Open Research Forum 9th March 2022

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

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

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 ventilationrecruiting personnel successfully via online interviewsVitamin 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

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 BoonMarcello De MariaKirsty HodgsonSophie 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 BoonSophie 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

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 Open Research Fund Call 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

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

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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

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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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Open Access Week 2021 – Publishing on the Wellcome Open Research platform, an interview with Dr Al Edwards

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Open Access week 2021

Wellcome Open Research was launched in 2016 as a platform for the publication of a wide range of submissions from Wellcome Trust-funded researchers. The platform, based on the same model as F1000Research, works on the publish first and peer review later model. The platform uses open peer review and enables versioning of articles in response to peer review comments. In launching the platform, the Wellcome Trust stated that the benefits would include faster publication of research, improved reproducibility and reliability of research and the publication of null and negative results. The platform was seen as particularly relevant for early career researchers (ECRs) as their work would be more visible, would include studies reporting negative or null results that can be difficult to publish elsewhere and would encourage dialogue with peer reviewers over the improvement of their articles.

I spoke to Dr Al Edwards about his experiences of publishing his work on the Wellcome Open Research platform. A version of this video is also available to University of Reading staff and students via Microsoft Stream.

Introductions
I work in the School of Pharmacy at University of Reading and my research is concentrated on biomedical technology, particularly diagnostics and vaccine technology. We were working on a vaccine for coronavirus a couple of years ago.

Why choose this platform?
I’ve published there twice for slightly different reasons. The first time was related to the Covid19 pandemic. We published a methodology paper for testing things during a pandemic and this paper was built on work we’d done with Wellcome Trust funding. This made us eligible to publish on the platform. Pandemic aside, our second publication was also from work funded by the Trust and was something that we thought we might struggle to publish elsewhere. The paper was a systematic analysis of lots of different cameras that we thought might be useful for everyone .

How does the platform work?

The publishing process at Wellcome Open Research. From the Wellcome Open Research website under a CCBY licence.

It is a very logical way to publish but is a bit unconventional. The idea is combining a preprint archive with the final approved version and all the peer reviews and data behind the article. You write your article as usual; you have to include all your data in the submission. The paper is checked. Most of the checks are about accessibility and transparency. If you’ve said your data is available elsewhere, they will go and check. It does take a week or so to complete these checks. The article is then published and is made freely available. It then goes through an open peer review process whereby the reviews are visible with the article. If there’s a recommendation for any changes, you can then submit a new version that will then be re-reviewed. Once approved by two reviewers, the article is then considered to be indexed. The authors’ comments to the reviewers are also open so that the reader can see the dialogue that took place between the peer reviewers and the author. In theory it is a great idea.

The peer review process is open and transparent at Wellcome Open Research. Screenshot from website under a CCBY licence

Are the reviewers still invited to review?
There are author-suggested reviewers and those suggested by the platform based on keywords in the article. You can ask for certain reviewers not to be invited. The platform then sends out invitations to the selected reviewers. Most people just don’t have time to review – it is the same as with any other conventional journal.

Were you worried about the peer reviews being open?
My biggest concern about open peer review is that if I wrote one, I’d be much more careful if I knew it was going to be published. I think open peer review is harder because you are essentially writing something for publication. This means that it can be even harder to recruit reviewers. Until the culture changes, this might be a real barrier. I’m more worried about finding willing reviewers rather than what they might say about my work. I can always explain why a public comment on my work might be wrong or unreasonable and a fair and open debate can take place. If the review is private, it is harder to enter into a discussion with the reviewer.

What about the pace of peer review?
We’ve published a couple of papers. The first was in the summer of 2020. It took a long time but eventually we got couple of reviews. It was slower than most conventional journals. But it has the bonus that the research is already out there even while you are waiting for reviews. Nobody’s going to blame you for the delay because they can see that there are obviously difficulties in recruiting reviewers. For the second paper, because of the time I published it in March this year, I wouldn’t necessarily expect any reviews yet. I believe that authors have to suggest more reviewers once the initial list has been exhausted. I haven’t had the time to go back onto the platform and suggest some additional reviewers. Normally that would be the journal editors job and they have time pressures on them to keep the times between submission and acceptance as short as possible.

Did you have to provide the underlying data to accompany your article?
It is a very strong rule on the platform that everything should be shared if it can be and if the raw data is meaningful. We are lucky that we have very good support available at the University of Reading. For the first article, we used the University Research Data Archive. It was very easy to set up as we had so much guidance on how to do it. What that meant that was all the checks that the platform requires had already been done on our dataset. When we submitted, as everything was correct, it was very straightforward. You can use other places to archive your data. If you use a repository or archive recommended by the publisher, it will already have a lot of the features required in place such as correct labelling and having a DOI. It is a reasonably straight-forward process if you have any kind of data that can be shared and/or reused.

Have you updated your article in response to feedback or peer reviews?
We haven’t done the updates yet for the one that has peer reviews added to it. This is mainly due to the pressure of having lots of other articles currently under review that need looking at. The cool thing would be if we can publish the real research based on the methodology that we described in the original paper. We could argue that having published the method, we were then able to go out and use that method to develop benefits to society and work on solving a real problem. Things are rapidly changing due to Covid. If the research doesn’t come to anything, it won’t be because of where we published the article. Some things just don’t work out the way you’d hoped.

Do you have to pay to publish on this platform?
Anyone who has had Wellcome funding can use the platform to publish their research free of charge. That was a good reason for us to use the platform.

Do you have any advice for others thinking of publishing on this or similar platforms?
My basic advice is give it a go. It is quite interesting to look at the articles on the platform. A lot of the articles are different to ones that you might find in conventional journals. Lots of them are prospective planning or methodology articles or might be wider and more sweeping articles that can be difficult to submit to conventional journals perhaps because they are too long. Have a go but be patient. Assume that it might be slow to get reviews – but that can be true of conventional journals too.

The articles by Al Edwards are openly available on the Wellcome Open Research website:

Jégouic SM, Jones IM and Edwards AD. Affordable mobile microfluidic diagnostics: minimum requirements for smartphones and digital imaging for colorimetric and fluorometric anti-dengue and anti-SARS-CoV-2 antibody detection [version 1; peer review: awaiting peer review]. Wellcome Open Res 2021, 6:57 (https://doi.org/10.12688/wellcomeopenres.16628.1)

Various metrics are available for each article published on the Wellcome Open Research platform. Screenshot from the website under a CCBY licence

Dataset: http://dx.doi.org/10.17864/1947.262
Jegouic, Sophie  and Edwards, Al  (2020): Dataset associated with the article ‘Affordable mobile microfluidic diagnostics: minimum requirements for smartphone digital imaging for colorimetric and fluorometric viral antibody detection’. University of Reading. Dataset. http://dx.doi.org/10.17864/1947.262 

Needs SH, Bull SP, Bravo J et al. Remote videolink observation of model home sampling and home testing devices to simplify usability studies for point-of-care diagnostics [version 1; peer review: 4 approved with reservations]. Wellcome Open Res 2020, 5:174 (https://doi.org/10.12688/wellcomeopenres.16105.1)

Dataset: Figshare: Data associated with the article ‘Remote videolink observation of model home sampling and home testing devices to simplify usability studies for point-of-care diagnostics’. https://doi.org/10.6084/m9.figshare.12622373 (Needs, 2020a)
OpenSCAD files for the 3D printed components is available from GitHub: https://gitlab.com/sneeds/model-home-testing-devices
Archived version at time of publication: http://doi.org/10.5281/zenodo.3928471 (Needs, 2020b)

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Open Access Week 2021 – Why publish your work as a preprint? An interview with Dr Al Edwards

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Open Access week 2021

There has been a huge increase in the number of outputs uploaded to preprint servers over the last few years. Why are researchers opting for this route and what benefits does it bring?

What is a preprint?
A preprint is a full draft research paper that is shared on a publicly available platform before it has been through formal peer review. Most preprints are given a digital object identifier (DOI) which allows them to be cited by the author and others in advance of formal publication in a peer-reviewed journal.
There are several reasons why researchers choose to upload a preprint:

  • Research is available faster than it would be via conventional publishing routes
  • Preprints can have several versions as the manuscript evolves and improves
  • The wider research community can help to improve a manuscript by suggesting changes and offering feedback
  • The authors can stake a claim to a novel result or a new method in the preprint and so reduce the chances of being ‘scooped’
  • Preprints can be viewed and cited ahead of the formal publication process leading to increased attention

It is important for readers of preprints to be aware that the research reported has not been peer reviewed and so should be treated with caution, particularly where medical issues are involved. Preprint servers have clear warnings about the status of publications on each output.

I talked to Dr Al Edwards about why he choses to use a preprint server for some of his work. This version of the video interview (hosted on Microsoft Stream) will only be accessible for University of Reading staff and students.

Please introduce yourself and tell us a bit about your research

Dr Al Edwards

My name is Al Edwards and I’m based in the School of Pharmacy at University of Reading.  I’m interested in technology that could be used in biomedicines. This includes things like diagnostic testing and vaccines. I also teach undergraduates.

Why did you choose make your work available as a preprint?
There are lots of different reasons to choose to upload a manuscript as a preprint. One of the simplest ones is that it can be a very quick way to get something out and available for others to read. This has been particularly significant in recent times with the rapid growth in research on COVID19. More recently I’ve been interested in using the preprint route to make my research available especially if I’m planning to publish in a journal where the final version may not be open access because we can’t pay the article processing charge (APC) or because the publisher’s embargo on the author-accepted version in our institutional repository will be too long. By using a preprint, we can make sure that our work is available to everyone even if the final peer-reviewed, accepted and typeset version of the article isn’t available for a while.

I did have an early experience with a preprint where I had a grant proposal under review and had some comments from the reviewers that I needed to address. I was able to get a manuscript uploaded as a preprint and referenced the data in the paper in my response to the reviewers knowing that they would be able to read the preprint. I’ve no idea if it had any effect but we did receive the funding from the application so it felt like a positive boost to my preprint experience.

How did you choose the platform for hosting your preprint?
I didn’t think about it too much. I’d heard of the original preprint site arXiv and there was a subject-specific version available in bioRxiv so that seemed an appropriate place to host the preprint. Once I’d used bioRxiv and had a good experience with it, I’ve used it ever since. Once you are familiar with a site, it makes sense to stick with it.

One of the benefits of the site is that a digital object identifier is assigned to your preprint. This makes it very easy for people to cite your output and for you to track attention to the item using tools such as Altmetric.

Having a DOI means that Altmetric attention can be captured

Does it cost anything to publish a preprint?
There is no direct cost to use the preprint platform but there’s a cost associated with everything you do. In this case it is the extra work that you have to put in to make sure that you are happy with the manuscript before you upload it to the preprint server. The extra work isn’t massive but with a preprint it is going to be out there for ever and so you want it to be right. With a peer-reviewed article there are several steps in the publication process where you get to check and proofread the article prior to it being publicly available. I tend to spend a bit more time on a preprint before I upload it because I know it is going to be immediately visible. [It is possible to make changes to a preprint and update the document with versioning in place if you do notice mistakes or want to respond to feedback].

What benefits do you think there are to making the work available to everyone ahead of a formal journal submission?
For me, the driving reason is because I genuinely believe that it is the right thing to do. There are secondary reasons such as wanting to show that you’ve got progress on a particularly research problem. It can take six months for a paper to make it through a journal submission system and by using the preprint route, the information is out there much quicker. It can be very useful to have the information publicly available at an early stage, for example, if you are going to a conference you can present you findings and people can look at the full detail of the work very easily. Another reason is that if your accepted journal article is not published open access and the author-accepted manuscript is under a publisher embargo in your institutional repository, the preprint version is still accessible to interested readers. This allows greater dissemination of my work

Preprints on bioRxiv are clearly marked as non-peer reviewed

Will you submit the paper to a journal eventually? Will the preprint version stay on the preprint server if you do?
Yes, absolutely. We have one article that is currently available as a preprint and has been through so many revisions with so many different journals but has still not been formally accepted for publication. The original preprint was made available probably four or five years ago and I think the information has probably been split up into three or four different journal articles now. One preprint is almost identical to the final peer-reviewed version that appeared in a journal so it seems to be a roll of the dice as to how the publication process works.

Have you received much feedback on your preprints? Was it helpful?
I don’t think I’ve received much feedback. I’m not sure if that is just a feature of research in my field. I don’t tend to be a proactive discusser of my work anyway. We work with lots of different people, for example, in industry, with clinicians and with other academics. Most of the discussions about the work take place within the research group. I know that other people have had useful feedback and used it to improve their manuscripts.

Would you do it again?
We’ve already got several preprints out there. I don’t do it for every paper. It tends to be on a case by case basis and sometimes there are compelling reasons to use a preprint server. If we know we are targeting a journal in a specialist field and that journal has a particularly high open access article processing fee, we might consider using a preprint in that instance. Some of the journals we are using, for example PLOS journals, are fully open access anyway and so the final peer-reviewed version will be publicly available. We have also used the Wellcome Open Research platform for our outputs. The route we choose varies from paper to paper.

Any advice for others thinking of doing the same?
I would make sure that there’s a good reason to try it. I mentioned my own example of when we just wanted the information out in the public arena quickly. Just do it and give it a go. If you are unsure and want to dip a toe in the water first, choose an article or a subject that you are not so intensively involved in and try that first. You might have a smaller paper or an article that you know is not the most important thing you’ve done and use that as a way of trying out the preprint route to see what it feels like.

It is important not to be too obsessed with getting everything perfect. When you read other people’s preprints, it is clear that you don’t expect perfection and you don’t notice typos or mistakes. Don’t be too precious about the manuscript and try to be relaxed about the process. Once you’ve done it once, you’ll find it much easier to consider again.

Al’s preprints are available on the bioRxiv preprint server. The site clearly shows which preprints have not been subject to peer review.

High Dynamic Range Bacterial Cell Detection in a Novel “Lab-In-A-Comb” for High-Throughput Antibiotic Susceptibility Testing of Clinical Urine Samples
Jeremy Pivetal, Martin J. Woodward, Nuno M. Reis, Alexander D. Edwards
bioRxiv 199505; doi: https://doi.org/10.1101/199505
This article is a preprint and has not been certified by peer review

Mixing is required for uniform reconstitution of filter-dried protein antigens in a single-injection vaccine formulation
Napawan Thangsupanimitchai, Alexander D. Edwards
bioRxiv 247403; doi: https://doi.org/10.1101/247403
Now published in Vaccine doi: 10.1016/j.vaccine.2018.07.001

High-throughput, multiplex microfluidic test strip for the determination of antibiotic susceptibility in uropathogenic E. coli with smartphone detection
Sarah H. Needs, Zara Rafaque, Wajiha Imtiaz, Partha Ray, Simon Andrews, Alexander D. Edwards
bioRxiv 2021.05.28.446184; doi: https://doi.org/10.1101/2021.05.28.446184
This article is a preprint and has not been certified by peer review

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