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

Posted on October 29, 2021 by Karen Rowlett
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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

Posted on October 28, 2021 by Karen Rowlett
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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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Open Access Week 2021 – Publishing a Registered Report: an interview with Jayne Morriss

Posted on October 27, 2021 by Karen Rowlett
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One of the aims of the Open Research movement is to make the research process more transparent, accountable and reproducible.

Writing a Registered Report has been proposed as a way of eliminating publication bias from the scholarly communication process. Usually studies reporting positive results are easier to get published than those that report negative or inconclusive ones. This publication bias can skew research priorities in some subjects, lead to selective reporting of results and possibly the changing of hypotheses in order to fit unexpected results.

What is a Registered Report?
The Registered Report format is suitable for all areas of science where there might be the potential for bias. The author writes the intended methods and proposed analyses that they will use in their study in the Registered Report format. The protocols are then peer reviewed prior to the research being conducted (Stage 1). After the proposed study has passed peer review, the study begins. Once the author has completed the study, they write the results and discussion sections of the article and then resubmit the article for Stage 2 peer review. If the authors can show that they conducted their study according to the initial protocols, the publication of the article should be straight forward.  The advantages of the Registered Report format are that the study should be much easier to replicate by others and, as the journal commits to publishing the report regardless of the outcome, there is no possibility of the methods or analyses being changed to alter the final results of the study.   

Steps to publication of a registered report compared with conventional article

Many journals in several disciplines now include the Registered Report format as an article type. According to the Center for Open Science, there are now over 300 journals that include Registered Reports in their list of acceptable formats. The subject range includes journals on psychology, neuroscience, linguistics, biology, ecology, oncology, veterinary science, computer science, nutrition, sociology, medicine and education.  Several publishers also provide guidelines for authors, including Wiley, Royal Society, Taylor & Francis and BioMed Central.

What do researchers think of the Registered Report initiative? I spoke to Dr Jayne Morriss who has used the Registered Report format several times in her work on the neurobiology of anxiety.

Please introduce yourself and tell us a little bit about your research

Portrait of Jayne Morriss

I’m a senior postdoctoral research fellow based at the School of Psychology and Clinical Language Sciences at the University of Reading. My research focuses on the neurobiology of anxiety.

Why did you choose to structure your work as a registered report?
There are multiple advantages to a registered report. In particular, with a registered report the timeline of the research project is clear, and it forces the researcher to be up front about their hypotheses and analysis plan. Furthermore, the research is published on the basis of sound hypotheses rather than whether the results are ‘positive’ or not.

Was it difficult to write the registered report?
It is a lot easier to write a registered report because there is a clear timeline of events i.e. write the introduction, hypotheses and analysis plan at stage 1 and the results and discussion at stage 2.

What benefits do you think there are to declaring what you are going to do in your study before you actually start collecting the data?
You can receive useful feedback from reviewers before starting the project. Thus, the rationale and design of the study tends to be more detailed and thorough.

Was it difficult to stick to the protocol that you had registered? Did it cause any issues in the conduct of the research?
Not at all. Although, if you notice potential problems with the design while piloting the experiment, you can go back to the editor and recommend further changes to the protocol. This works as long as you haven’t collected/started the real experiment yet.

Did having the registered report make it easier or harder to write up the final paper?
It was much easier to write up the final paper because the introduction and method had already been finalised at stage 1. Moreover, reviewers can only comment on the results/discussion at stage 2.

What was the peer review like on the final paper?
As the method had already been scrutinised in advance, the peer review on the final paper was much quicker and more streamlined.

Would you publish a registered report again?
Yes, I have published three registered reports so far in different journals.

Do you have any advice for others thinking of doing the same?
The process of preparing a registered report is worth learning. If you have a replication study or a ‘risky’ study, I would recommend the preregistered report route. Another thing to remember is that there is actually some flexibility with a registered report. For example, say you realise that there may be an alternative way of analysing the results, you can do these analyses if you state that it was posthoc and not part of the registered analysis plan. Posthoc tests can be added in the results section under the planned analyses or in a supplementary material.

The Registered Reports written by Dr Morriss are listed below.

Morriss, J., Biagi, N. and Dodd, H. (2020) Your guess is as good as mine: a registered report assessing physiological markers of fear and anxiety to the unknown in individuals with varying levels of intolerance of uncertainty. International Journal of Psychophysiology, 156. pp. 93-104. ISSN 0167-8760 doi: https://doi.org/10.1016/j.ijpsycho.2020.07.009

Morriss, J., Wake, S., Lindner, M., McSorley, E. and Dodd, H. (2020) How many times do I need to see to believe? The impact of intolerance of uncertainty and exposure experience on safety-learning and retention in young adults. International Journal of Psychophysiology, 153. pp. 8-17. ISSN 0167-8760 doi: https://doi.org/10.1016/j.ijpsycho.2020.04.012

Currently at stage 2 of review:
Wake, S. J., Dodd, H., & Morriss, J. (2020, March 30). Intolerance of uncertainty and novelty facilitated extinction: The impact of reinforcement schedule. PsyArXiv Preprints. doi: https://doi.org/10.31234/osf.io/7qgrh

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Open Access Week 2021 – Publishing Open Software, an interview with Brendan Williams

Posted on October 26, 2021 by Karen Rowlett
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Software can be an important research output in some disciplines such as the physical and life sciences. One of the aims of the open research movement is to encourage researchers who generate software or code as part of their projects to make it open and accessible to others. This not only means that the software can be checked and verified by others but that it can also be archived and licenced appropriately to enable reuse by others and possibly further development or re-purposing of useful tools.

Brendan Williams

I spoke to Brendan Williams, a Research Fellow in the Centre for Integrative Neuroscience and Neurodynamics at University of Reading about why he decided to publish the software tool that he developed as part of his PhD research.

Introduction 
The work that I am involved in, mainly for my PhD, is on adaptive decision making and how people can respond to change and how the brain supports the behaviour which we see when people are responding to change. 

What does the software that you developed do?
The software that I helped to develop is called pyfMRIqc and it is a useful piece of software for providing quality assurance metrics for neuroimaging data.  One of the problems with new MRI imaging data is that it is multi dimensional and not the kind of data that you can check by hand. The software helps individuals make decisions about the quality of their data and then decide if they can use the data set or whether they need to repeat the data collection step. Because the software was developed in Python, it is nearly platform-independent and therefore can be used by the lots of researchers in the neuroimaging community.

Why did you decide to publish your software?
It was important to publish the software in order to make it more discoverable for others who might want to use it. Quality assurance in neuroimaging is a really big thing and so having software that is easily accessible for others who want to check the quality of their data is really important.

Why was it important that it was openly available?
It was important that the publication that matches the software was also open access. One of the great benefits is that it allows anybody, regardless of who they are, to access not only the software but the publication that describes the software and how to use it.

Are you more careful to check everything if you are publishing your software openly?
The software was designed with the average user at our Centre in mind. We have researchers who are relatively junior, from MSc level, right up to Professorship level. We don’t want to assume any prior knowledge when people come to use our software. We want it to be available and easy to use for anyone who needs to perform quality assurance on their MRI data. It was important to make the software easy to use but also to make sure that the documentation matches up exactly with how it works. Making everything accurate has reduced the amount of time we’ve had to spend answering support queries as well as helping the users.

How did you choose the right place to publish your software?
We published our article in the Journal of Open Research software as it seemed the most appropriate place. It is a fully open access (Gold open access) journal so anyone can read the papers in the journal without needing a subscription.

Did you have to pay an APC to publish in the journal?
Yes we did but as it was a fully open access journal that was listed in the Directory of Open Access Journals, the University of Reading’s open access fund covered the costs. That was very helpful in getting our work out there.

What are the benefits of making your software open to everybody? Do you think it might be built on by others in the future?
One of the benefits of publishing the software openly is that it can be used by anybody who wants to run quality assurance on their data with no cost to themselves or the need to write their own code. This is very important as it democratises the research process and allows anybody from anywhere, regardless of who they are, to be able to do these kinds of important checks on their data. With regard to the tool being built on by others, there’s definitely scope for that. The code is open source so if anybody wants to add new features or additional metrics they can certainly do so and we are totally supportive of people taking what we started and developing it further.

Have you received much feedback from others?
Yes, we’ve had some really positive feedback about how people have used the software and how it helped them to run quality assurance on their data. One really interesting piece of feedback was from a group that have used the tool for spinal cord imaging data. At CINN, we are usually just imaging the brain so we developed the tool with that area of the body in mind. As the functions within the tool are agnostic to the part of the body that has been scanned it was very cool to hear that others are using the software for different studies like looking at the spinal cord.

Do you think the availability of the software has had an impact on your research community?
Definitely. From personal experience with my data, it has given me more confidence that the data I was analysing for my PhD was of sufficient quality. It has also been used within the broader CINN community. If the data coming out of CINN is good quality, it will ensure that the research conducted by our community will be of a high standard.

Any tips or advice for others thinking of publishing their software?
One of the really important things for us when we were developing the software was making sure that we had our end user in mind. If you want other people to use your software you have do understand what their needs are and what their level of skills and expertise are. You can then design your software so that it is suitable for those that want to use it. I think that makes a good project.

Brendan’s paper on the software tool is openly available:

Williams, B. and Lindner, M., 2020. pyfMRIqc: A Software Package for Raw fMRI Data Quality Assurance. Journal of Open Research Software, 8(1), p.23. DOI: http://doi.org/10.5334/jors.280

The pyfMRIqc code is available on GitHub
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Open Access Week 2021 – The benefits of publishing open access: an interview with Brooke Bessesen

Posted on October 25, 2021 by Karen Rowlett
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Publishing your work as open access (OA) with a creative commons licence allows your work to be accessed by everyone with an internet connection and also repurposed and built on by others with appropriate credit to you. In this interview for Open Access Week 2021, I spoke to PhD researcher Brooke Bessesen.

Brooke sampling seawater in the study area. Photo courtesy of Brooke Bessesen

Please introduce yourself and tell us a bit about your research 
I’m Brooke Bessesen, a PhD candidate in the department of Ecology and Evolutionary Biology at University of Reading under the supervision of Dr Manuela González-Suárez. My research takes place in a rare tropical fiord in southwestern Costa Rica, where I’ve been working as a principal investigator for more than a decade (though I started at Reading in 2019). My studies focus on the ecology of an endemic population of yellow sea snakes, Hydrophis platurus xanthos. But because the root of my research is understanding and conserving the embayment’s biodiversity, sometimes multiple species are involved, as is the case with our recent paper: ‘The value and limitations of local ecological knowledge: Longitudinal and retrospective assessment of flagship species in Golfo Dulce, Costa Rica’. 

Why did you choose to publish your work in a fully open access journal? Why was open access important to you?
Open access was important to us on several levels. Whenever intellectual data comes from a community, those community members
deserve to know what was learned from their contributions.

Brooke videoing a sea snake from a boat
Brooke videoing a sea snake from a boat. Photo courtesy of Brooke Bessesen

Because our study was centered on interviews with local fishermen and tour boat guides, we wanted to make sure the findings were accessible to them. Also, because we hoped to serve conservation in a bio-rich area of Costa Rica that is currently under pressure, our work needed to reach as many stakeholders as possible. Through OA we were able to provide valuable assessment data to myriad policymakers and practitioners. On a more global level, we wanted to share insights about an interdisciplinary methodology that might help conservation biologists and social scientists surveying marine biodiversity in other parts of the world. Our goals were best achieved through OA. 

How did you pay for the APC for the journal article? Was it easy to sort out the request and payment?
Because the University of Reading is a member of the Wiley JISC Read and Publish agreement, sorting out gold open access was very easy. The publisher identified the paper as originating from University of Reading via the corresponding author’s email address and just needed quick confirmation of eligibility from the Library’s open access requests team. The process was incredibly easy and didn’t involve me dealing with any invoices or purchase orders. 

I can see that you also archived a dataset relating to your work using Figshare. What benefits do you think making the data set open brings to your research?
By providing our dataset, our results can be substantiated and potentially contribute to future research, as new questions may be answered by our efforts. The advantage of putting the dataset in Figshare is that it has a digital object identifier (DOI) of its own and can also be cited separately from the paper. The dataset can also be tracked for Altmetric attention.
Dataset citation: Bessesen, Brooke; Gonzalez Suarez, Manuela (2021): Local ecological knowledge regarding flagship species in Golfo Dulce, Costa Rica. figshare. Dataset. https://doi.org/10.6084/m9.figshare.14442029.v1

I know that there is now a Spanish translation of your work available so that the work is accessible by a wider audience and to the people living in the area of your study. Did publishing open access make it easier to distribute the translation?
The translation (by Daniel Colgan) stemmed from a request by Costa Rican government officials, but it was also an essential step toward knowledge-sharing in the community. Broad dissemination was made possible only because the original journal article was OA, and we were pleased to follow suit by making the Spanish version open access too (through a CC BY 4.0 license). It’s available on CentAUR with a DOI and can be freely downloaded by readers across Latin America and beyond.

Screenshot of the translated paper in the CentAUR repository
The translated paper in the CentAUR repository

Have you had any feedback or response to your work?

Altmetric score of 5

The original People and Nature article, which came out in May, has an Altmetric score of 5 (we appreciate the downloads and tweets and hope its reach will continue to grow). The translation was published in September, and government officials, local conservation directors, and our study participants have already expressed gratitude.

Do you have any tips or advice for others trying to publish open access or engage with open research? Given the growing focus on data sharing, there are more and more OA journals to choose from. And since institutional partnerships are usually listed, it’s possible to see if the university will assist with payment. While certain concerns can make full transparency of research findings imprudent (for example, localities of vulnerable taxa that might lead to exploitation), most investigations benefit from reaching a wider readership, potentially sparking future contributions and collaborations, and drawing the public audience into the journey of discovery.

Brooke sillhouetted against an orange sunset on a boat
Costa Rican sunset. Photo courtesy of Brooke Bessesen

Read Brooke’s Open Access article in People and Nature:
Bessesen, BL, González-Suárez, M. (2021) The value and limitations of local ecological knowledge: Longitudinal and retrospective assessment of flagship species in Golfo Dulce, Costa Rica. People Nat. 3: 627– 638. https://doi.org/10.1002/pan3.10219

Spanish translation:
Bessesen, B. L. and Gonzalez-Suarez, M. (2021) El valor y limitaciones del conocimiento ecológico local: Una evaluación longitudinal y retrospectiva de especies bandera en Golfo Dulce, Costa Rica.  https://doi.org/10.48683/1926.00100401

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Open Research Forum 15th September 2021

Posted on September 24, 2021 by fredbreese

Thank you again to all those who attended our second Open Research Forum meeting on Wednesday 15th of September. If you missed it on the day a recording of the meeting is available to view via this link (University of Reading members only).

We enjoyed two great presentations, with our first visit from an external speaker, each followed by a lively discussion of all things Open Research. There were also updates on the activities of our busy Open Research Champions. The next Open Research Forum is set for early December (date tbd)

Organising ourselves for world domination: how junior academics can work together to improve research culture

Jessica Butler, Senior Research Fellow, Centre for Health Data Science and Lead for UK Reproducibility Network, University of Aberdeen

You can find the slides here

Jess discussed how junior academics can work to reshape our current research culture. For the last 10 years we have been hearing about the reproducibility crisis and Jess set out to contextualise this within the broader research landscape. She argues that improving research quality is uncontroversial and that we know how to do it. If you read A manifesto for reproducible science, published in 2017, you will see a broad range of recommendations in favour of innovation in methods, improvements to reporting and Open Science practices.

Jessica Butler: “We can’t do better science if doing better science is dangerous to our careers”.

Jess argued that the issue is with institutional barriers which remain in place, slowing the adoption of better practices and drew our attention to a number of resources. UKRI’s Research Integrity: A Landscape study summarised the top 5 factors having a negative impact on Research Quality, and of these 4/5 are institutional factors.

UKRI (2020) p. 7

In addition Jess suggested that there is an opposition between the ideal of best practice, and the reality of how job applications are evaluated: on the basis of 3/4* REF publications and grant money won. You can see this in a recent study of criteria used to evaluate promotion and advancement at biomedical schools, where Open Research criteria remain almost entirely absent from consideration. (Rice et. al 2020)

It’s widely acknowledged there are issues with research culture. Wellcome’s What researchers think about the culture they work in found that 55% of researchers reported a negative sentiment towards research culture vs. 33% positive. 54% indicated they felt pressed to meet KPIs or metrics, i.e. for REF or grant funding.

So, how can these issues be addressed? Jess encouraged us to keep up to date with the latest developments, and ask questions. First get a sense of how your University functions politically and economically, find out which committees make the decisions. Find out if they have signed declarations such as DORA or The Concordat (or if there are institutional policies, such as Reading’s Open Research Action Plan) and what these endorse.

Her message is to pass solutions upwards. Does the boss of your lab know about your institution’s policies on Open Research? Senior management are generally sympathetic, but have a big ship to run . Suggest small concrete actions – “other institutions are doing this, why don’t we follow their lead?” For example UKRI have recently  adopted the use of narrative CVs. Ask if your institution provides training for writing one.

Finally, remember you’re not alone. There is a thriving community on Twitter at #researchculture and #ReimageineResearch and you can follow Jess @JessButler284. See if there is a Reproducibilitea group at your University, look out for RIOT science club events. You can help other people find you by having your own visible online presence and making use of your own University web page

The UNESCO Open Science Recommendation, Open Research and ethics

Marzia Briel, PhD student, School of Law

You can find the slides here.

Marzia is one of our Open Research Champions, and presented on the UNESCO Open Science Recommendation, adopted in May 2021. This was arrived at after consultation with global stakeholders including CERN, Coalition S and OpenAIRE, and debated online between over 100 member states. The recommendation is a non-binding legal instrument formulating principles and norms for international regulation, in this case of Open Science. Marzia highlighted 8 key points

  • Open Data and Open Licenses. Not just open publications
  • Inclusive of natural sciences, social sciences and humanities. Principles of Open Knowledge apply to all disciplines
  • Equal opportunity and indigenous knowledge protection. Open Science infrastructures should have long term sustainable visions, guaranteeing participation in research from less privileged institutions and countries. Indigenous rights over traditional knowledge should not be infringed
  • Use of Open Science to solve complex problems across disciplinary boundaries.
  • Prevent the extraction of profit from publicly funded science. The recommendation supports not for profit community driven publishing models.
  • Academic freedom and the continuing right to protect intellectual property
  • Transparency and public accountability of science as a form of evidence based knowledge.
  • Monitoring Oversight of Open Science must be kept public and not delegated to the private sector.

Marzia continued by referencing the broader relevance of Open Science practices, as seen in the case of the AstraZeneca vaccine, reported as being 97% funded by taxpayers or charitable trusts. Moves have been made to make the vaccine available under an open license, although these have been hindered by questions around quality control and the need for consensus between a large number of stakeholders.

The Recommendation also gives consideration for the potential negative consequences of Open Science practices such as predatory behaviour from publishers. It’s this area which Marzia is focusing on in her own research, mapping the impact and probability of these consequences.

Finally Marzia highlighted the 2013 McKinsey Open Data report which estimated Open Data could unlock $3.2 – 5.4 trillion per year in areas such as education. You can see the effects of this in the $7.5 billion acquisition of  GitHub by Microsoft in 2018. She described Research Data as the next frontier after personal data for Big Tech, and warns we must be aware of the possible cultural, legal and ethical consequences. The UNESCO Recommendation is playing an important role in the rapidly developing Open Research landscape, and sends a clear message about how this development should be approached.

Research Champions Business

Tahlia-Rose Virdee: Gathering Testimonials on Open Access Publishing

Tahlia and the other Champions in the School of Law have been talking to members of their Department and gathering testimonials from those who have published Open Access, to be published on the Open Research Champions website. In the spring term this will be expanded into a video panel, advising on Open Research in the humanities and social sciences. There are also plans with for a mini conference on Open Research and Open Access publishing.

Marcello De Maria and Auvikki de Boon: Open Research Survey

Ethical approval has now been granted for our planned University-wide survey on Open Research. The details of the survey are now being finalised. The survey is planned to run during October and we are hoping for responses from both staff and students.

Al Edwards: Open Hardware Hackathon

Unfortunately the planned hackathon in September had to be postponed, and a new date is going to be set around the New Year. There are still lots of Open Hardware activities being organised, so if you are interested please contact Al.

Karen Rowlett: Open Access Week

Open Access Week is coming up in the last week of October. The Library’s Research Engagement Team is planning a number of events including an Open Access publishing drop in for staff and students. Any help publicising these events in your School or department would be much appreciated, and if you would like to participate in Open Access week please get in touch.

References

Azoulay A. (2021). Draft text of the UNESCO Recommendation on Open Science. UNESCO

Manyika, J., Chui, M., Groves, P., Farrell, D., Van Kuiken, S., Almasi Doshi, E. (2013). Open data: Unlocking innovation and performance with liquid information. McKinsey

Metcalfe, J., Wheat, K., Munafò, M. & Parry, J. (2020). Research integrity a landscape study. Vitae, UKRN & UKRIO

Munafò, M. R., Nosek, B. A., Bishop, D. V., Button, K. S., Chambers, C. D., Du Sert, N. P., … & Ioannidis, J. P. (2017). A manifesto for reproducible science. Nature human behaviour, 1(1), 1-9.

Rice, D. B., Raffoul, H., Ioannidis, J. P., & Moher, D. (2020). Academic criteria for promotion and tenure in biomedical sciences faculties: cross sectional analysis of international sample of universities. Bmj, 369.

Safi, M. (2021). Oxford/AstraZeneca Covid vaccine research ‘was 97% publicly funded’. The Guardian

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Open Research Forum 7th July 2021

Posted on July 8, 2021 by fredbreese

Thank you to all who attended our first Open Research Forum meeting on Wednesday. A recording of the meeting is available to view for University of Reading members via this link (University members only).

These regular meetings give an opportunity for Open Research Champions and others to share experiences with Open Research at the University of Reading, and updates for ongoing projects. Another meeting is planned in September, for more information email researchdata@reading.ac.uk and we’ll add to you to the Open Research mailing list.

Four presentations were given by Research Champions at this event, slides are downloadable below.

Open Research survey (Auvikki de Boon and Sophie Read)

Our Champions have been developing an Open Research survey to map the current landscape of Open Research practices at Reading, among both staff and students. The plan is to launch the survey at the beginning of Autumn term, with all respondents being entered into a prize draw.

The aim of this project is to better inform our work promoting Open Research across the University, and to guide our offering of Open Research training opportunities. For more information contact marcello.demaria@reading.ac.uk

Download Slides

An open hardware community for the University (Al Edwards)

Open Hardware is a movement which already has a large following outside of Research Science.  For researchers participating in Open Hardware is an opportunity to share information about equipment used in research platforms. This can assist with reproducibility, showing other researchers the exact instrumentation used to produce results, and is in line with the values promoted by the Open Research movement. Al’s interest in Open Hardware grew out of a project in 2019 with a 3D printer and a Raspberry Pi which you can read more about here.

Al would like to grow an open hardware community at the University of Reading. Are you interested in making low-cost easily reproducible scientific equipment? Al is especially keen to work with developers of open software, as there is so much overlap between software and hardware, not least in 3D CAD for printing exciting random plastic things. There are also plans for an Open Hardware Hackathon in September. Contact r.sariyer@pgr.reading.ac.uk if you’d like to take part.

Electronic lab notebooks pilot project (Cristiana Bercea)

Electronic lab notebooks are software systems for documenting research work, intended to replace the use of paper notebooks. They are easy to use and offer extra functionality over traditional lab books. This includes simple collaborative features, making the notebook searchable, timestamping entries and integration with other software and data sources.

Cristiana is leading a project to pilot electronic lab notebooks in the Schools of Chemistry, Food and Pharmacy and Biological Sciences. The pilot group will start in August and test three different platforms for the Notebooks. If you are interested in taking part you can find out more here and let Cristiana know at c.bercea@reading.ac.uk

Download Slides

Open data and land corruption (Marcello De Maria)

Marcello and PhD student Niko Howai recently won funding to explore the use of open data to counteract land corruption. Marcello discussed their final report and the broader impact open data can make in this important area. Their methodology has informed a number of other studies, showing the role open research practices can allowing interaction with a larger community of stakeholders.

There is growing availability of digital land data, but openness remains limited; 1% of countries have land ownership records open and in digital form. The report made a number of recommendations, in particular highlighting the need for public engagement, tech know-how, pollical will and a strong legal framework to achieve concrete change towards open platforms. You can read the full report online here.

Download Slides

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University of Reading Open Research Award 2021

Posted on June 10, 2021 by Robert Darby

The University of Reading’s Open Research Award 2021 online celebration took place on the afternoon of Wednesday 9th June.

Wellcome Trust Lecturer in English Literature Dr Alanna Skuse won the Award with an outstanding case study on the challenges and benefits of publishing Open Access in the humanities; while Dr David Brayshaw and Dr Hannah Bloomfield took the prize for best presentation and shared third place in the Award with a discussion of the role of data sharing in the meteorology-renewable energy interface. Dr Ting Sun and Professor Sue Grimmond took second place with a study of Open Source software development in urban climate modelling; and Dr Luke Barnard and Professor Mathew Owens shared third place with another study of Open Source software development, this time in modelling solar wind.

Just under 90 people from across and outside the University joined us to celebrate researchers who have used open practices to make their research more accessible, transparent or reproducible. We had a superb set of researchers to celebrate, and heard four excellent presentations providing insights into a diverse range of Open Research experiences. Summaries of presentations and the Award Panel’s assessment are provided below, and slides from all speakers are available for download. A recording of the event can be found here.

We were also privileged to welcome our keynote speaker Sarah de Rijcke, Professor in Science, Technology, and Innovation Studies and Scientific Director at the Centre for Science and Technology Studies (CWTS), Leiden University. Professor de Rijcke is co-author of the Leiden Manifesto for Research Metrics and the UNESCO Recommendation on Open Science. Sarah discussed the impoverishment of research when it is governed by a narrow range of value criteria and assessment indicators. The San Francisco Declaration on Research Assessment (DORA), the Leiden Manifesto, the pioneering work of the Research on Research Institute (RoRI), and the UNESCO Recommendation on Open Science are all signposts to a more equitable, inclusive, collaborative and transparent research culture built on open foundations. Key to reforming research culture is the implementation of assessment and evaluation systems that are aligned to Open Research principles and that reward accessibility, transparency and reproducibility.

Professor Parveen Yaqoob, Deputy Vice-Chancellor and PVC for Research and Innovation, also presented an update on University progress in Open Research, and highlighted some of the milestones on our recent journey, including this year’s launch of the University’s Open Research Action Plan (download from Useful links on this page) and the Open Research Champions programme. Dr Phil Newton, Research Dean for Environment and senior management champion for Open Research, gave a welcome address at the start of the event and sent us on our way with some closing remarks. Both Professor Yaqoob and Dr Newton highlighted the University’s progressive position in the UK sector: it was the first to publish an institutional Statement on Open Research (in January 2019), and the Open Research Award competition, first run in 2019, has established a model that has since been replicated in several UK universities.

Slides

Winning entries in the Open Research Award 2021

Presenters are marked with a †. Following an abstract of the presentation, text in italics summarises the assessment of the Award Panel.

Winner of the Open Research Award (prize: £500)

Dr Alanna Skuse†: Surgery and Selfhood: lessons from open humanities publishing

Surgery and Selfhood in Early Modern England: Altered Bodies and Contexts of Identity is an Open Access monograph published in 2021. It is the product of a Wellcome Trust-funded postdoctoral fellowship undertaken 2016-2019. This is the second Open Access monograph I have published. I explore the challenges of publishing Open Access for humanities researchers, where there may be a limited range of suitable Open Access venues. I also discuss the benefits of taking the Open Access route for long form publications, including increased readership and opportunities for engagement with a non-academic audience.

This was a deserved winner, demonstrating a clear-eyed appreciation of both the benefits and the challenges of publishing Open Access in the humanities, and evincing a clear commitment to embedding openness in humanities research.

Alanna has been an early adopter of Open Access monograph publication. The Panel was impressed that Alanna is also working to influence emerging policy through her membership of the UKRI Early Career Researcher Forum, and to help her colleagues at Reading make informed Open Access choices through her role as an Open Research Champion.

Second place (prize: £250)

Dr Ting Sun† and Professor Sue Grimmond: Urban climate modelling using SuPy: enhancing the SUEWS community

Over 55% of the world’s population live in cities, so their activities are critical to the global environment; but cities occupy less than 0.1% of global land, and their weather and climate is poorly understood. It is essential to understand urban atmosphere-environment interactions, at various scales (building – neighbourhood – city) in order to build resilient cities under changing climates. We developed the Open Source urban climate model SuPy (Surface Urban Energy and Water Balance Scheme or SUEWS in Python) with the goal of delivering reproducible research and exciting urban climate teaching. In this case study we discuss how we developed an active Open Source user community by making strategic decisions about how to package, distribute and support the software.

This was an outstanding case study of a well-considered development and distribution of Open Source software for urban climate modelling research. A commitment to making the software user-friendly and developing the user community has resulted in re-use of the software in teaching and student projects and research workshops around the world.

The entry derived strong lessons about the need to support open resources with good documentation and user support, and to use the right online platforms to engage and sustain an active user community.

Third place and best presentation (prizes: £150 + £150)

Dr David Brayshaw†, Dr Hannah Bloomfield†, Dr Paula Gonzalez, Professor Andrew Charlton-Perez, Professor John Methven, Dr Phil Coker, Dr Dan Drew, Dr Dirk Cannon: Meteorological data for the transition to future clean energy systems

Rapid increases in renewable electricity generation (such as wind and solar), mean that the need for high quality, openly available, climate information for managing energy-system risk has never been greater. The Energy-Meteorology research group has been at the forefront of addressing this interdisciplinary challenge for more than a decade. It has created numerous open-access datasets and models enabling researchers to explore climate risk to energy systems, including long term ‘artificial histories’ of renewable generation and tailored sub-seasonal weather forecasts up to 6-weeks ahead. The methods and datasets the group has developed are now in widespread use by academia and industry.

There was real substance to this case study of a research team engaging in sustained distribution of open data over a period of several years, and using these data to create a bridge between the fields of meteorology and renewable energy research.

David and Hannah’s presentation really brought out the team effort, and Hannah was articulate about her own learning journey from fist venturing into data sharing as a PhD student. She highlighted the critical importance of providing good documentation and designing datasets with the target users in mind. It was inspiring to see a research group building capacity in data sharing and developing data curation skills in the new generation of researchers.

Third place (prize: £150)

Dr Luke Barnard† and Professor Mathew Owens, Open Source modelling of space weather

We have produced a new, computationally efficient, numerical model of the solar wind. We made this model Open Source because we believe it is useful to researchers, educators, and space weather forecasters. Within a year this has resulted in new international collaborations, uptake by external university courses, and the further development of our model into an operational forecast tool at the UK Met Office, including our own research outputs. Open research practices have significantly raised the quality and the impact of our research outputs; for us, this clearly justifies the resources and effort required to implement open research practices effectively.

This was a well-articulated case study, which clearly set out the rationale for adopting an Open Source pathway to distribute novel computationally-efficient modelling software.

Luke spoke persuasively of the benefits realised as a result of making the software Open Source, which has led to new research collaborations, improvement in the model and quality of the resulting research, and has enabled him to win funding to develop the tool for operational use by the Met Office.

Speakers

Dr Luke Barnard is a postdoctoral researcher in the Department of Meteorology. Luke’s research focuses on how the Sun creates and controls the space environment near Earth. In particular, Luke is interested in how sporadic eruptions of mass and radiation from the Sun create the space weather that affects us on Earth from day-to-day. Using cameras on spacecraft that observe the Sun’s atmosphere with numerical models of the solar wind, Luke develops methods to improve the skill and reduce the uncertainty of space weather forecasts.

Dr Hannah Bloomfield is a PDRA in the Meteorology department working in the Energy-Meteorology research group. Her interests include understanding the impacts of climate variability and climate change on current and future power systems. Hannah has created numerous open access datasets of renewable energy generation and electricity demand which are used in academia, industry and teaching.

Dr David Brayshaw is an Associate Professor in the School of Mathematical, Physical and Computational Sciences (Meteorology Department), where he founded the Energy-Meteorology research group in 2012. He has been involved in numerous academic and commercial research projects on weather and climate risk in the energy sector, including a leadership role in two major European energy-climate service prototypes. He leads several initiatives supporting interdisciplinary exchange and education in energy-climate science and climate services more broadly.

Sarah de Rijcke is Professor of Science, Technology and Innovation Studies and Scientific Director at CWTS, Leiden University, and Co-Chair of the Research on Research Institute (RoRI). Sarah specializes in social studies of research evaluation, which she considers in relation to epistemic cultures, knowledge infrastructures, valuation processes, and roles of research in and for society. She has a strong international public academic presence with global outreach activities in science policy, speaking frequently on the topic of research evaluation and metrics uses. She recurrently acts as expert advisor in European and global science policy initiatives. Most recently, she was invited to represent the Netherlands in a high-level UNESCO Expert Group to write a global recommendation on Open Science. Her present research is funded by a grant from the European Research Council (ERC). Her team regularly collaborates in research consortia funded by the European Commission’s Framework programmes and national research councils across Europe and the UK.

Dr Phil Newton is Research Dean for Environment and senior management champion for Open Research. He is a member of the Committee on Open Research and Research Integrity and has been a driving force behind the Open Research initiative at Reading in the last few years. He published the University’s Statement on Open Research in 2019 and secured funding to implement the University’s Open Research Action Plan 2021-23.

Dr Alanna Skuse is a Wellcome Trust University Award holder in the Department of English Literature. Her research focuses on early modern representations of self-wounding. She has been a Wellcome Postdoctoral Fellow at Reading and Long-term Fellow at the Folger Shakespeare Library, and has taught at Bristol and Exeter universities. Alanna has published two Open Access monographs, Surgery and Selfhood in Early Modern England (CUP, 2020) and Constructions of Cancer in Early Modern England (Palgrave, 2015), as well as numerous journal articles. She has written for The Conversation and organised numerous public engagement events as well as speaking at a variety of heritage and charity events.

Dr Ting Sun is a NERC Independent Research Fellow in the Department of Meteorology. His research is in the fields of urban climate and hydrology with a focus on understanding urban-atmospheric interactions for enhancing urban resilience and sustainability. He is an advocate for Open Research as a lead developer of several Open Source models, notably SuPy and SUEWS, and through these is a key contributor to the Open Source climate service tool UMEP (Urban Multi-scale Environmental Predictor).

Professor Parveen Yaqoob is Deputy Vice-Chancellor and PVC for Research and Innovation. As Chair of the Committee on Open Research and Research Integrity, Professor Yaqoob provides strategic direction for the University’s initiative to develop its culture of Open Research.

Open Research Award Panel

Professor Parveen Yaqoob, Deputy Vice-Chancellor and PVC for Research and Innovation (Chair); Dr Etienne Roesch, Associate Professor, School of Psychology and Clinical Language Sciences; Dr Phil Newton, Research Dean for Environment; Professor John Gibbs, Head of School, School of Arts and Communication Design; Dr Robert Darby, Research Data Manager.

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Electronic lab notebooks pilot study

Posted on June 2, 2021 by Robert Darby

This post is by Open Research Champion Cristiana Bercea

As one of the leads for Open Research for the School of Chemistry, Food and Pharmacy, I would like to invite colleagues to participate in a pilot study on the use of electronic lab notebooks (ELNs) between the end of June and the end of September. You do not have to be in Chemistry, Food and Pharmacy to take part: for example, members of the School of Biological Sciences may also be interested in the pilot.

In short, the plan is to provide you with a list of free software packages that we propose might be suitable, and ask you to choose one that you are willing to try. This would be especially useful to involve new PhDs in. We will organise an induction workshop where I will briefly show you around the packages and discuss any questions. If you are interested, please complete this Doodle poll to indicate your availability.

Anyone is welcome to join, or alternatively you can designate a rep for your lab, who will also liaise with me regarding feedback.

There are many advantages to switching to ELNs, of which a few are:

  • backup means information cannot be lost
  • keywords being searchable means it’s easy to find methods and data from a while ago, or from people who leave the lab
  • time and date stamps
  • data integration means it would be easier to prepare publications.

During the pilot, I will ask the participants to take a look at this feedback form and fill in your assessments. This checklist was adapted from similar pilots held at other universities, so we feel it’s comprehensive, and I would like to organise a feedback presentation (Doodle poll to come in July) to discuss the outcomes with you. However, if you have any other comments or suggestions, please let us know. I set up the form such that each group testing a package can copy and paste a Sheet, rename it with the name of the rep, the name of your group, and package, and fill it in. There is an example with my name, our lab, and OneNote.

As Open Research Champion representative on the Committee on Open Research and Research Integrity (CORRI), at the end of the pilot I will write a report of our experience and discuss it with CORRI. If there is interest, we can also discuss obtaining university subscriptions, which would allow access to further software features.

If you are interested in taking part in this pilot study please take a look at the list of proposed software. If you have other packages you are already using or have used in the past, that would be great as well.

Here are some more information resources:

If you have any questions or would like to discuss taking part, please contact me.

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Open Research Award 9th June 2021

Posted on May 18, 2021 by Robert Darby

The University of Reading’s Open Research Award 2021 online celebration will take place at 13.00-15.30 on Wednesday 9th June. Four finalists (listed below) will present their Open Research case studies and the winner of the 2021 Award will be announced. There will be prizes for the winner of the Award, and second and joint third places, as decided by the Award Panel, and a prize for best presentation, which will be determined by audience vote.

The online celebration will feature a keynote from Sarah de Rijcke, Professor in Science, Technology, and Innovation Studies and Scientific Director at the Centre for Science and Technology Studies (CWTS), Leiden University. Professor de Rijcke is co-author of the Leiden Manifesto for Research Metrics and the UNESCO Recommendation on Open Science.

Professor Parveen Yaqoob, Deputy Vice-Chancellor and PVC for Research and Innovation, will present an update on University progress in Open Research.

Book your place now at the Open Research Award online celebration.

A recording of the event will be made available afterwards.

If you have any enquiries please contact Robert Darby, Research Data Manager.

Open Research Award 2021 finalists

†Presenters.

Programme

Welcome (Phil Newton) 13.00
Fostering Open Research through responsible research assessment (Sarah de Rijcke, Leiden University) 13.05
UoR progress in Open Research (Parveen Yaqoob) 13.40
Break 13.55
Presentations by Open Research Award finalists (Ting Sun, Alanna Skuse, David Brayshaw and Hannah Bloomfield, Luke Barnard) 14.05
Audience vote and result 15.05
Announcement of Award and runners-up (Parveen Yaqoob) 15.10
Wrap up 15.20
Close 15.30

Keynote

Fostering Open Research through responsible research assessment

Sarah de Rijcke is Professor of Science, Technology and Innovation Studies and Scientific Director at CWTS, Leiden University, and Co-Chair of the Research on Research Institute (RoRI). Sarah specializes in social studies of research evaluation, which she considers in relation to epistemic cultures, knowledge infrastructures, valuation processes, and roles of research in and for society. She has a strong international public academic presence with global outreach activities in science policy, speaking frequently on the topic of research evaluation and metrics uses. She recurrently acts as expert advisor in European and global science policy initiatives. Most recently, she was invited to represent the Netherlands in a high-level UNESCO Expert Group to write a global recommendation on Open Science. Her present research is funded by a grant from the European Research Council (ERC). Her team regularly collaborates in research consortia funded by the European Commission’s Framework programmes and national research councils across Europe and the UK.

Finalists’ presentations

Urban climate modelling using SuPy: enhancing the SUEWS community (Dr Ting Sun)

Over 55% of the world’s population live in cities, so their activities are critical to the global environment; but cities occupy less than 0.1% of global land, and their weather and climate is poorly understood. It is essential to understand urban atmosphere-environment interactions, at various scales (building – neighbourhood – city) in order to build resilient cities under changing climates. We developed the Open Source urban climate model SuPy (Surface Urban Energy and Water Balance Scheme or SUEWS in Python) with the goal of delivering reproducible research and exciting urban climate teaching. In this case study we discuss how we developed an active Open Source user community by making strategic decisions about how to package, distribute and support the software.

Dr Ting Sun is a NERC Independent Research Fellow in the Department of Meteorology. His research is in the fields of urban climate and hydrology with a focus on understanding urban-atmospheric interactions for enhancing urban resilience and sustainability. He is an advocate for Open Research as a lead developer of several Open Source models, notably SuPy and SUEWS, and through these is a key contributor to the Open Source climate service tool UMEP (Urban Multi-scale Environmental Predictor).

Surgery and Selfhood: lessons from open humanities publishing (Dr Alanna Skuse)

Surgery and Selfhood in Early Modern England: Altered Bodies and Contexts of Identity is an Open Access monograph published in 2021. It is the product of a Wellcome Trust-funded postdoctoral fellowship undertaken 2016-2019. This is the second Open Access monograph I have published. I explore the challenges of publishing Open Access for humanities researchers, where there may be a limited range of suitable Open Access venues. I also discuss the benefits of taking the Open Access route for long form publications, including increased readership and opportunities for engagement with a non-academic audience.

Dr Alanna Skuse is a Wellcome Trust University Award holder in the Department of English Literature. Her research focuses on early modern representations of self-wounding. She has been a Wellcome Postdoctoral Fellow at Reading and Long-term Fellow at the Folger Shakespeare Library, and has taught at Bristol and Exeter universities. Alanna has published two Open Access monographs, Surgery and Selfhood in Early Modern England (CUP, 2020) and Constructions of Cancer in Early Modern England (Palgrave, 2015), as well as numerous journal articles. She has written for The Conversation and organised numerous public engagement events as well as speaking at a variety of heritage and charity events.

Meteorological data for the transition to future clean energy systems (Dr David Brayshaw and Dr Hannah Bloomfield)

Rapid increases in renewable electricity generation (such as wind and solar), mean that the need for high quality, openly available, climate information for managing energy-system risk has never been greater. The Energy-Meteorology research group has been at the forefront of addressing this interdisciplinary challenge for more than a decade. It has created numerous open-access datasets and models enabling researchers to explore climate risk to energy systems, including long term ‘artificial histories’ of renewable generation and tailored sub-seasonal weather forecasts up to 6-weeks ahead. The methods and datasets the group has developed are now in widespread use by academia and industry.

Dr David Brayshaw is an Associate Professor in the School of Mathematical, Physical and Computational Sciences (Meteorology Department), where he founded the Energy-Meteorology research group in 2012. He has been involved in numerous academic and commercial research projects on weather and climate risk in the energy sector, including a leadership role in two major European energy-climate service prototypes. He leads several initiatives supporting interdisciplinary exchange and education in energy-climate science and climate services more broadly.

Dr Hannah Bloomfield is a PDRA in the Meteorology department working in the Energy-Meteorology research group. Her interests include understanding the impacts of climate variability and climate change on current and future power systems. Hannah has created numerous open access datasets of renewable energy generation and electricity demand which are used in academia, industry and teaching.

Open Source modelling of space weather (Dr Luke Barnard)

We have produced a new, computationally efficient, numerical model of the solar wind. We made this model Open Source because we believe it is useful to researchers, educators, and space weather forecasters. Within a year this has resulted in new international collaborations, uptake by external university courses, and the further development of our model into an operational forecast tool at the UK Met Office, including our own research outputs. Open research practices have significantly raised the quality and the impact of our research outputs; for us, this clearly justifies the resources and effort required to implement open research practices effectively.

Dr Luke Barnard is a postdoctoral researcher in the Department of Meteorology. Luke’s research focuses on how the Sun creates and controls the space environment near Earth. In particular, Luke is interested in how sporadic eruptions of mass and radiation from the Sun create the space weather that affects us on Earth from day-to-day. Using cameras on spacecraft that observe the Sun’s atmosphere with numerical models of the solar wind, Luke develops methods to improve the skill and reduce the uncertainty of space weather forecasts.

Open Research Award Panel

Professor Parveen Yaqoob, Deputy Vice-Chancellor and PVC for Research and Innovation (Chair); Dr Etienne Roesch, Associate Professor, School of Psychology and Clinical Language Sciences; Dr Phil Newton, Research Dean for Environment; Professor John Gibbs, Head of School, School of Arts and Communication Design; Dr Robert Darby, Research Data Manager.

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