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
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
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. 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.
The translated paper in the CentAUR repository
Have you had any feedback or response to your work?
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.
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
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
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 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
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.
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
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 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
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.
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 Skusewon 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.
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.
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.
introduction to ELNs: what ELNs are, how they work, what the features and functionality are, options for storage and security, and advice about how to pick one
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.
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.
Do you collect research data that is difficult or impossible to anonymise, or that would lose significant value if identifiable/confidential information were removed?
Would you use a secure solution for archiving these research data in such a way that they can be safely shared with other researchers, subject to authorisation and under conditions designed to preserve confidentiality?
The Research Data Manager and Data Protection Officer are investigating the feasibility of implementing a University service for the secure archiving of confidential/identifiable research data, and the sharing of such data with authorised researchers under a standard data access agreement, subject to approval by a Data Access Committee.
We believe a University-managed solution would give researchers the confidence to preserve and share data safely, where otherwise they might be lost to research or exposed to the risk of inappropriate disclosure.
We would consider within scope any datasets that cannot be shared openly because of the confidential nature of the information they contain or because a higher risk of re-identification exists. In such cases it may still be possible for data to be shared on a restricted and managed basis.
These are examples of data that might be suitable for archiving in this service:
Datasets containing participant-identifying or other confidential information (such as commercial information), e.g. unredacted interview transcripts; video and photographic data containing images of identifiable participants; biometric data, such as facial scans or fingerprint images; records of commercial activities;
Data that have been anonymised but that because of the sensitivity of the information they contain or a risk of identification through linkage to other publicly-accessible data are considered higher-risk and not suitable for public sharing.
The service would provide the following features:
A dataset with related documentation can be formally deposited in the service, with a linked publicly-accessible metadata record published via the University of Reading Research Data Archive. The dataset will be assigned a DOI that links to this metadata record. The public metadata record does not contain any sensitive information, but it means the dataset is citable and discoverable by potential legitimate users.
The dataset will be held in closed internal storage, accessible only by authorised persons (e.g. service administrators and the PI of the project in which the data were collected).
A researcher affiliated to a recognised research organisation may apply to access the data for non-commercial research purposes. The researcher’s credentials will be validated and their application will be subject to approval by a Data Access Committee (DAC). The original project PI or a suitable representative will join the DAC in order to consider the access request. The DAC may either grant or refuse the request.
If the request is granted, the requester’s organisation will sign a Data Access Agreement with the University. This agreement requires the recipient to use the data in confidence and to destroy their copy of the data by an agreed date. Once the agreement is signed the data will be securely shared with the recipient. The University will follow up to ensure that the data are destroyed by the agreed date.
The proposed model is based on a successful service established by the University of Bristol.
If you collect data that you think might fall within scope of this service, we want to hear from you.
Would you use this service? What type of data might you wish to deposit?
Robert Darby (Research Data Manager) and Rebecca Daniells (Data Protection Officer) will be holding an open consultation at 13.00-14.00 on Wednesday 26th May. Come along to find out more about the proposal and ask questions.
The University’s 2021 Open Research Award is now open for entries.
The Open Research Award will recognise and reward researchers or research students who have used open practices to make their research more accessible, transparent or reproducible. Entry is open to both members of staff and research students, who may enter either as individuals or as teams. Entry is by means of a case study describing how open practices have been used in a research context.
The winner of the Open Research Award, and second and joint third places, will be determined by a panel of judges chaired by Professor Parveen Yaqoob, Pro-Vice-Chancellor (Research & Innovation). The winner will be announced at the Open Research Celebration following the presentation of case studies. Prizes will be awarded as follows:
Winner of the Open Research Award: £500
Second place: £250
Joint third place: £150 each.
There will also be a £150 prize for best presentation decided by audience vote on the day.
Prizes awarded to members of staff will be paid into SDA accounts. Prizes awarded to research students will made as cash payments.
Shortlisted entries will be published on the University website as Open Research case studies, and will be promoted in the University’s Open Research communications.
The Award is administered by the Committee on Open Research and Research Integrity.
Dr David Brayshaw
Dr Alanna Skuse
This post is by Open Research Champion 
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