The Open Science Notice Board

Open science skills for competing for funding from Horizon Europe

In the European Commission’s latest framework programme for research and innovation, Horizon Europe 2021-2027, applicants are required to account for how open science practices are to be implemented in their project and how these benefit the project’s overall aim. Open science practices are exemplified as open access publishing, pre-print publishing, registered reports, sharing of data, software, code or algorisms, engaging citizens and other stakeholder. It can also encompass other ways of enhance accessibility, transparency and reproducibility in research. In this blog entry, I have been talking to Anneli Wiklander and Teresia Rindefjäll, research funder advisors at Research Services to learn more about the implications of these new requirements.

Karolina: What impact do the descriptions of open science practices in applications have in the evaluation of proposals?

Teresia: The section where applicants describe the implementation of open science practices is included in the research methodology, which is part of the excellence section of the applications. Applications to EU have three parts, excellence, impact and implementation. Previously, open access publication was addressed in the impact section. Now the EU is talking instead of open science, which is a broader concept. The excellence section has a larger impact on the overall evaluation of the proposal compared to the impact and implementation sections. Therefore, descriptions of open science practices has a larger impact now than in any previous research programs.

Anneli: It is very important for researchers to understand what the concept Open Science and its components entail. Demands on making research data available and FAIR has been included in previous announcements but then with the possibility of opting in or out, this is not the case now. Open science is new for researchers and we need to see more evaluations of the applications to see the expectations from the EU and evaluators. We think it is important that LU provides support in the open science area to assist researchers that have questions. If you get 5 points in the other two sections of the proposal and 4,5 on the excellence section due to shortcoming relating to open science you might be out of the game.

Karolina: What questions have you received from researchers about open science relating to the calls that are part of this research program?

Teresia: We do not have a large material to draw conclusions from since not that many applications have been evaluated within the Horizon Europe 2021-2027 program yet. Personally, I have not received many questions and most have been rather general. For these questions we can refer researchers to their faculty libraries and to resources available online, but from what we have seen many applicants address more established open science practices such as open access publishing and to a lesser degree other aspects of open science. As we see more evaluation reports we will analyse point reductions related to descriptions of how open science is implemented in projects and identify what kind of additional support researchers may need.

Anneli: It is common that researchers describe how they will make their publications open access, if they will publish pre-prints and then it is of course mandatory to have a data management plan. From the evaluations that we have seen this far it is clear that evaluators expect more. There will not be one solution for all research areas, but a more equal approach with time, still adjusted to suit the research and project. Then there may also be differences between different calls within the program. In some calls, it is explicit that public engagement or involvement of stakeholders must be addressed. Another thing is that if a researcher do not plan to implement, say for example citizen science, in their project it can be good to describe the reasons for not doing so in case it could be seen as a relevant open science practice for the project by evaluators. However, this requires the research to know how to express this. I think more skills and competence related to open science is required at Lund University. For open access publishing and for writing data management plans the libraries offer plenty of support.

Karolina: From what you say, implementation of open science practices appear to have become an important aspect in applications when competing for funding from the EU.

Anneli: Yes, it has!

Teresia: Yes, and in the national strategy for Sweden’s involvement in Horizon there is a call for increasing participation. At Lund University, there is also an interest in increasing the number of successful applications to the EU. It is therefore important to highlight that the skills to adequately address open science practices in applications is a matter of being in a position to compete for these grants.

February 24, 2022

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Digital archaeology and infrastructures for sharing – an interview with Nicolò Dell’Unto

Nicolò Dell’Unto is an associate professor and senior lecture in archaeology. His research focus on developing digital methodologies for archaeological analysis. He is part of a team that is maintaining and developing the Lund University Digital Archaeological Laboratory (DARK Lab) which is a research infrastructure that develops visualization strategies for analysis of archaeological data.

Karolina: How does open science connect with archaeology?

Nicolò: Open Science (OS) is the key to progress in archaeological studies; however, several cultural and methodological changes are necessary to achieve Open Science in archaeology. I think we need to start implementing digital infrastructures capable of promoting FAIR principles and, most importantly, enable users to produce knowledge. We need also to identify strategies for linking OS to career paths, e.g., how data published through a digital infrastructure can be cited through a DOI and in this way have an impact on the cv of the researcher that shared the data. The covid 19 pandemic was an important moment for mapping limits and potentials of the different infrastructures available. For example, we noticed that many infrastructures mainly provide information about the location where archaeological materials can be retrieved. This is of course very useful, but not sufficient for triggering a process of knowledge production. Since 2020, we have been exploring web visualization systems for making our data, mainly 3D models, available and useful in situations like the covid pandemic. We experimented with systems based on 3D web visualization, designed to provide people with access to all information they need for running research from home without necessarily installing any software or downloading any dataset to their computer. The Digital Collections available through the DARKLab website were designed with this purpose in mind.

Karolina: Could you explain what the DARK lab’s digital collections contain?

Nicolò: The digital collections available through the DARKLab website are organized into three main categories: Excavations, Monuments and Artefacts. Excavations provide access to 3D datasets acquired during different field investigations. Currently, it is possible to review and reuse data from the archaeological field investigations carried out in Kämpinge, Gribshunden, Västra Vång and Södra Sallerup. Some of these systems were used during the pandemic to support courses in field archaeology, at for example Stockholm University, and link researchers working remotely with material from Gripshunden and Västra Vång. In Monuments, it is possible to access the datasets acquired during the Republican Forum Romanum project, the Swedish Pompeii Pompeii project and the Lund Cathedral project. Furthermore, the 3D web system designed to publish monuments allows the users to explore the models at different resolutions gaining spatial information and morphological details that would be difficult to see on site. The Artefacts are published through the Dynamic Collections web platform, is an ongoing research project developed in collaboration with the Lund University Historical Museum and the National Research Council of Italy CNR-ISTI. The Dynamic Collections project aims to develop a novel 3D web infrastructure to support higher education and research in artefacts analysis. At the onset of the COVID-19 pandemic, all teaching at Lund University moved online, reinforcing the urgency for such an infrastructure. The Lund University Digital Archaeology collections are part of the VR funded infrastructure Swedigarch. This new infrastructure is a large consortium which includes many Swedish universities and Heritage institutions. The idea is to experiment and find solutions for connecting archives, which are very different in purpose. This will give us the possibility to work in synergy.

Karolina: What information can you access and what can you do in Dynamic Collections?

Nicolò: Through the system, you can (1) retrieve several measures such as length and of angles, (2) create different sections of the artefacts, (3) produce high-resolution orthoimages and (4) access meta and para data. Furthermore, it is possible to remove the colour information and manipulate the light to highlight information usually invisible on the original object. The system allows different recording types of annotations. Once “interpreted”, the artefacts and the annotated interpretation can be saved on the user’s personal computer and shared with others. For example, when studying a specific artefact or group of artefacts you can use the system to annotate your thoughts, retrieve measurements etc. Once finished, you can download and forward your interpretation to a colleague. This person can upload your interpretation on the 3D web platform and further implement the research. This dynamic interaction can also be performed between the teacher and the students in class. The Dynamic collections is an archive (or a repository) of 3D objects. However, a collection is a different things… A collection is an expression of a specific scientific culture. The platform developed for the Dynamic collections project allows users to create personal collections of artefacts assembled to address specific research questions. Furthermore, the collections created through the web system can be authored, described, annotated and shared! This is, in my opinion, the coolest tool that we have developed so far because it allows researchers to use the system to generate new knowledge!

Karolina: In your view and from your experiences, which are the possibilities and challenges related to open science in archaeology?

Nicolò: Open science, in general, is a very broad concept, and this could be confusing… However, working with a broad definition leave us a larger space for experimenting with different solutions. It is utopistic to think that archaeology or any other discipline can become completely open in a very short time. Therefore, we need to work hard to:

Construct new and more innovative infrastructures.
Create new generations of researchers capable of engaging with digital data.
Include and promote research methodologies that require datasets available across different disciplines.

Although there is still a layer of concern among the community of researchers about implementing a fully Open Science approach, I am confident that this process will lead us all into new and more effective research trajectories. Things are changing rapidly, and being part of this change is just great!

More information about Nicolò’s research is available here.

February 17, 2022

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Open Access and transformative agreements

The number of scientific article published open access by researchers affiliated with Lund University has increased from 26 % in 2015 to 69 % in 2021[1]. A consortium of Swedish universities, colleges and national agencies called BIBSAM, has for approximately 30 years, negotiated agreements for access to electronic resources. Today these agreements also encompass publishing fees in open access and hybrid journals. Åsa Sellgren and Anna-Lena Johansson work at the University Library and manage the agreements that LU has joined and provide access to these for researchers and PhD-students at LU. In this blog entry they tell us more about transformative agreements.

Karolina: Could you briefly describe what a transformative agreement is?

Anna-Lena: Yes, with previous agreements, we paid for reading rights but with transformative agreements, we pay for both reading and publishing rights in hybrid journals, that is, journals that publish both open access content and content that is behind paywalls. A transformative agreement means that the journals that are included in these will gradually be transformed into full open access journals.

Karolina: When did transformative agreements first appear and how have these changed over time?

Anna-Lena: The first agreement that Lund University participated in came into effect in the summer of 2016. That was an agreement with Springer.

Åsa: Today we have approximately 25 agreement with different publishers. The agreements have evolved gradually. Initially many agreements covered the cost for a yearly agreed number of publications. The costs associated with the number of publications that arose above those included in the agreements were split between participating universities according to the number of publications from each of these. For example, previous agreements with Wiley and Taylor & Francis were such agreements. In order to pay for the publications beyond the agreements we had to apply for funding centrally from Lund University. This kind of agreements are, with a few exceptions, no longer made and BIBSAM do not want to enter into agreements that only cover an agreed number of publications anymore. BIBSAM have other criteria as well. To enter into an agreement that exceeds a period of one year the publisher must have a plan for a transformation towards open access. If they do not have that in place, only one-year agreements encompassing reading rights are made. I think that is a good thing, in that way BIBSAM put pressure on the publishers. Large publishers that BIBSAM have transformative agreements with, such as Elsevier, do however continue to launch subscription-based journals. In that way some publishers go against the transformation towards open access.

Karolina: Is there any difference regarding attitude towards transformative agreements and open access between commercial publishers and university presses?

Åsa: Yes, there is a difference. The large commercial publishers have said that this transformation is going to take a long time for them to complete while the university presses push towards open access. One such example is Cambridge University Press. They have a clearly stated plan for transforming the majority of their journals to open access no later than 2025. It is very good that there are publishers that choose that path. One wonders why university presses do not play a larger part in publishing.

Karolina: If you look ahead, what do you think will happen concerning open access publishing and with publisher agreements in the years to come?

Åsa: I think that we will see these transformative agreements for quite some time; they will not be replaced as soon as we might have hoped. Nevertheless, I think that we will also see that alternatives to these will grow. I hope that the university presses, Open Journal System (for LU’s application see this page) and Open Monograph Press (for LU’s application see this page) will play a bigger role. Publishing is however a large issue that reaches beyond what we do, it is also very much about the role played by publications when research qualifications are evaluated and therefore an issue that needs to be addressed on higher levels at universities.

Karolina: What effects have the transformative agreements had?

Åsa: I think it has made research done at LU more visible. One of the ideas with these agreements were also that they would make it easier for researchers to publish open access. But the agreements differ from each other and publishers use different platforms, some are easy to use and others are more difficult. Still, the agreements have made it easier than it has been previously. I also think that the increasing amount of open access publishing in journals at Lund University is a consequence of these agreements.

Anna-Lena: Another advantage with the transformative agreements is that we now have an overview of the costs spent on publishing. When researchers paid their own publishing fees, we did not have that.

Karolina: If researchers or PhD students at Lund University want to learn more about the possibilities for publishing open access, to whom can they turn and where can they find more information?

Anna-Lena: Information about all agreements Lund University has entered into is available here. If they want to search for journals included in our agreements, they can use the search service called SciFree. Researchers and PhD student can always turn to their faculty library if they have questions about open access publishing, they can also contact publicera@ub.lu.se.

[1] Numbers are based on data from SciVal and only includes gold open access.

January 27, 2022

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Share your experiences of open science! – Workshop for researchers and PhD-students

Researchers and PhD students that would like to share their experiences and needs related to implementing open science approaches in their research are most welcome to register for the open workshops that the ‘Open science at Lund University’ project will organise in February and March.

Open science has today gained a prominent position in research policy in Sweden as well as in the EU. The Swedish government’s goal is that publications and research data from projects funded by public funding should be openly available no later than 2026. Universities and colleges are ascribed an important role in achieving this goal. Research funders are today also increasingly demanding that research outputs such as publications and data from projects they fund should be made openly accessible.

In order to improve conditions for researchers at Lund University to implement open science aspects in their research we are very interested in learning more about your practices and needs related to open science. Open science do not only refer to making publications and data open. It may include sharing software and code, the publication of pre-prints or participating in open peer-review, registered reports, citizen science or in other ways engage in practices that make research available, transparent and reproducible. The information gathered during the workshops constitute an important contribution and background for the suggestions that will be handed over to the research board from the project.

Dates for workshops and registration is available here.

If you have questions about the projects or the workshops, please contact Karolina Lindh (karolina.lindh@ub.lu.se).

January 20, 2022

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European Science Cloud (EOSC) – a major project on open science in Europe

Lund University decided in November 2021 to apply for membership in the EOSC Association, which will be beneficial both for the University in general and for researchers involved in different projects related to EOSC. But what is EOSC? Here follows a short background.

The European Open Science Cloud (EOSC) is an environment for hosting and processing research data to support EU science. The ambition of EOSC is to provide European researchers, innovators, companies, and citizens with a federated and open multi-disciplinary environment where they can publish, find and re-use data, tools and services for research, innovation and educational purposes. This environment will be realized through the EOSC Portal.

EOSC was originally started in 2015 by the European Commission. The aim was to federate existing research data infrastructures in Europe and realize a web of FAIR data and related services for science, making research data interoperable and machine actionable following the FAIR guiding principles. In the initial phase of development until 2020, the Commission invested around €320 million to start prototyping the EOSC through project calls in Horizon 2020. EU countries and countries associated with Horizon 2020, represented in the EOSC Governance Board, agreed unanimously to run the EOSC as a co-programmed European Partnership under Horizon Europe from 2021. In July 2020, an EOSC Association was set up to provide a single voice for advocacy and represent the broader EOSC stakeholder community. This association became operational in 2021 and is rapidly expanding its membership.

Benefits with a membership for Lund University:
• Opportunity for an active engagement in the development of EOSC, which means both access to resources within EOSC and valuable contacts.
• Opens up for valuable collaborations for our researchers.
• Opens up for valuable collaborations for our research infrastructures.

If you have any questions, contact kristoffer.holmqvist@ub.lu.se

January 18, 2022

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Open software for collecting images and detecting emotions in political ads online – interview with Michael Bossetta

Michael Bossetta is a researcher and associate senior lecturer in media and communication studies at Lund University. His research explores how social media are used by politicians and citizens during elections and how the design of platform shape the use of social media in politics. One of his recent studies explored the emotions expressed by presidential candidates in images used in ads on Facebook. For that project, Michael Bossetta and his colleague Rasmus Schmøkel, PhD Student at Southern Denmark University developed two open science tools.

Karolina: Hello Michael! Could you tell us a little about the open software tools that you and your colleague have developed?

Michael: The FBAdLibrarian basically helps researchers download images from Facebook’s Ad Library, which is a searchable database of political ads on Facebook and Instagram. While verified researchers can collect textual data from the Ad Library as a spreadsheet, our tool allows researchers to extract the ads’ images. Images can carry important information that is non-textual, like facial expressions or political symbols.

The other tool is called Pykognition . It creates an easier way for researchers to access the Amazon Rekognition API, which performs emotion and object detection. It gives you a prediction of what emotions people are expressing in images. I think it is important to know that this tool by Amazon is used more by companies, it is not actually built for research. What we did with Pykognition was to make it easier to connect with that product in a way that provides the data in a way more suitable for researchers, not for software developers.

Karolina: Could you say something about the background, which were your reasons for developing these particular tools?

Michael: Facebook launched this Ad Library in 2018, so 2020 was the first US presidential election that we could study political ads on Facebook. In recent years, researchers have made huge strides in developing computational methods software for R, an open source programming language. We wanted to create something in that open source spirit, but most of the existing R software is built for analysing text. However, when it comes to political advertisements on social media, images are probably are more powerful than text in shaping what people think about candidates. So our idea was to develop tools that could collect and analyse images. The paper FBAdLibrarian and Pykognition: open science tools for the collection and emotion detection of images in Facebook political ads with computer vision details how to use the tools, and it’s really a stepping-stone to apply FBAdLibrarian and Pykognition in a bigger research project.

Karolina: Both tools have the GNU GPL license that permits freedom to use, change and share the software. How would you like other people to use or develop these tools?

Michael: I hope people will first try them out and think of other ways to use them. We know facial recognition software has limitations, so how do others deal with those? The way that we actually used Pykognition was to automatically classify happy images, which is where the tool performs best. So we could use Pykognition as a filtering mechanism to remove happy images where we didn’t need human coders. This was not what we originally built it for, but we found it was very useful for reducing the amount of data we needed to code manually. There are probably other, unexpected ways that these tools can help research, and maybe not in the ways that we originally intended. I also hope that people do use these tools to researcher images on social media. A lot of social media research is on text, but images seem to be more powerful. There’s many things we do not know about political images, in terms of how candidates present themselves and the impact their images have on voters.

More information about Michael’s research is available here

January 10, 2022

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Citizen Science

Citizen science refers to ways of engaging non-researchers in research projects. The most common way of doing this is that volunteers help to either gather or organise data of some kind. A good example of the latter is Galaxy Zoo where anyone can go online and help researchers categorize galaxies. A well-established Swedish database is Artportalen, to which anyone can report sights of animal and fauna.

National initiatives that aim to facilitate carrying out citizen science projects have been lacking but this week the first iteration of a national portal for citizen science was launched, medborgarforskning.se. Medborgarforskning.se is connected to the European citizen science portal eu-citizen.science, which includes many interesting resources for anyone interested in engaging in citizen science.

Keynotes from the conference where medborgarforskning.se was launched are available here: https://www.youtube.com/watch?v=Wdi19QVNX_Y