Amending the literature through version control | Biology Letters

Abstract:  The ideal of self-correction in science is not well served by the current culture and system surrounding amendments to published literature. Here we describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. We report a survey (n = 132) that highlights academics’ dissatisfaction with the status quo and their support for such an alternative approach. Authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and requires nothing but buy-in from the scientific community—a community that is already evolving towards open science frameworks. This would remove a number of frictions that discourage amendments leading to an improved scientific literature and a healthier academic climate.


The Benefits of Accessibility and Open Educational Resources – The Future is Open

“When creating and distributing open educational resources (OERs), it is important to consider accessibility to make sure that everyone can benefit from these resources, including those with disabilities. By designing and developing OERs with accessibility in mind, we can help make sure that everyone has the opportunity to benefit from these resources.

The use of alternative formats is an important aspect of accessibility in OERs. This includes providing text in a format that can be read by assistive technology, such as a screen reader, as well as providing captions for videos and audio content. Additionally, images and other non-textual elements should include alternative text (alt text) descriptions so that users who are visually impaired can understand the content….”

Close to open—Factors that hinder and promote open science in ecology research and education | PLOS ONE

Abstract:  The Open Science (OS) movement is rapidly gaining traction among policy-makers, research funders, scientific journals and individual scientists. Despite these tendencies, the pace of implementing OS throughout the scientific process and across the scientific community remains slow. Thus, a better understanding of the conditions that affect OS engagement, and in particular, of how practitioners learn, use, conduct and share research openly can guide those seeking to implement OS more broadly. We surveyed participants at an OS workshop hosted by the Living Norway Ecological Data Network in 2020 to learn how they perceived OS and its importance in their research, supervision and teaching. Further, we wanted to know what OS practices they had encountered in their education and what they saw as hindering or helping their engagement with OS. The survey contained scaled-response and open-ended questions, allowing for a mixed-methods approach. We obtained survey responses from 60 out of 128 workshop participants (47%). Responses indicated that usage and sharing of open data and code, as well as open access publication, were the most frequent OS practices. Only a minority of respondents reported having encountered OS in their formal education. A majority also viewed OS as less important in their teaching than in their research and supervisory roles. The respondents’ suggestions for what would facilitate greater OS engagement in the future included knowledge, guidelines, and resources, but also social and structural support. These are aspects that could be strengthened by promoting explicit implementation of OS practices in higher education and by nurturing a more inclusive and equitable OS culture. We argue that incorporating OS in teaching and learning of science can yield substantial benefits to the research community, student learning, and ultimately, to the wider societal objectives of science and higher education.


The gaping problem at the heart of scientific research – The Week

“The benefits of open access have been proved beyond doubt….

National science agencies from nations including the UK, Australia, Italy, the United States and Brazil called for publishers to make coronavirus research immediately and freely accessible, which in the most part they did.

But the very need for these groups to call for research to be made available in the middle of a global emergency demonstrates the failure of the current publishing system. Making research immediately free to read, which, when combined with the use of an open publishing licence, is known as open access’ is a hot topic in science.

Global health bodies know how important open research is, especially in times of emergency, which is why they have repeatedly called for research to be made open….

The consequences of lack of access to research can be dire.

In 2015 a group of African researchers claimed that an earlier Ebola outbreak could have been prevented if research on it had been published openly….

As 2023 unfolds, it seems that the benefits of open access have been proved beyond doubt.

The next emergency in front of us, climate change, is much more complex, and there too are calls for open access.

Serious investment in a variety of approaches is essential to ensure a diverse, equitable, open access future.”

Does it pay to pay? A comparison of the benefits of open-access publishing across various sub-fields in Biology | bioRxiv

Abstract:  Authors are often faced with the decision of whether to maximize impact or minimize costs when publishing the results of their research. For example, to potentially improve impact via increased accessibility, many subscription-based journals now offer the option of paying a fee to publish open access (i.e., hybrid journals), but this solution excludes authors who lack the capacity to pay to make their research accessible. Here, we tested if paying to publish open access in a subscriptionbased journal benefited authors by conferring more citations relative to closed access articles. We identified 146,415 articles published in 152 hybrid journals in the field of biology from 2013-2018 to compare the number of citations between various types of open access and closed access articles. In a simple generalized linear model analysis of our full dataset, we found that publishing open access in hybrid journals that offer the option confers an average citation advantage to authors of 17.8 citations compared to closed access articles in similar journals. After taking into account the number of authors, journal impact, year of publication, and subject area, we still found that open access generated significantly more citations than closed access (p < 0.0001). However, results were complex, with exact differences in citation rates among access types impacted by these other variables. This citation advantage based on access type was even similar when comparing open and closed access articles published in the same issue of a journal (p < 0.0001). However, by examining articles where the authors paid an article processing charge, we found that cost itself was not predictive of citation rates (p = 0.14). Based on our findings of access type and other model parameters, we suggest that, in most cases, paying for access does confer a citation advantage. For authors with limited budgets, we recommend pursuing open access alternatives that do not require paying a fee as they still yielded more citations than closed access. For authors who are considering where to submit their next article, we offer additional suggestions on how to balance exposure via citations with publishing costs.


The challenge of preprints for public health The challenge of preprints for public health

“Despite disagreements over whether this form of publication is actually beneficial or not, its advantages and problems present a high degree of convergence among advocates and detractors. On the one hand, preprint is beneficial because it is a quicker way to disseminate scientific content with open access to everyone; on the other hand, the lack of adequate vetting, especially for peer reviews, increases the risk of disseminating bad science and can lead to several problems 2. The dissent lies in considering to what extent possible risks overcome possible benefits (or vice versa).


The argument about this rapid dissemination has strong supporting evidence. A study on preprint publication showed that preprint are published on average 14 months earlier than peer-reviewed journal articles 1. This is expected considering that the time-intensive process of peer reviews and revising manuscripts is totally bypassed. However, in this strength lies its very fragility: how to assure that this shorter process will not compromise the quality of the publication?


ASAPbio (Accelerating Science and Publication in Biology) 3 is a group of biology researchers that promotes preprint publication and has produced a number of studies that attempt to allay concerns about its quality, claiming, for example, that published articles previously submitted to a preprint server did not show relevant changes for its publication 4. Authors from this group have argued that the current approaches to evaluate research and researchers hold back a more widespread adoption of the preprint methodology 5, which would explain its relatively small participation on the general panorama of scientific publication.


Despite claims to the contrary, however, there are examples of poor studies published as preprints, which caused undesirable consequences in public health. Two methodologically flawed studies about a protective effect of tobacco smoking against COVID-19 (one of which has an author with known connections with the tobacco industry), for example, increased the commercialization of tobacco products in France and Iran 6 and a virology study that erroneously stated that the SARS-COV-2 virus had “HIV insertions” fueled conspiracy theories about the former virus being a bioweapon, which lingered on even after the preprint was removed from the server due to its egregious errors 7. Studies have found that much of the public discussion and even policy was indeed driven by what was published in preprints rather than in scientific journals 7,8,9,10, thus, quality issues are a major cause of concern.


On the other hand, similar errors have been observed within traditional publishing; the publication of a poor quality paper with undisclosed conflicts of interest in one of the most prestigious medical journals, The Lancet, which became the trigger for the contemporary wave of anti-vaccine activism, is a major, and regretful, example. Understanding to what extent this problem is likely to occur with or without gatekeeping mechanisms is necessary….”

Clinical Trial Data-sharing Policies Among Journals, Funding Agencies, Foundations, and Other Professional Organizations: A Scoping Review – Journal of Clinical Epidemiology

Abstract:  Objectives

To identify the similarities and differences in data-sharing policies for clinical trial data that are endorsed by biomedical journals, funding agencies, and other professional organizations. Additionally, to determine the beliefs, and opinions regarding data-sharing policies for clinical trials discussed in articles published in biomedical journals.


Study Design

Two searches were conducted, a bibliographic search for published articles that present beliefs, opinions, similarities, and differences regarding policies governing the sharing of clinical trial data. The second search analyzed the gray literature (non-peer-reviewed publications) to identify important data-sharing policies in selected biomedical journals, foundations, funding agencies, and other professional organizations.



A total of 471 articles were included after database search and screening, with 45 from the bibliographic search and 426 from the gray literature search. A total of 424 data-sharing policies were included. Fourteen of the 45 published articles from the bibliographic search (31.1%) discussed only advantages specific to data-sharing policies, 27 (27/45; 60%) discussed both advantages and disadvantages, and 4 (4/45; 8.9%) discussed only disadvantages specific. A total of 216 journals (of 270; 80%) specified a data-sharing policy provided by the journal itself. One hundred industry data-sharing policies were included, and 32 (32%) referenced a data-sharing policy on their website. One hundred and thirty-six (42%) organizations (of 327) specified a data-sharing policy.



We found many similarities listed as advantages to data-sharing and fewer disadvantages were discussed within the literature. Additionally, we found a wide variety of commonalities and differences — such as the lack of standardization between policies, and inadequately addressed details regarding the accessibility of research data — that exist in data-sharing policies endorsed by biomedical journals, funding agencies, and other professional organizations. Our study may not include information on all data sharing policies and our data is limited to the entities’ descriptions of each policy.

Why price transparency in research publishing is a positive step | Hindawi

“In 2019, Hindawi took part in the price transparency framework pilot run by Information Power on behalf of cOAlition S. Three years later and the coalition’s new Journal Comparison Service (JCS) is up and running. Hindawi is proud to be one of the publishers that has contributed data to this service. Taking part has helped us focus on the rigour of our own reporting system and has enabled us to give researchers greater choice when choosing a journal by giving more visibility to our services in our new and publicly available journal reports.

Only a few publishers took part in the pilot and the framework remains untested. It’s not yet clear how useful the JCS will be to the institutions who might want to access the service and use the data, or how the JCS will increase transparency about costs as well as pricing across the publishing industry more generally. In part, this is because it’s seen by some to provide an overly simplistic view of publishing. Compartmentalising publishing services into seven or eight different categories  (see page 20 of the JCS guidance for publishers) inevitably constrains the many different and often overlapping services that publishers provide. In addition, limiting the price breakdown of these services into the percentage that each contributes to a journal’s APC also means that the real costs aren’t visible. There are also pragmatic reasons that make it very difficult for some publishers to collect data consistently, especially for those with large portfolios that operate on multiple platforms or have journal-specific workflows. Finally, fully open-access publishers who don’t have an APC business model can’t take part, even if they want to be more transparent. However, we believe the upsides are large. Hindawi has more than 200 journals in our portfolio and the following outlines a few of the ways we, and we hope those who contribute to and access our journals, are benefiting. Our focus is on the ‘Information Power’ framework for the JCS and on the ‘Journal Quality’ information specifically (columns P-Z in the template spreadsheet). This information relates to data on the journal workflow, especially peer review (such as timings and the no of reviewers involved). We know that there is a long way to go to make all publishing services transparent, but we are learning from our participation in the JCS and will continue to explore ways to improve transparency….”

AAU president: ‘It is time we moved from talking to walking’

“He added that, as the celebration focused on the theme ‘Open Science – Bringing Equity to Research and Publishing’, it was appropriate that discussions were aligned to addressing the bigger picture.

“I strongly believe that it is time we moved from talking to walking and to implementing the various recommendations that we come up with – at our departmental, institutional, and continental levels, year after year. The time to act is, indeed, now,” he said….

Oyewole said, contrary to the fear and apprehension that was held by some against open science when it started, he was confident that many have now been convinced that it is the way to conduct research.

“Indeed, we all had first-hand experience about the benefit of open science when, at the peak of the COVID-19 pandemic, both researchers and publishers in the scholarly sector made efforts to freely make available and in real-time, their COVID-related research, in a bid to help stem the rising tide of infections,” he added….

In addition, he said, the African continental publishing platform, one of the pillars of open science, is open access. The AAU, in collaboration with UbuntuNet Alliance (a regional research education network, or REN) is providing a cloud-based platform to host institutional journals….”

How the OA Switchboard fits into the ecosystem (PART 4/THE FUNDER)

“As an intermediary, the OA Switchboard simplifies the sharing of information between publishers, institutions and funders, thereby reducing the transactional cost for stakeholders, and it provides a safe space for publication metadata. With this, OA Switchboard adds to the tools and data sources currently available to funders.


The two use cases the OA Switchboard supports are also (indirectly) relevant for research funders:

Reporting Made Easy

Matching Publication Costs with Publication Funds…


Sometimes research funders engage directly in the dealings with publishers and covering publication charges, sometimes this is an indirect relationship (e.g. via institutionally managed block grants).


The value of the OA Switchboard for a funder can be one or more of the following:

Direct benefits (e.g. information and data on funded research output)

Indirect benefits (e.g. better implementation of OA policies on a publication-level)

Community benefits (e.g. the ecosystem works better for everyone)…”

Surveying research data-sharing practices in US social sciences: a knowledge infrastructure-inspired conceptual framework | Emerald Insight

Abstract:  Purpose

This study develops a conceptual framework and a series of instruments for capturing researchers’ data-sharing practices in the social sciences, by synergizing the theory of knowledge infrastructure and the theory of remote scientific collaboration.


This paper triangulates the results of three studies of data sharing across the social sciences, with 144 participants in total, and classifies the confusion, “frictions” and opportunities arising from such sharing into four overarching dimensions: data characteristics, technological infrastructure, research culture and individual drivers.


Based on the sample, the findings suggest that the majority of faculty and students in social science research do not share their data because many of them are unaware of the benefits and methods of doing so. Additional findings regarding social scientists’ data-sharing behaviors include: (1) those who do share qualitative data in data repositories are more likely to share their research tools than their raw data; and (2) perceived technical support and extrinsic motivation are both strong predictors of qualitative data sharing (a previously underresearched subtype of social science data sharing).


The study confirms the previously hypothesized nature of “friction” in qualitative data sharing in the social sciences, arising chiefly from the time and labor intensiveness of ensuring data privacy.

Attitudes, behaviours and experiences of authors of COVID-19 preprints

Abstract:  The COVID-19 pandemic caused a rise in preprinting, apparently triggered by the need for open and rapid dissemination of research outputs. We surveyed authors of COVID-19 preprints to learn about their experience of preprinting as well as publishing in a peer-reviewed journal. A key aim was to consider preprints in terms of their effectiveness for authors to receive feedback on their work. We also aimed to compare the impact of feedback on preprints with the impact of comments of editors and reviewers on papers submitted to journals. We observed a high rate of new adopters of preprinting who reported positive intentions regarding preprinting their future work. This allows us to posit that the boost in preprinting may have a structural effect that will last after the pandemic. We also saw a high rate of feedback on preprints but mainly through “closed” channels – directly to the authors. This means that preprinting was a useful way to receive feedback on research, but the value of feedback could be increased further by facilitating and promoting “open” channels for preprint feedback. At the same time, almost a quarter of the preprints that received feedback received comments resembling journal peer review. This shows the potential of preprint feedback to provide valuable detailed comments on research. However, journal peer review resulted in a higher rate of major changes in the papers surveyed, suggesting that the journal peer review process has significant added value compared to preprint feedback.


Open Access Research Outputs Receive More Diverse Citations | Zenodo

Huang, Chun-Kai (Karl), Neylon, Cameron, Montgomery, Lucy, Handcock, Rebecca N., & Wilson, Katie. (2022). Open Access Research Outputs Receive More Diverse Citations (Version 1). Zenodo.

The goal of open access is to allow more people to read and use research outputs. An observed association between highly cited research outputs and open access has been claimed as evidence of increased usage of the research, but this remains controversial. A higher citation count also does not necessarily imply wider usage such as citations by authors from more places. A knowledge gap exists in our understanding of who gets to use open access research outputs and where users are located. Here we address this gap by examining the association between an output’s open access status and the diversity of research outputs that cite it. By analysing large-scale bibliographic data from 2010 to 2019, we found a robust association between open access and increased diversity of citation sources by institutions, countries, subregions, regions, and fields of research, across outputs with both high and medium-low citation counts. Open access through disciplinary or institutional repositories showed a stronger effect than open access via publisher platforms. This study adds a new perspective to our understanding of how citations can be used to explore the effects of open access. It also provides new evidence at global scale of the benefits of open access as a mechanism for widening the use of research and increasing the diversity of the communities that benefit from it.


The relationship between open access publishing and referencing

“49.9% of papers published in 2019 and 2020 are currently available as OA and 51.3% of references from all papers published during those two years are to papers that are currently available as OA. These two percentages are more similar than the percentage of the papers published between 2010 and 2020 that are OA (i.e., 43.3%), suggesting that the OA percentage of the references of papers is not simply a reflection of the access status of the available papers. When we investigate by OA access type, we observe a similar pattern. The exception is gold OA, with a difference of 9.2 percentage points as opposed to 11.9 percentage points. The results suggest that references in recent papers are more open than one would expect, given OA publication practices in the last decade and that they are more open that the publications in which they appear. This demonstrates that the use of OA exceeds the production of it.”