Open Access Week 2022 – The evolution of Open Access for journal articles at University of Reading

Posted on October 24, 2022 by Karen Rowlett

Open Access – part of the University’s commitment to Open Research

A tray of small iced cupcakes with the open access logo in green or gold on top At the University of Reading, we’ve been encouraging our researchers to make their work Open Access for many years either by publishing their outputs as Gold Open Access or by using the University’s CentAUR repository to make them available via the Green Open Access route. This is part of the University’s commitment to Open Research. To date, the emphasis has been on making journal articles Open Access rather than books and book chapters, but this is likely to change as funders’ requirements also evolve to include a wider range of research outputs in their Open Access mandates.

For outputs published in journals, improved access to funding for Gold Open Access, both from funders such as UKRI and from the University’s own Gold Open Access Fund, and the growth of Transformative Agreements with publishers has led to an increase in the number of items that are published Open Access. This means that a large percentage of the University of Reading’s outputs published as journal articles are now openly accessible, discoverable and free to read, reuse and repurpose by users all over the world.

As part of our Open Access Week activities, this post looks at how Open Access for journal articles has evolved at University of Reading over the last 10 years.

How have Open Access publishing practices for journal articles changed over the last 10 years?

The Scopus database was used to find journal outputs where at least one of the authors declared a University of Reading affiliation. The Unpaywall simple query tool was then used to find out whether the articles were published as Gold Open Access or became open through the Green Open Access route via CentAUR or another institutional repository.

Bar chart showing the breakdown of Gold, hybrid and Green open access publications at University of Reading 2013-2022

The graph shows the breakdown of the different types of access to articles published from 2013 to the end of September 2022. In 2013, when the Research Councils UK funder mandate for Open Access began, only a small proportion of articles authored by University of Reading authors were published as Gold Open Access, 7.2% as hybrid Gold Open Access and 10% in pure Gold Open Access journals. In the same year, the University of Reading also developed its own policy on Open Access for research articles, encouraging authors to choose the Open Access route if they were able to do so. Authors began to be more aware of Open Access as a movement and something that they should think about when publishing their research outputs. This cultural shift also encompassed the use of institutional repositories to archive author-accepted versions of articles. The Green Open Access route was also not as well developed in 2013 as it is now, with only 22% of outputs available as author-accepted versions of published manuscripts. As an indication of the state of Open Access at this time, the data show that around 50% of the outputs published in 2013 may still be behind publisher paywalls (the black segment in the bars of the graph).

As the requirement for funded authors to publish Open Access became more established and the Open Access requirement for the REF2021 was imposed on UK University-based researchers, the pattern of Open Access publishing began to change. In 2016, the University of Reading also established a Gold Open Access fund that allowed unfunded staff and students to publish their work in pure Gold Open Access journals or hybrid journals with a relatively low article processing charge (APC). The effect of these measures can be seen in the chart above. By 2017, over 40% of journal outputs were published as Gold Open Access, split roughly 50:50 between pure Gold and hybrid journals. The proportion of outputs available via the Green Open Access route also grew to 37%. Overall, under 13% of total outputs for 2017 are currently behind publisher paywalls and available to subscribers only.

Transformative Agreements drive Gold Open Access in hybrid journals

Since 2020 there has been a growth in Transformative Agreements with publishers. These agreements have the aim of transforming publishers’ business models from subscription-based ones, where libraries pay to access content, to an ‘author pays’ model whereby journals are funded by the APCs paid to publish Open Access. The University of Reading has signed up for several of these JISC-negotiated national agreements and they are changing the pattern of Open Access publishing across the University, increasing the number of Gold Open Access outputs in hybrid journals. The deals include some of the major publishers, for example Springer, Wiley, Elsevier and Taylor and Francis, but also some smaller and Learned Society publishers such as Portland Press and Microbiology Society. Since 2019, the percentage of outputs published as Gold Open Access in hybrid journals has increased from 15% of total outputs to over 31% for the first nine months of 2022.

The continuing importance of Green Open Access

Green Open Access Logo of an open padlock

Despite the increase in the percentage of University of Reading’s outputs being published as pure Gold
or hybrid Gold Open Access, there is still a significant role for the Green Open Access route. At University of Reading, the Green Open Access route is particularly important for authors who are publishing in journals that charge a very high APC that cannot be funded from the University’s budgets. All researchers are able to fulfil funder’s mandates and increase the reach of their research by making the author-accepted version of their work available.  For most years, over 30% of articles are available via an author-accepted version of the article hosted in the institutional repository. The impact of publisher embargoes on the availability of these versions can be seen in the chart; for 2022 the proportion of articles that are available to journal subscribers only is over 22%. However, within 6 to 12 months, as publisher embargoes expire, more of this content will become available through the Green Open Access route. The new 2022 UKRI policy on Open Access requires that author-accepted versions in repositories are now made available to users without embargoes at the same time as the publisher’s version of record is released. This new requirement for funded authors should also reduce the time lag on the availability of items in the CentAUR repository.

Will all University of Reading’s journal articles be published Open Access in the future?

open Access LogoThe proportion of closed articles that are available to journal subscribers only is usually around 10% of the total articles published by University of Reading researchers each year. There may be several reasons that this content is not made available Open Access in some form. The journal may not have any mechanism for publishing Open Access or have a self-archiving policy in place, the researcher may not be bound by any Open Access mandates and so choose not to publish openly, the researcher may not be able to deposit the author-accepted manuscript in an appropriate repository or (despite University policy) the researcher may simply forget to deposit their manuscript.

It is possible that more publishers will negotiate Transformative Agreements over the next few years  and this could enable more of University of Reading research to be published Open Access. New deals would involve a large number of smaller publishers and it may be difficult to justify the time and money needed to set up lots of individual arrangements. As the aim of Transformative Agreements is to change the publishing model, it is also expected that many journals should flip from the hybrid model to pure Gold Open Access over the coming years. However, the cost of any further agreements or paying APCs as authors publish may well be prohibitive. A recent estimate of the cost of making the remainder of Reading’s journal outputs open access gave a figure of over £2 million per year in addition to the current six-figure spends from the UKRI block grant and the University Gold Open Access Fund.

How is Open Access funding managed at University of Reading?Screenshot of the University of Reading's Open Access Libguide

You can find out more about how researchers at University of Reading can publish their outputs Open Access by visiting our Open Access Libguide.

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Open Research Forum 18th May 2022

Posted on May 30, 2022 by chloebolsover

The recording for the Open Research Forum is now available to watch via Stream (University of Reading members only):

On 18th May, we held our most recent Open Research Forum on open peer review. We were delighted to be joined by a range of speakers who contributed fascinating and thought-provoking perspectives and insights into the world of open peer review.

We kicked off our session with a quick poll to capture the initial thoughts of our attendees. We asked whether they were in favour of open peer review. The results of this are shown below:

We were interested to see whether people’s attitudes would change during the session.

The Future of Peer Review: Four Schools of Thought

Presented by Stephen Pinfield, Professor of Information Services Management/Associate Director of the Research on Research Institute, University of Sheffield

Stephen Pinfield- Slides

The Research on Research Institute (RoRI) is an international consortium of researchers, research funders, and other key stakeholders. It aims to co-design and co-produce research projects together with stakeholders in the research system, providing evidence-informed insights that can be translated into practical solutions.

A recent RoRI report on the future of peer review  identified open and transparent peer review as an area of significant innovation. It identified four schools of thought regarding peer review which offer different perspectives and highlight aspects of peer review which are problematic.

The Four Schools are:

  1. Quality and Reproducibility
  2. Democracy and Transparency
  3. Equity and Inclusion
  4. Efficiency and Incentives

Whilst the Schools complement each other in some areas, there are significant tensions between them. Conversations between schools are suggested to provide creative ways to resolve these. There needs to be more heterogeneity in the peer review system, allowing for co-existence of different forms of review. The publishing peer review system needs to be aligned with broader developments in the research system. Finally, a requirement was identified for the research on research community to develop a rigorous evidence-informed understanding of the peer review system.

Open Peer Review at F1000Research

Presented by Eleanor-Rose Papas, Editorial Operations Manager and Peer Review Manager, F1000Research

F1000 Research- Slides

F1000Research and associated publishing platforms, including Wellcome Open Research, Gates Open Research, and Open Research Europe are platforms that aim to change the way science is communicated through the open and transparent publication of articles, associated data and peer review reports.

Since 2012, F1000Research have offered an open and transparent review model. The basis of this is that articles are published first before being subjected to open peer review. This has the benefit of  increasing dissemination, with authors able to revise articles according to the feedback they receive. All peer review reports are available to read, with reviewers acknowledged on the report. This means that the reviews can become part of academic literature, so are assigned DOIs and are data minable.

The review process is formal and invited, with reviewers provided with a code of conduct that they must adhere to. Therefore, F1000Research can preserve integrity, ensuring that readers can trust the peer review process.

eLife’s mission and the PRC model

Presented by Ailís O’Carroll, eLife Community Manager

eLife- Slides

eLife is a not for profit peer-reviewed open access scientific journal for the biomedical and life sciences. Its mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours.

eLife’s ‘publish, review, curate’ model involves researchers uploading a preprint to an appropriate server. The preprint will be subjected to consultative peer review with an evaluation summary provided. Public Reviews are posted alongside the preprint, with a response from the authors if they choose to produce one. Authors then have the option to transfer to another journal or to revise and publish with eLife. Public Reviews are also offered with a wider public audience in mind.

For this new system to work, eLife emphasizes the need for the research community to become involved. They work alongside PREReview, Sciety and eLIFE Community Ambassadors to improve the peer review process.

Open Research Forum on open peer-review- A personal account

Presented by Rémi Tailleux, Associate Professor of Physical Oceanography, Department of Meteorology, Open Research Champion for MPCS

Remi Tailleux- Slides

Remi discussed his experiences of open peer review as both an author and a reviewer for Copernicus journals and Nature Communications.

Remi highlighted the positives of open peer review. The paper is immediately available and has a DOI, meaning that it can be cited even if it has not yet been accepted for publication. The open discussion tends to discourage unprofessional reviews. Authors are also able to receive a wider range of comments, as anybody can comment on papers. This can help authors to receive greater feedback, resulting in a better paper.

Despite this, Remi discussed how in his experience, open peer review can lead to superficial responses. Reviewers and authors must take care in monitoring the responses they provide, as they will remain public forever. Traditional models of publishing enable editors to moderate exchanges between authors and reviewers. Editors in some models only intervene at the end of the open discussion, playing less of a filtering role than in the standard model.

Open Peer Review: A Journal Editor’s Perspective

Presented by Angelique Chettiparamb, Professor of Urban Planning and Governance, Henley Business School (Real Estate and Planning), Managing Editor: Planning Theory

Angelique Chettiparamb- Slides

Planning Theory is a high-ranking journal in spatial planning. The editorial board decided to join the Web of Science Transparent Peer Review (TPR) Program through their publishers-Sage Publishing-on a pilot basis. The board decided to review the initiative after one year of implementation and then evaluate whether the journal should continue with the program.

Authors could choose to opt in for TPR at submission. Reviewers had to opt in for the process, as opting out would have meant that the entire content for the peer review process of the article would not be published. However, reviewers could preserve their anonymity, as they had a choice to do so.

Since TPR came into operation on 1st April, statistics from Sage Track show:

  • 6 new submissions- all authors have opted in
  • 2 first revision submission- authors have opted in
  • 1 second revision submission- author has opted out of TPR
  • All reviewers have opted out of sharing their identity.

There was enthusiastic support from some participants, as TPR aligns with principles of openness and transparency. However, there were questions raised of whether TPR improved reviews in terms of providing constructive and substantial feedback. Some members of the editorial board were unsure what TPR was aiming to solve. There were concerns surrounding post-publication exercise of power, authors possibly refusing to review, and reviewers writing for an audience rather than producing a substantive review. However, open peer review acknowledges the contribution that reviewers make to a manuscript. This was suggested as challenging authorial ‘glory’ since publishing the review process shows how reviewers’ inputs can shape the final published output.

Panel Discussion/Q&A

We invited our speakers to contribute towards a panel discussion on open peer review. The discussion first focused on the unintended consequences of the process such as exercises of power and the quality of reviews.

The panel also reflected on changes or interventions within the wider ecosystem that would encourage a greater adoption of open peer review models. This included a spectrum of balancing concerns and incentives, such as enabling authors to preserve their anonymity and promoting the contribution reviewers can make to the publishing process. Thus, incentive systems need to be aligned to facilitate the open peer review process. Currently, review is a voluntary contribution from researchers as it is the expected activity of the academic community.

To inspire a cultural shift, aspects such as paying reviewers were touched on. However, this does not resolve wider issues, as there is a need for institutions to recognise peer review more as a scholarly output. Training researchers how to write good peer reviews could contribute towards this. Training sessions and structured mentoring programmes could help, as well as early career researchers receiving guidance from their supervisors.

After hearing from our speakers, this was the end poll:

It was fascinating to see how the talks influenced our audience’s attitudes towards open peer review.

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Open Research Forum 9th March 2022

Posted on March 16, 2022 by rogandixon

The recording for the Open Research Forum on Wednesday 9th March 2022 is now available to watch via Stream (University of Reading members only):

Ersilia, a hub of Open Source AI/ML models for infectious and neglected diseases

Ersilia – Slideshow

Presented by Gemma Turon, a co-founder of Ersilia, and an appointee to a Software Sustainability Institute Fellowship.

The Ersilia Open Source Initiative is a non-profit organisation which provides artificial intelligence (AI) and machine learning (ML) models to support health research and strengthen research capacities in Low and Middle Income Countries.

While low and middle income countries suffer the greatest impact from infectious diseases, they produce less than 10% of the scholarly output in this field, leading to a significant western bias in biomedical research, and drug development.

Ersilia seeks to redress this imbalance by providing reusable Open Source AL/ML models, building community tools and governance models, and improving the documentation and accessibility of resources.

One Image: Exploring Open Source Digital Imaging for Research

One Image 2022 – Slideshow

Presented by Eva Kevei, Associate Professor in Biomedical Sciences, and a member of the Open Hardware community at the University of Reading.

The One Image project, funded for 12 months by the University of Reading, was launched in January 2022 with the purpose of designing, building and testing imaging instruments for a variety of scientific applications and disciplines using Open Hardware design principles.

Money for research is always limited, even in the developed world, and existing, often bespoke, imaging equipment can be prohibitively expensive. One Image’s output will be cheap, accessible and customisable, with design files, code and documentation being made available under open licences. Open hardware makes experimental research more accessible at lower cost and has a role to play in correcting the existing bias in research towards higher income countries.

Annotating for Transparent Inquiry in qualitative research: making archival documents accessible

Annotating for Transparent Inquiry – Slideshow

Presented by Joseph O’Mahoney, Lecturer, Politics, Economics and International Relations, and Open Research Champion at the University of Reading

The Annotation for Transparent Inquiry Initiative developed a tool for qualitative researchers that enables them to create enhanced annotations in articles and link to digital copies of archival sources in trusted repositories.

One problem in archives-based research is the accessibility of primary resources: often the sources only exist as a single, physical copy which can only be accessed in person with no digital surrogates, which raises questions about the authenticity and credibility of quotations and citations in scholarly output.

The Annotation for Transparent Inquiry augments papers with an interactive overlay which provides extended metadata, annotated notes and facsimiles of the document, providing a much needed context for the source material.

Joseph was involved in the project to pilot this valuable tool and has published a practical guide based on his experience. You can find more information in his Open Research Case Study.

Open Research Champions business / updates

Open Research Survey

Marcello De Maria and Kirsty Hodgson presented the findings of the 2021 Open Research Survey to a meeting of the Committee on Open Research and Research Integrity on 8th March. It was extremely well received and generated a great deal of discussion at the Committee, particularly in respect of the gaps in perceptions and requirements that were observed across different demographics represented in the survey.

 Electronic Lab notebooks

A question was raised regarding the employment of electronic lab notebooks. Christiana Bercea discussed her pilot project using OneNote, which was recently undertaken in the School of Chemistry, Food and Pharmacy. This pilot was discussed at the 7th July 2021 Forum. It has proved successful, with a number of participating lab groups committed to continued use of OneNote.

 Thank you 2021 Champions!

Your work this year has been invaluable, we are extremely grateful to everybody for their contributions over the last year under what have not been the easiest of circumstances.

 2022 Research Champions Applications

While the Open Research Forum took place before the closing date for applications, we would like to thank everyone who showed interest and submitted applications.

 The Next Open Research Forum

Date TBC

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CentAUR stats for January 2022

Posted on February 14, 2022 by Karen Rowlett

For 2022 the CentAUR statistics infographics are using the new COUNTER-compliant data available from IRUS. IRUS collects raw usage data from institutional repositories such as CentAUR and processes these data into COUNTER-conformant usage statistics. This provides repositories with comparable, authoritative, standards-based usage data.

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CentAUR in 2021

Posted on January 18, 2022 by Karen Rowlett

Our institutional repository, CentAUR, hosts research outputs from the University of Reading. Users from around the world are able to access large numbers of full text articles, books, book chapters, theses etc via a combination of green open access (authors’ accepted manuscripts) and items that were published as gold open access (versions of record as on the publishers’ sites). Here’s a quick snapshot of what was added in 2021 and how users interacted with our content.

New items

In 2021, 2,289 items were added to CentAUR, slightly down from the 2020 figure of 2,942. The number of deposits does vary year to year and the slight drop in 2021 might be due to a lull in publishing activity after the submission of the UK REF2021 possibly combined with the impact of staff changes and the training of new repository staff.

Deposits to the repository in 2021 included 1,774 journal articles (78%), 204 book chapters (9%), 59 books (3%) and 137 theses (6%). Of the journal articles, over 60% had a full text publicly available to download reflecting the adoption of gold open access across the University and the expansion of the read and publish deals available from publishers. The repository now contains over 51,400 items.

It is always interesting to look at which new items added to the repository are accessed the most. For 2021, it was a PhD thesis that took the crown of being the most downloaded item added in the same year. Dr Jo Hamilton’s thesis, entitled “Emotional Methodologies for Climate Change Engagement: towards an understanding of emotion in Civil Society Organisation (CSO)-public engagements in the UK” was downloaded almost 700 times after being added to the repository in January 2021. The thesis was accessed by researchers in 49 different countries/territories with most of the downloads originating from the USA (45%), UK (19%) and Canada (7%). Other top newcomers included: “The “other” time: a review of the subjective experience of time in organizations“ by Shipp and Jansen, “Music as a coevolved system for social bonding” by Savage et al., “Glove industry spikes during Covid-19 pandemic: a case study of Comfort Gloves Berhad (CGB)” by Dr Mandy Mok from our Malaysia campus and “Fifteen years of customer engagement research: A bibliometric and network analysis” by Hollebeek et al.

Downloads from CentAUR

For 2021, total downloads of repository items were 734,118, up from 566,147 in 2020. As the number of items available for download grows each year, you would expect the total downloads to grow year on year. However, looking at the number of downloads per downloaded item, this grew from 42.3  in 2020 to 49.5  in 2021.  In 2021, 14,831 items were downloaded more than once, 8,321 items were downloaded more than 10 times and 1,613 items were downloaded more than 100 times. There were 53 items, including 44 journal articles, that were downloaded more than 1,000 times.

Using IRUS R5 COUNTER-compliant data, it is possible to track where in the world the download requests originated. For 2021, users from 229 different countries/territories downloaded items from the repository. The highest number of downloads were from the UK (23.4%), followed by the USA (15.4%), China (5.1%), India (4.2%), Germany (3.8%) and Australia (2.7%). Looking at the data on the continent level,  45.1% of downloads were from Europe, 25.2% from Asia, 18.5% from North America, 5.5% from Africa, 3.2% from Oceania and 1.9% from South America.

Notable items

There’s one paper in the repository that is consistently downloaded more than others. Professor Will Hughes’ article on “What makes a good research paper“, originally published in 2001 and added to the repository in 2010, is regularly downloaded between 500 and 800 times a month, in tune with the academic year in the Northern hemisphere.

In 2021, it was downloaded over 9,500 times. In 2021, most downloads of this article were from users in the Philippines (28%), followed by users in the USA (16%) and the UK (11%).

Another notable item with high downloads was Professor Emily West and Dr Rose Knight’s article “Mothers’ milk: slavery, wet-nursing, and black and white women in the Antebellum“. This item, added to CentAUR in 2017, has now accrued over 46,500 downloads, including over 9,000 in 2021.

Some of the items with high downloads in 2021 were related to the COVID-19 pandemic. For example, papers on air filtration technology for healthy building ventilation, recruiting personnel successfully via online interviews, Vitamin D and COVID, and on barriers to implementing e-learning all showed high downloads during 2020 and 2021.

Visitors to CentAUR

We use Google Analytics to track visits to the CentAUR repository. For 2021, the total number of visitors grew from 283,624 in 2020 to 878,148, an increase of over 200% year on year. The number of sessions and page views also grew substantially to 947,949 and 1,271,817, respectively. According to Google Analytics, almost 80% of the traffic to CentAUR was from China but visits were recorded from over 220 territories/countries.

Data sources

To compile the statistics on CentAUR we used the JISC IRUS service, IRstats available in CentAUR and Google Analytics.

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Open Research Forum 15th December 2021

Posted on December 16, 2021 by fredbreese

Thank you to all who attended the Open Research Forum meeting on Wednesday 15th of December. A recording of the meeting is available to view on Stream if you missed it on the day (University of Reading members only).

We heard updates on the fantastic work of our Open Research Champions, including the Open Research Survey which received responses from over 400 staff and students across the University.

Event Announcement: Open Hardware Hackathon

7th January. Book your place here

Join the Open Hardware Hackathon and make a digital microscope! Teams will build a sophisticated microscope using Open Source designs and low-cost parts (all equipment provided). There will be prizes. This is an opportunity to learn about open hardware and get involved with the emerging UoR maker community. All are welcome to join the UoR Open Lab Team. Contact Al Edwards for enquiries.

Preliminary findings of the Open Research Survey

Auvikki De Boon, Marcello De Maria, Kirsty Hodgson, Sophie Read and Brendan Williams

The Open Research Survey has been an initiative carried out by a group of Open Research Champions this Autumn, with a view to gaining a better understanding of the current Open Research landscape at Reading. The survey was designed to give information about current knowledge and use of Open Research practices and to reveal needs for training and development. It received a broad uptake with over 400 staff and students responding with 70% actively involved in research. There was broad coverage with responses received from all Schools in the University except one.

Preliminary analysis of the data has begun drawing out key concepts associated with Open Research. When asked “What does the term ‘Open Research’ mean to you”, research accuracy and transparency were the most commonly mentioned. Responses were also coded for positive and negative statements and notably only 5 negative responses were received. Awareness of Open Research was not uniform among the sample, with a quarter of respondents indicating they were either unaware or had low levels of understanding of Open Research.

The survey also posed questions around factors which encourage and discourage engagement with Open Research practices. Potential for broader dissemination and accessibility of research were reported most frequently as encouraging engagement. In contrast the perception that Open Research wasn’t relevant until after publication was a key discouraging factor. The issues of the cost and time commitment of Open Research featured in both positive and negative answers, a finding it will be interesting to see explored in the full analysis. Finally, the survey asked how Open Research practices are currently being used. A lack of information, training resources and dedicated funding were highlighted as key challenges.

Following presentation of the survey results, discussion centred on the survey’s findings of a gender difference in the perception of Open Research, with men found to have a more positive perception compared with women. It was suggested that the view of Open Research as introducing administrative burdens for researchers could be off-putting in an environment where this workload is already carried disproportionately by women.

The speakers would like to extend thanks to all who promoted the survey and helped achieve such a wide reach across the University. We all look forward to the sharing of the full findings in the new year. Champions will report findings from the survey and recommendations to the Committee on Open Research and Research Integrity in March.

Oxford | Berlin Summer School on Open Research

Auvikki de Boon, Sophie Read and Zoë Dennehy

A group of Open Research Champions reported on this year’s Oxford | Berlin Summer School on Open Research, which provided a free four-day programme of classes on transparent and reproducible research practice for early career researchers.

The course was held online this year and split between lectures and workshops, with an online community facilitated through a slack channel. Lectures dealt with 4 overarching themes: the importance of Open Research; methods and statistics; the use of coding; and Open Research Tools. Workshops then returned to these ideas in more detail. You can access slides for these sessions, along with some recordings, through the links below.

Importance of Open Research

  1. Setting the scene
  2. Ethics and integrity
  3. Reducing waste/increasing value

Keynote: Research Culture – a job for everyone

Methods and statistics

Lectures

  1. What to expect from replications
  2. How bias leads to entrenched errors

Workshops

  1. Data visualisation
  2. Safeguarding research integrity

Coding

Lectures

  1. Writing Readable code
  2. Free code and open data

Workshops

  1. Introduction to R and reproducible workflows
  2. Simulations of data in R
  3. Reproducible manuscripts in Rmarkdown
  4. Version control with Git (personal workflow or collaborative workflow) 

Open Research tools

Lectures

  1. FAIR data for humans and machines
  2. Open Access, preprints and scholarly publishing models
  3. Using meta-research to improve science

Workshops

  1. Creative commons
  2. Introduction to planning Research Data Management
  3. Planning writing and dissemination
  4. Preregistration
  5. Systemic reviews and meta analyses

All three speakers highly recommend the Summer School and are happy to be contacted if you are planning on applying next year. In particular they highlighted how the summer school showed that Open Research practices can be adopted in small steps. Attempting to apply a whole suite of new approaches at once can be overwhelming. Individually however, practices such as writing reproducible code and tools such as Rmarkdown are designed to make your life easier.

Applying for the school is a straightforward process, only requiring a 300 word statement of motivation, describing how the knowledge and skills acquired will be used for ongoing research. A statement of support from a supervisor or PI is also required. Financial support is available from the Summer School itself and also through the university’s own Open Research Fund.

Electronic lab notebook pilot study: an update

Cristiana Bercea has been leading a pilot study in the school Chemistry, Food and Pharmacy, encouraging the move from paper based lab notebooks to OneNote. The electronic notebooks are used to record protocols, raw data and for data analysis. So far there have been 7 participants in the school, who have provided feedback on a number of different electronic notebook software platforms. OneNote has been well received with 3 labs committing to switch permanently. Cristiana is currently planning on expanding the pilot to other schools at the University beginning the school of Biological Sciences.

Open Research practices in meteorology – panel discussion

Gabriel Perez is organising a panel discussion on Open Research in Meteorology as part of the department’s lunchtime seminar series on the 15th of February. There are plans for panels focusing on the needs of ECRs and for more senior staff. Gabriel hopes the panel discussions will initiate a department wide conversation about the impact Open Research can have on meteorology and climate science. This will help identify existing barriers to adoption and lay out ideas on how to increase uptake of open research practices.

There are a number of factors specific to Open Research in Meteorology which will be discussed during the panels. These include projects such as CMIP (Climate Model Intercomparison Project) which are already established drivers of reproducibility. But there are other subject-specific practices which can be barriers to reproducibility and the democratization of research, for example the continued use of obscure and poorly maintained codebases. In addition large data storage and data processing requirements can be barriers to researchers, particularly those without access to resources such as JASMIN – researchers in the Global south, for example. Some Open Research tools such as RMarkdown or jupyter also don’t meet the complex needs of meteorology research.

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Open Research Fund

Posted on December 2, 2021 by Robert Darby
Do you need funds to help you deliver an Open Research activity or project, or to support Open Research learning and development?

The Open Research Fund provides small amounts of money up to £500 to researchers, members of staff connected with research and research students (either individually or as members of a team) to enable them to deliver an Open Research activity, project or output, or to support Open Research learning and development.

Any member of University staff active in research or a research-related role, research student, or team, can apply to the Fund at any time. The Fund can be used:

  • to enable delivery of an Open Research activity or project, such as organising a workshop or developing an open resource;
  • to cover the cost of archiving/enabling access to data or other digital resources;
  • to attend an Open Research-related event or training course.

Applications must be submitted using the online application form. If you are interested in applying, please read the OpenResearchFund-Call (PDF) for full details.

If you have any questions or would like an informal chat, please contact Robert Darby, Research Data Manager (0118 378 6161).

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Open Research in practice – an interview Prof Aleardo Zanghellini

Posted on November 23, 2021 by Karen Rowlett

As part of the efforts to improve the Open Research culture at the University of Reading, according to the Committee on Open Research and Research Integrity action plan, the Open Research champions for the School of Law, Marzia Briel and Tahlia-Rose Virdee, conducted a brief interview with Professor Aleardo Zanghellini on his experiences of Open Research and Open Access Publishing.

Professor Zanghellini is a Professor of Law and Social Theory at the University of Reading’s School of Law. His research interests are legal, political and moral philosophy, gender and sexuality, socio-legal studies, and Law and literature.

Tahlia: When did you first come across Open Access publishing, and how did you find out about it?

Professor Zanghellini: A few years ago I started seeing open access (OA) journals appear at about the same time as OA started being discussed by the University; so it was a mixture of witnessing the emergence of a phenomenon while also being told about it.

Tahlia: Where have you published Open Access?

Professor Zanghellini: Most recently in Philosophia (a hybrid journal with open access options). My first OA piece was, I think, in Laws (a pure gold, fully open access journal). Other articles I have published in recent years in Open Access format include one that appeared in Jurisprudence (a hybrid journal with OA options) and one in Sage Open (fully  OA). There have been others.

Tahlia: What were your motivations for publishing Open Access? Had you published traditionally before?

Professor Zanghellini: I had published traditionally before. The main reason for OA publishing is increased visibility of my work. E.g., Sage Open is Sage’s most read journal.

Tahlia: How does the Open Access process differ from publishing traditionally? Are there different outcomes than publishing your work traditionally?

Professor Zanghellini: The main different outcome is more visibility and hence greater potential for influencing debates and perceptions, and also higher citation numbers. That said, if your topic is of niche interest it tends to remain so, whether published in OA journals or not.

There are, however, some possible drawbacks to OA publishing when you publish on politically controversial topics. Basically, the increased visibility of your work beyond academic circles may expose you to trolling, online character assassination, and attacks on your professional integrity. Some sections of the general public have no qualms in misrepresenting academic work which they have a reason to hate, stopping at little in order to get attention. This includes the use of hacks that will improve the google ranking and general visibility of webpages the non-academic activist has created about you and your OA work, for example by giving those pages the look of your official webpage or of a personal blog authored by you.

The fact that OA publishing almost always involves the payment of an article processing charge on the part of your University (for the journal needs to make up the money it loses by not putting the article behind a paywall) may also be turned into a false allegation that your article was published only because you paid for it. This is of course nonsense: OA publishing in reputable journals has exactly the same standards of peer review as traditional publishing.

Foxhill House houses the University of Reading Law department

No doubt, most OA work is published without anyone batting an eyelid, but when it is on controversial topics, as critical legal scholarship may often be, the sort of situations I mentioned above can be a risk. This can be unsettling for everyone, especially less seasoned, early-career researchers. I think that Universities, in encouraging their research active staff to publish OA, have not quite caught on yet to some of the possible adverse consequences on staff. As far as I am aware, they do not have dedicated mechanisms in place to assist scholars in managing and countering some of the potential negative consequences of OA. In a world in which populism (typically, but not always, of the right-wing variety) increasingly takes the form of animus against academic and intellectual ‘elites’, I think this will have to be taken much more seriously.

Tahlia: What advice would you give to a student or early career researcher considering publishing their work Open Access?

Professor Zanghellini: Many Universities set aside funds for publishing OA to pay for the article processing charge, and most traditional journals these days also offer the option to publish OA. Familiarise yourself with the process and go for it — but be mindful of the issues I noted in response to your previous question, especially if your work is politically controversial!

Acknowledgements

The School of Law Open Research Champions (Marzia and Tahlia) would like to thank Professor Aleardo Zanghellini for his time, for sharing his experiences of Open Access Publishing, and for contributing to the culture of Open Research and Knowledge Sharing on this project.

Interview conducted, designed and transcribed by Tahlia-Rose Virdee and Marzia Briel.

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Open Access Week 2021 – Free Research Resources LibGuide

Posted on November 1, 2021 by Karen Rowlett
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Open Access week 2021

Recently, the University of Reading Library launched a LibGuide about free, Open Access resources. This project aligns closely with this year’s theme for International Open Access Week, as the LibGuide is designed for our diverse, alumni community and researchers anywhere to use to achieve their future goals.

What inspired us to create the guide?
On leaving the University, graduates will no longer have access to subscribed resources since most research is behind a paywall. This applies to anyone in the world who does not have access to an academic library or cannot afford expensive subscription fees. We understand that learning is for life. People may wish to carry out research to help better themselves, their work, and their community. One of the benefits of Open Access is that members of the public can acquire research which their taxes have funded. However, they may not know where to look or what is freely available legally. It is also a real possibility that they will not be local to the University or to any academic library. To remedy this, the Library’s Research Group, comprising of experts from across the Library and University Museums and Special Collections, created a new LibGuide to free, online Open Access resources. Our guide brings together a recommended selection and continues the Library’s relationship with our alumni.

What’s in the guide?
We share our knowledge of finding academic articles, books and other resources useful for research. Our LibGuide brings together available resources from the University Library and external, wider sources. All of the resources that we highlight are available to read online or download for free.

We have kept the LibGuide’s style consistent, so that alumni who are familiar with using Library support resources can navigate with ease. The homepage advises users to make use of the key sections to explore by type of resources. We have defined what Open Access is and how users can tell if a resource they are reading is Open Access. We have provided links so that users can find out more about the history and current developments within Open Access as well as further information about Creative Commons licenses.

The LibGuide has been split into six sections:

The LibGuide on free research resources from University of Reading

“E-books” – The guide links to some of the main providers of free online books (including Project Gutenberg, Hathi Trust, Google Books, DOAB, and OAPEN Library).

“Journal articles” – As many repositories are indexed by Google Scholar, this can be an excellent starting point for finding Open Access articles. The guide includes some of the best browser extensions available to download so that users can access research behind paywalls. There are links to preprint servers (including ArXiv and SSRN) and academic social networks (ResearchGate and Academia.edu), as many researchers are eager to share their work openly. The “Access to research” service has been featured. It is available in many public libraries, through which users can access articles for free on library computers.

“Other Material” – This section is dedicated to finding other resources such as theses, images, film, audio, primary sources, maps, and data. Sites such as the University of Reading Museums and Collections Virtual Reading Room allow exploration of high quality galleries of items from the University’s special collections, art collections and Museum of English Rural Life (The MERL). For users looking for information on particular topics, users can use links to access our Subject guides, as they often include links to free resources.

University of Reading Library

“Libraries”– The guide has advice for visiting libraries (subject to Covid-19 government guidance), including the University of Reading Library, The British Library, as well as legal deposit (e.g. Bodleian Library and Cambridge University Library), and public libraries. Users are advised to use catalogues like WorldCat and Jisc Library Hub Discover to find out which particular resources academic libraries have before they visit. For historical, unique or rare materials like manuscripts, there are links to special databases (including Archives Hub and the ESTC).

“Referencing” – In this section, there is a link to a LibGuide on citing references. Links for key referencing tools are included (such as Mendeley, EndNote, and Zotero), so that users can store details of useful resources that they find.

“Alumni” – In this final section, there is guidance for the University’s alumni community if they wish to visit the Library and borrow physical resources (subject to Covid-19 government guidance).

How does the LibGuide build structural equity?
Sharing resources and knowledge with the public fits with the University of Reading’s strategy of engaging with our wider community, in order to have a positive impact. Our LibGuide goes further than simply highlighting the number of academic books and articles which are free to access and download without an inconvenient and unaffordable paywall. It facilitates access to knowledge for everyone, contributing to the building of a fair and equitable research landscape. The guide is well-used; since it was first launched in summer 2021, it has received over 1,000 views. It provides an opportunity for continuing lifelong learning and developing new knowledge.

·        Explore the guide here: https://libguides.reading.ac.uk/freeresearchresources

This post was adapted by Chloe Bolsover from an article featured in CONNECTED, the magazine for alumni at the University of Reading. Link to article: https://sites.reading.ac.uk/connected/2021/07/08/library-guide-for-alumni/

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Open Access Week 2021 – Writing an open peer review: an interview with Shirley Williams

Posted on October 30, 2021 by Karen Rowlett
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Open Access week 2021

Open peer review is one aspect of the Open Research movement which aims to make the research process more transparent, accountable and reproducible.

The peer review system for academic publications is traditionally a closed process whereby the author does not know the identity of the reviewer but the reviewer may know the identity of the author.  In order to improve the transparency and fairness of the peer review process, several journals now operate open peer review models. Some journals publish individual reviewer comments while others make a combined decision letter from all the reviewers openly available. Some journals also make the replies to the reviewers public so that the whole process is clear and available for others to make their own judgments about the fairness and stringency of the review process.

Portrait photo of Emerita Professor Shirley Williams
Emerita Professor Shirley Williams

I spoke to Emerita Professor Shirley Williams about her experience of writing an open peer review for the publishing platform F1000Research. Shirley retired around six years ago from the University of Reading’s School of Systems Engineering. Over the years Shirley’s research interests evolved from the technical to the more social aspects of computing. When she received her promotion to Professor, she chose the title Professor of Learning Technologies which reflected her research interests.

Why did you decide to contribute an open peer review?
The paper on the F1000Research platform was related to a study that  Dr Tharindu Liyanagunawardena and I had undertaken on Medical MOOCs (Massive Open Online Courses). Someone flagged to us that this new paper was up for review and we decided to act as reviewers.

How much guidance did you get on what to include/consider in your review?
The platform asks reviewers to adhere to the principles of the Open Science Peer Review Oath and to the Committee for Publication Ethics’ guidelines for peer reviewers. There is a set of questions for reviewers which gives some guidance about what to include in your review.

What do you think about the publish first, review after model that the platform uses?
I think in these days lots of academic work appears in the grey literature. Platforms that allow work to be published but then reviewed certainly have a place. Reviewing in traditional journals (certainly in my discipline) can be a very lengthy process that can delay the publication of new research. Articles that pass peer review in F1000Research are then included in the PubMed Central database.

I can see that you did the review in conjunction with another researcher. Was this a way of helping them get experience as a peer reviewer?
No, not in this instance. At the time we were asked to contribute the review, Tharindu and I were working together so it seemed natural to write the review together and for us to both add our names.
I understand that the F1000Research platform does allow early career researchers who might not normally qualify as peer reviewers to contribute reviews in conjunction with their supervisor or principal investigator so it could be a good way of gaining experience if this was appropriate.

Did you have any concerns about your peer review being open to everyone to see? 
I didn’t have any worries about the peer review being open. I was happy that others could see what we’d said about the paper and our suggestions for improvement. Everyone can read the review online and it is also possible to cite the peer review as the platform assigns a Digital Object Identifier (DOI) to all reviewer comments.

Screenshot of the F1000Research article with the open peer review
The F1000Research article reviewed by Prof Williams showing the open peer review process (screen shot from the website, https://f1000research.com/articles/6-1699, CCBY)

I can see that the authors updated their paper after your review and their responses to your comments are also open. Do you think this makes the review process more transparent and collaborative?
I felt the ability for authors to respond to the review was a positive aspect of the process. Sometimes with traditional blind review I have felt that it would have been be an advantage for the authors and reviewers to engage in a conversation to help to improve the article.

Have you ever had an open peer review on one of your own papers?
I haven’t submitted a paper for an open review. Since I retired I see my research role as supporting co-researchers and I have left the choice of publications and the submission process up to them.

Do you have any advice to anyone thinking of contributing an open peer review?
As there are lots of different peer review models being used across the scholarly publishing landscape, I’d recommend making sure that you understand the review process, the publishing process and the degree of openness used by the journal before you accept to undertake the peer review. Most journals will have detailed instructions for reviewers available on their websites.

The article reviewed by Shirley and Tharindu is available for all to read, along with the reviewers’ reports and the authors’ responses to the reviewers.
Bendezu-Quispe G, Torres-Roman JS, Salinas-Ochoa B and Hernández-Vásquez A. Utility of massive open online courses (MOOCs) concerning outbreaks of emerging and reemerging diseases [version 2; peer review: 2 approved]. F1000Research 2017, 6:1699 (https://doi.org/10.12688/f1000research.12639.2)

The citation for the open peer review that Shirley and Tharindu submitted is:
Williams SA and Liyanagunawardena TR. Peer Review Report For: Utility of massive open online courses (MOOCs) concerning outbreaks of emerging and reemerging diseases [version 2; peer review: 2 approved]. F1000Research 2017, 6:1699 (https://doi.org/10.5256/f1000research.13685.r28591)

Further reading
Aleksic J, Alexa A, Attwood TK et al. An Open Science Peer Review Oath [version 2; peer review: 4 approved, 1 approved with reservations]. F1000Research 2015, 3:271 (https://doi.org/10.12688/f1000research.5686.2)

The University of Reading Open Research LibGuide covers all aspects of open research including a section on open peer review.

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