstone of public health, then reaffirming the public good is its overriding purpose, and unethical platforms ought to be excluded from the commons and its benefits.

DOI : https://doi.org/10.1017/S0963180120000456