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Announcing: UCL Statement on Principles of Authorship
By Kirsty, on 25 October 2024
As we conclude International Open Access Week, we have been inspired by a wealth of discussions and events across UCL! This week, we have explored balancing collaboration and commercialisation, highlighted the work of Citizen Science initiatives, discussed the role of open access textbooks in education, and addressed key copyright challenges in the age of AI to ensure free and open access to knowledge.
Today, we are excited to introduce the UCL Statement of Principles of Authorship. This new document, shaped through a co-creation workshop and community consultation, provides guidance on equitable authorship practices and aims to foster more inclusive and transparent research collaboration across UCL.
The team at the UCL Office for Open Science & Scholarship is pleased to launch the UCL Statement of Principles of Authorship. These principles have been built up from a co-creation workshop and developed in consultation with our academic community and are now available for wider use, linked from our website.
Participants during ‘Challenges of Equity in Authorship’ workshop in 2023
In August 2023, the OOSS Team posted a discussion about the challenges of equity in authorship and the co-production workshop held during that year’s Open Science & Scholarship Conference. We outlined some preliminary considerations that led to the workshop, summarised the discussion and emerging themes, including the need to more widely acknowledge contributions to research outputs, the power dynamics involved in authorship decisions, and ways to make academic language and terminology accessible for contributors outside the academic ‘bubble’.
The outcomes of the workshop were then used as the basis for developing the new Statement of Principles of Authorship. This document provides general advice, recommendations and requirements for authors, designed to complement the UCL Code of Conduct for Research and align with existing published frameworks, such as the Technicians Commitment or CRediT. The document outlines four core principles and a variety of applications for their use across the broad range of subject areas and output types that are produced across the institution. It also proposes standards for affiliations and equitable representation of contributors.
While it is true that academic publishing is a complex and changing environment, these principles are intended as a touchstone for discussions around authorship rather than explicit expectations or policy. They can guide decision making, help understand how affiliations should be presented for best consistency and traceability in the long term, and empower people to request inclusion or make plans to include citizen scientists or other types of collaborators to their work.
We look forward to hearing the many ways that these principles can be used by the community!
For a full overview of our #OAWeek 2024 posts, visit our blog series page. To learn more about the Principles of Authorship and stay updated on open science initiatives across UCL, sign up for our mailing list.
Copyright and Open science in the age of AI: what can we all do to ensure free and open access to knowledge for all?
By Rafael, on 24 October 2024
We are approaching the end of International Open Access Week, and we have been enjoying a series of interesting insights and discussions across UCL! Earlier this week, we explored the balance between collaboration and commercialisation, highlighted the important work of Citizen Science initiatives and the growing significance of open access textbooks.
Today, Christine Daoutis, UCL Copyright Support Officer, will build on our ongoing series about copyright and open science, focusing on how we can ensure free and open access to knowledge in the age of AI, by addressing copyright challenges, advocating for rights retention policies, and discussing secondary publication rights that benefit both researchers and the public.
Open Access Week 2024 builds on last year’s theme, Community over Commercialisation, aiming not only to continue discussions but to take meaningful action that prioritises the interests of the scholarly community and the public. This post focuses on copyright-related issues that, when addressed by both individual researchers and through institutional, funder, and legal reforms, can help create more sustainable and equitable access to knowledge.
Rights retention infographic. Source: cOAlition-s
Retaining author rights
Broadly speaking, rights retention means that authors of scholarly publications avoid the traditional practice of signing away their rights to publishers, typically done through a copyright transfer agreement or exclusive licence. Instead, as an author, you retain at least some rights that allow you to share and reuse your own research as openly as possible. For example, you could post your work in an open access repository, share it on academic networks, reuse it in your teaching, and incorporate it into other works like your thesis.
Many funders and institutions have specific rights retention policies that address related legal issues. If such a policy applies, and publishers are informed in advance, authors typically need to retain rights and apply an open licence (usually CC BY) to the accepted manuscript at the point of submission.
Rights retention ensures that your research can be made open access without relying on unsustainable pay-to-publish models, and without facing delays or restrictions from publishers’ web posting policies. Importantly, rights retention is not limited to published research—it can be applied to preprints, data, protocols, and other outputs throughout the research process.
Secondary Publication Rights (SPRs)
Secondary publication rights (SPRs) refer to legislation that allows publicly funded research to be published in an open access repository or elsewhere, at the same time as its primary publication in academic journals. Some European countries already have SPRs, as highlighted by the Knowledge Rights 21 study conducted by LIBER, and LIBER advocates for #ZeroEmbargo on publicly funded scientific publications. There are ongoing calls to harmonise and optimise these rights across countries, ensuring that the version of record becomes immediately available upon publication, overriding contractual restrictions imposed by publishers.
SPRs can apply to different types of research output and are meant to complement rights retention policies. However, introducing SPRs depends on copyright reform, which is not an action individual researchers can take themselves, though it’s still useful to be aware of developments in this area.
Source: Computer17293866, CC BY-SA 4.0, via Wikimedia Commons
Artificial Intelligence and your rights
The rise of Generative AI (GenAI) has introduced broader issues affecting researchers, both as users and as authors of copyrighted works. These include:
- Clauses in subscription agreements that seek to prevent researchers from using resources their institution has subscribed to for AI-related purposes.
- Publishers forming agreements with AI companies to share content from journal articles and books for AI training purposes, often without clear communication to authors. A recent deal between Taylor & Francis and Microsoft for $10 million has raised concerns among scholars about how their research will be used by AI tools. In some cases, authors are given the option to opt in, as seen with Cambridge Press.
- For works already licensed for reuse, such as articles under a CC BY licence or those used under copyright exceptions, questions arise about how the work will be reused, for what purposes, and how it will be attributed.
While including published research in AI training should help improve the accuracy of models and reduce bias, researchers should have enough information to understand and decide how their work is reused. Creative Commons is exploring ‘preference signals’ for authors of CC-licensed works to address this issue.
The key issue is that transferring your copyright or exclusive rights to a publisher restricts what you can do with your own work and allows the publisher to reuse your work in ways beyond your control, including training AI models.
Using Copyright exceptions in research
UK copyright law includes exceptions (known as ‘permitted acts’) for non-commercial research, private study, criticism, review, quotation, and illustration for instruction. As a researcher, you can rely on these exceptions as long as your use qualifies as ‘fair dealing’, as previously discussed in a blog post during Fair Dealing Week. Text and data mining for non-commercial research is also covered by an exception, allowing researchers to download and analyse large amounts of data to which they have lawful access.
Relying on copyright exceptions involves evaluating your purpose and, for some exceptions, making a decision around what is ‘fair’. This also involves some assessment of risk. Understanding copyright exceptions helps you exercise your rights as users of knowledge and make confident assessments as to whether and when a copyright exception is likely to apply, and when permission is necessary. [see links for UK legislation at the end of this article]
Source: www.freepik.com
Engage with copyright at UCL
The conversations sparked during Open Access Week continue throughout the year at UCL as part of ongoing copyright support and education. To engage further with these issues, you can:
- Add your voice to how copyright literacy is shaped at UCL. Provide feedback on the draft UCL copyright literacy strategy and consider joining the new UCL copyright literacy community.
- Attend a copyright training session or email copyright@ucl.ac.uk to arrange a bespoke session. The newly introduced ‘Copyright, Open Science and Creativity’ game is a fun way of engaging with current debates and learning about recent developments. More dates for this will be released soon.
- Follow copyright news on the Open@UCL blog and the Copyright blog.
Useful Legislation
- Copyright, Designs and Patents Act 1988, Section 29: Research and Private Study
- Copyright, Designs and Patents Act 1988, Section 29A: Text and Data Mining for Non-Commercial Research
- Copyright, Designs and Patents Act 1988, Section 30: Text and Data Mining
- Copyright, Designs and Patents Act 1988, Section 32: Copying for non-commercial research
OA Textbooks: UCL Press Perspective
By Rafael, on 23 October 2024
As we continue celebrating International Open Access Week, it’s inspiring to see how open access is shaping research and collaboration across UCL! Earlier this week, we explored the balance between collaboration and commercialisation, and highlighted the important work of Citizen Science initiatives.
Midway through the week, Dhara Snowden, Textbook Programme Manager at UCL Press, shares her insights below on the growing significance of open access textbooks and their role in the broader landscape of open access publishing.
UCL Press is the UK’s first, and largest, fully open access university press. We have been publishing books and journals for almost ten years, covering a wide range of subjects and formats. In 2021, the press launched a new programme focusing on open access (OA) textbooks. I joined at that time, and over the past three years, I’ve been responsible for managing our progress in this area. As part of this year’s International Open Access Week, I wanted to share some of our thinking and planning around this activity and offer some musings about OA textbook publishing in general and what the future holds.
What are Open Access Textbooks?
Firstly, it’s useful to clarify what we mean by “textbooks.” Through conversations with academics across faculties, I’ve realised this term can mean different things depending on the context and level of study. In the broadest sense, a textbook is a resource that supports the delivery of a course or module. Textbooks can provide a wide-view survey of a field or subject, to be “adopted” as the main guide for study, or they can be part of a reading list that includes chapters from various sources, like journal articles.
Although textbooks were traditionally published in print, there has been increasing demand for digital versions of commercial textbooks, which can be purchased by individuals and licenced to institutions for use for multiple users.
Open access publishing, meanwhile, involves making scholarly content freely available online, removing subscription or purchase barriers. In the context of textbooks, this means students and educators can access high-quality educational resources without significant costs. OA textbooks are typically published under a Creative Commons (CC) licence, which allows for redistribution, adaptation, and modification, promoting a collaborative and inclusive educational environment.
The creation and uptake of OA textbooks has seen a sharp increase in recent years, particularly in the US and UK, with non-profit-funded publishers like OpenStax, collaboratively funded projects like CORE Econ, and platforms like Pressbooks. The Open Textbook Library, supported by Open Education Network, currently indexes 1,542 published open textbooks.
Why do we create them?
The UCL Press textbook programme was set up in direct response to issues around pricing for institutional access to essential e-textbooks, which were exacerbated during the Covid-19 pandemic. The current ecosystem presents an unstable and unsustainable financial model for institutional libraries, as well documented by the eBooks SOS campaign, which calls attention to the lack of regulation in pricing by commercial publishers.
An article published by Insights in 2022, ‘Perspectives on e-books and digital textbooks and the way ahead’, claims that ‘combined spending on book across nationally negotiated library purchasing frameworks increased from £55M in 2019/20 to £73M in 202/21, with e-textbook provision increasing by 281% to £25.1M during that time’.
In addition to concerns about affordability and sustained access, the Insights article outlines that post-pandemic, “shifts in teaching practice are accelerating demand for features that enhance blended learning”, with more flexibility and adaptability in resources being required, which isn’t being delivered by traditional academic publishing.
UCL Press’s aims to disrupt the current academic publishing ecosystem, offering authors and readers an alternative to the commercial model. This connects the theme for OA Week 2024, which calls for community over commercialisation. Bringing publishing back to the hands of academy, we can provide sustainable and high-quality textbooks to facilitate hybrid teaching and remove barriers to access for our content thereby reaching the widest possible audience and increasing chances to impact in scholarly communities.
How do we create them?
The UCL Press textbook programme commissions and publishes textbooks for undergraduate and postgraduate students across a wide range of subjects and topics. Every new proposal (and final manuscript) undergoes a rigorous peer-review process to ensure high-quality and relevant content.
Our approach is to collaborate with lecturers to create resources that provide high-quality guidance for students. Taking a personal and flexible approach to each project, we avoid rigid templates or a one-size-fits-all mentality, tailoring our textbooks to the needs of students and subject matter.
To date, we’ve published two textbooks. The first, An Introduction to Waste Management and Circular Economy, came out in December 2023. This textbook supports a module taught at UCL but also has global relevance for courses in environmental engineering, resource efficiency, bioenergy, and waste-to-energy technologies.
More recently, we published Methods and Methodologies in Heritage Studies, an edited collection exploring the disciplinary debates, intellectual legacies, and practical innovations that shape contemporary understandings of heritage value.
Together, these two titles have been downloaded over 12,000 times in 152 countries and territories. Our forthcoming titles include, A Guide to Performing Systematic Reviews of Health and Disease and Fundamentals of Dark Matter, both due to publish early next year.
What are the benefits of writing or using OA textbooks? Where’s the value?
There are many benefits to writing and using OA textbooks and the European Network of Open Education Librarians have created a toolkit to encourage use of OA materials and Open Educational Resources (OER). Some key points are listed below.
- Reaching a Global Audience: downloads and views from readers across the globe, particularly the Global South.
- Cost-Effectiveness: One of the most significant advantages of OA textbooks is their cost-saving potential for both library and student. OA resources can alleviate this burden, allow to redistribution of saved funds and make education more accessible for all.
- Adaptability: open licences enable reuse, modification and adaptation, enabling educators to make the content work best for teaching.
- Showcase Teaching Excellence: OA textbooks can help platform new approaches or area of study, and celebrate examples of teaching excellence.
- Encourage lifelong learning: Provide students with resources they can use and reference after their studies and into their careers.
- Accessibility and Inclusivity: Open access textbooks are available to anyone with an internet connection, supporting diverse learners, including those in remote or under-resourced areas, and those outside academic institutions(e. professionals and policy makers)
- Up-to-Date Content: Traditional textbooks can quickly become outdated. OA textbooks can be updated and revised more readily, ensuring that students have access to the most current information.
- Enhanced Collaboration: Open resources encourage collaboration among educators, fostering a community of shared knowledge and innovation.
To measure impact, we use both qualitative and quantitative measures. Our Statistics dashboard shows the readership and reach of our books, including a map of access. In addition, we are collecting testimonials and feedback from academics and students and engaging with the societal impact of our books (as discussed in a recent article in The Scholarly Kitchen). We interrogate our user analytics to understand which communities are interacting with our content and how they are using it in their own work.
Value in this context is calculated not only in terms of cost-saving on commercial provision, but also in the added value student experience. This includes showcasing teaching excellence to encourage enrolment in a particular course or providing a teaching and learning resources for a module that are underrepresented in commercial provision (i.e. those with smaller cohorts/interdisciplinary topics/less mainstream perspectives).
What does the future hold?
The future of open access textbook publishing in the UK looks promising, with increasing institutional support and growing awareness among educators. As the demand for affordable and accessible educational resources continues to rise, the potential for OA textbooks to reshape higher education is significant.
Open access textbook publishing represents a vital shift in the academic landscape, providing a sustainable, equitable, and collaborative approach to education. As more institutions and publishers embrace this model, we hope to create a future where quality educational resources are accessible to all, empowering students and educators alike.
Significant sea change in the status quo requires a long-term outlook, and significant investment and commitment. If educators, students, and policymakers continue to discover and advocate for the adoption of open access resources within institutions, there is potential to foster an educational environment that fully supports and values accessibility, collaboration, and innovation.
UCL Press will continue to develop its programme of OA textbooks and to keep up to date with our publications, please do sign up to our mailing list or take a look at our website.
Empowering communities: How open access and citizen science work are shaping the future of research
By Rafael, on 22 October 2024
As we continue celebrating International Open Access Week, following our earlier post on balancing openness and commercialisation, we’re now turning our focus to Citizen Science initiatives. Sheetal Saujani, UCL’s Citizen Science Coordinator, highlights in her article below how community-driven research and open access are shaping the future of knowledge creation, empowering individuals to make meaningful contributions to global challenges.
Did you know that ordinary citizens are making significant contributions to solving some of the world’s biggest challenges – from climate change to wildlife conservation?
This year’s International Open Access Week continues to focus on the importance of community in scholarly research and open access initiatives.
Definition of citizen science at UCL
UCL supports a broad approach to citizen science, recognising that there are different applications and functions of citizen science in research, whether they are community-driven research projects or global investigations.
Citizen science is characterised as research conducted by the public, often in collaboration with academic institutions, and is a diverse practice involving academic and community researchers from various disciplines.
At its most inclusive and most innovative, citizen science involves ordinary people as partners in the entire research process, including determining research themes, questions, methodologies and means of disseminating results. The involvement of people in participatory research can range from short-term data collection to intensive involvement in the research process, from technical contribution to genuine research, and from open collaboration to co-creation of knowledge.
Citizen science promotes community-driven collaboration over profit-driven research
Citizen science is a model for open access and collective participation in research, ensuring the benefits of knowledge creation are accessible to all. It embodies community-driven collaboration because it is built on principles of openness, inclusivity, and shared ownership of knowledge. The focus is on addressing real-world problems and empowering communities to take part in research that benefits everyone – not on generating profit for a select few.
Why does open access matter?
Open access refers to the free, unrestricted access to research outputs like journal articles, data, and educational resources. It ensures that research reaches the widest possible audience, and that it can be used and shared easily.
Open access aligns with the values of community engagement and citizen science by making knowledge and data open to the public. This allows people to engage in research without the barriers of paywalls or proprietary information, unlike commercialised research, where data can be restricted for profit.
Citizen science as an open, community-driven approach
Citizen science is a community-driven approach that focuses on problem-solving and knowledge expansion, promoting open collaboration and ownership. Citizen science projects typically share their findings openly. Initiatives like Zooniverse and iNaturalist offer open access to tools, software, and platforms, democratising knowledge. By enabling people to participate in and shape real research based on publicly accessible data, this approach promotes accessibility and inclusivity. It builds trust between researchers and the public, strengthening the quality and impact of research by drawing on collective wisdom and diverse perspectives.
Case studies: open access in citizen science
Below are two examples of successful citizen science projects that embody this week’s theme.
Air quality monitoring by communities: In the Open AQ project, citizens use open-access, low-cost sensors to track air pollution in their neighbourhoods. The data collected is shared freely and openly, allowing communities to act and policymakers to respond. This contrasts with commercial entities that might charge for proprietary pollution data or sensor technology.
Biodiversity conservation: iNaturalist invites people to document plant and animal species in their area. The data is shared freely, benefiting researchers and conservationists worldwide. No one is excluded based on ability to pay or access to commercial tools – everyone has a stake in biodiversity protection.
Challenges and opportunities: advancing with community in mind
Challenges of commercialisation in citizen science do exist: some citizen science platforms are commercialised, locking data behind paywalls or limiting access to paying users. Profit-driven research models hinder knowledge access, distort priorities, exploit participants, and compromise objectivity. To benefit society and produce shared findings, it is important to prioritise the public good and fair access to research.
Promoting open access in citizen science can enhance participation, diversity, and openness. Because citizen science invites participation from all, it offers opportunities for underrepresented communities and developing countries to contribute to and benefit from research. This inclusive model breaks down barriers in commercialised research systems, ensuring marginalised voices are heard and valued in the research process.
We would encourage everyone to support open access movements and citizen science platforms and projects that rank community benefit over profit.
Empowering the public through open access and citizen science
Open access and citizen science align with the theme of “Community over Commercialization” by prioritising collaboration and transparency in research. Open access removes barriers, while citizen science empowers people to participate in research projects. This approach puts the interests of the public first and benefits the wider population.
Looking towards the future, prioritising community-driven approaches in research can lead to more equitable, inclusive, and impactful research. Citizen science and open access work together to resist commercialised research, leading to a more equitable, community-centred approach to research.
As we celebrate International Open Access Week, let’s remember that when we put community at the heart of research, we empower everyone to contribute to the knowledge that shapes our world and makes a lasting impact on society.
Community over Commercialisation?
By Kirsty, on 21 October 2024
Today marks the start of International Open Access Week 2024! Throughout the week, we’ll be sharing insights from UCL staff on how open access is shaping research, collaboration, and scholarship across the university. To kick off the series, Kirsty Wallis explores the significance of this year’s theme and the challenges and opportunities of balancing openness with commercialisation in ways that benefit both research and society.
The theme for this year’s International Open Access Week (OA Week), “Community over Commercialisation,” intends to provide a starting point for us to reflect on the importance of community in the work that we do relating to Openness, rather than letting financial or commercial interests take focus.
This is the second year focusing on this theme, which shows its significance in Open Science and Scholarship and the growing interest in these discussions.
The UNESCO Recommendations on Open Science highlight the issues of groups profiting from publicly funded research and advocate for non-commercial, collaborative publishing models.
This year’s OA Week invites reflection on critical questions around commercialisation, corporate control of knowledge and what we can do to encourage a shift towards more open practices. This post will focus on the progress in opening up research worldwide, but also bring to the fore some areas where commercialisation may be able to serve the public interest. Can commercialising research ever be for public good?
Last year in support of the theme, we launched our Citizen Science Community! It was the culmination of a lot of work from the team in the Office for Open Science and Scholarship. Our approach to Citizen Science at UCL foregrounds the need to prioritise community interests and aiming to make everything we do as inclusive as possible and integrate as many subject areas as we can.
We also explored how Creative Commons (CC) licences promote open, reusable research, making scholarly outputs accessible to a wider audience—from researchers to the general public.
International Open Access Week has created a list of profiles of global institutions showcasing how Open Science communities are embedding principles of shared knowledge and equitable access into their practices: visit the International Open Access Week list of Theme Profiles.
Continuing the Discussion in 2024:
As we move forward, OA Week 2024 offers the opportunity to build on the 2023 theme and further explore how community-based approaches can coexist with commercial interests in ways that serve both the research community and the public. Turning this dialogue into concrete action is essential for achieving the goals of Open Science—making knowledge accessible and equitable for everyone.
So, is there ever a scenario where commercialisation of research can work for community? After all, it is possible to share the outputs of research openly while also selling them as a product, for example in software. It is possible and even fairly common in some areas to make the underlying code open source but sell access to supported versions or additional features that can be used by companies and businesses that are unable to support products themselves. There are many examples of this, from the underlying code supporting Android phones and Chrome browsers to the Linux operating system and, also the ePrints repository software that we use here at UCL.
As another example, this time from within UCL itself is the Ventura CPAP Machine developed during 2020 at the height of the pandemic. The designs for the machine were made available free of charge via the UCLB licensing system. This enabled limitations to be put in place for who could use the designs, preventing companies from profiteering from the design while making it available to hospitals and other charitable organisations to build and test their own free of charge. It has always been UCL’s position that profit is not the end game, going back as far as Jeremy Bentham, the spiritual founder of UCL, who believed that education should be more widely available, a core underpinning value of UCL and the Office for Open Science and Scholarship today.
This year’s Open Access Week theme aligns with some of the behind-the-scenes work we’re doing to explore the relationship between openness and commercialisation and investigate scenarios where they may not be as much in conflict as the theme suggests. Keep an eye out for the report and recommendations coming later this academic year!
RPS and UCL Profiles have been updated
By Rafael, on 17 October 2024
Guest post by Alan Bracey, UCL Open Access Compliance Officer
As we prepare for a full week of events and updates during International Open Access Week, the UCL Open Access team is sharing recent improvements to UCL’s Research Publications Service (RPS) and its public interface, UCL Profiles. Below is a summary of the key changes implemented, including new HTML text entry boxes for easier formatting, refined search and filtering options, and improvements in readability and accessibility. Check it out!
Overview text boxes are now html
We start with one of the most popular feature requests from colleagues at UCL and other institutions, and are very pleased to announce that this has now been added by the supplier.
The text entry boxes in RPS for entering Overview, Research interests, and Teaching summary are now HTML rather than text, and have controls to add formatting and links:
Any formatting added here is applied in Profiles.
Better searching and filtering in Profiles
The update brings several improvements to searching and filtering. Firstly, the search algorithm itself has been updated. This means that although users will see fewer results as they add terms, those results should be more relevant, particularly where users are searching for multiple terms or multi-word terms. The supplier is keeping the new algorithm under review, so we welcome feedback on how the search is performing.
Profiles also now highlights where the search terms have been matched to major sections within a profile, helping users to understand the relevance of their results:
Plus, the display of zero search results has also been improved:
A search has also been added to the top of the publication and activity pages, so that users can search a list for content within that list (e.g. search an academic’s publications for an article):
The list of filters is now collapsible, making the full list of available filters more prominent and easier to navigate. Highlights also remind users what filters have already been applied, making search results easier to refine:
Other changes in Profiles
We are pleased to announce that Profiles has a new font, with a stronger weight and wider spacing, that improves readability:
The option to add pronouns has been available in RPS for a while now, but previously they did not display in Profiles. This has been updated so that pronouns added in RPS (on the Account Settings page) show in Profiles, under your name:
The X/Twitter icon has also been updated.
Other improvements you might notice in RPS
The RPS Edit Profile page (RPS > Edit my Profile) is better spaced out, making it clearer and easier to read. Updates have been made to the overall layout and to profile and field-level privacy controls. Accessibility improvements have also been made, including to the photo uploader.
Note: ‘Position’ and ‘Department’ no longer show in the Edit page, only the RPS ‘View profile’ page, which will help avoid potential confusion as these fields are sourced from HR and cannot be edited in RPS. See our FAQs for details of how to request changes to those fields.
This page used to show embedded publications (and a related graph), professional activities, teaching activities and grants. These have been removed because they were found to be confusing for users. (These tabs are still on the RPS View profile page.)
This means there are no shortcuts to Manage publications/professional activities/teaching activities/grants from the Edit profile page. Use the home button (top left of RPS) to return to your home page to edit publications/professional activities/teaching activities. Grants are not editable in RPS, but this data will be improved before it is added to Profiles in future.
We’d love to hear your feedback on these updates and any other features you’d like to see in Profiles! To share your thoughts, please contact UCL’s Open Access Team.
Announcing: UCL Open Science & Scholarship Award Winners 2024!
By Rafael, on 2 October 2024
On behalf of the UCL Office for Open Science & Scholarship and the UKRN local leads, we would like to thank everyone who engaged with the nominations and showed us how amazing the research community at UCL is. We were overwhelmed by the support for this process, and the judging panel had a really hard job selecting just a few winners from the over 50 applications and nominations we received!
We will be presenting the awards in a small ceremony during International Open Access Week on 2-3:30pm, Wednesday 23rd October (for the full list of events for that week, check our blog post). A selection of winners and honourable mentions will present their work, followed by a small reception sponsored by UCL Press.
We have limited tickets available due to the small venue, but tickets are available on Eventbrite for UCL staff and students.
Full information about all of these projects will be available on the day of the awards, so watch this space!
Category: Students
Winners:
• Sophie Ka Ling Lau and Divya Balain, postgraduate students at the Faculty of Brain Sciences and Life Sciences
Honourable mentions:
• Beth Downe, MSc in Ecology and Data Science at Division of Biosciences
• Gabrielle Pengyu Shao, Undergraduate student in Geography
Category: Non-academic Staff
Winners:
• Dr Eirini-Christina Saloniki, Senior Research Fellow in Health Economics (NIHR ARC North Thames) in the Department of Applied Health Research
• William Lammons, Patient and Public Involvement and Engagement Lead for the Applied Research Collaboration North Thames
Category: Open Publishing
Winner:
• Dr Emily Gardner, Research Fellow in the Department of Genetics & Genomic Medicine
Honourable mentions:
• Dr Deborah Padfield, Associate Professor at the Slade School of Fine Art
• Dr Adam Parker, Lecturer in the Division of Psychology and Language Sciences (with David Shanks, Courtenay Norbury, and Daryl Lee)
Category: Open-Source Software/Analytical Tools
Winner:
• Alessandro Felder (on behalf of the BrainGlobe team), Research Software Engineer in the Neuroinformatics Unit at the Sainsbury Wellcome Centre and technical lead for the BrainGlobe initiative
Honourable mentions:
• Hengrui Zhang, PhD student at the Institute of Health Informatics
• Mathilde Ripart, PhD student at the Great Ormond Street Institute of Child Health
• Prof Justyna Petke, Professor of Software Engineering at the Centre for Research on Evolution, Search and Testing
• Dr Enny van Beest, Senior Research Associate at the Institute of Ophthalmology, and Dr Célian Bimbard, Senior Research Fellow, Institute of Ophthalmology
Category: Advocating for Open Science/Community Building
Winner:
• Dr Joseph Cook, Lead of the UCL Citizen Science Academy at the Institute for Global Prosperity
Honourable mentions:
• Claire Waddington, PhD student at the Dementia Research Centre
• Fan Cheng, PhD student at the Faculty of Population Health Sciences
Book your tickets now and join us in celebrating the incredible open science work happening at UCL!
For more information about the UCL Open Science and Scholarship Awards, visit our webpage. You can also stay connected by following us on LinkedIn or BlueSky, and be sure to subscribe to our newsletter for the latest updates on the awards and all things open science at UCL!
Coming Soon: Open Access Week 2024!
By Rafael, on 24 September 2024
We’re excited to announce a packed programme of events for this year’s #OAWeek at UCL! Throughout the week, we’ll be sharing daily blog posts and updates on social media that highlight the latest activities from UCL Press and the UCL Copyright team, alongside exciting news on our growing Citizen Science Community on MS Teams. This year’s theme, ‘Community over Commercialisation’, will be at the heart of our discussions, exploring how we can prioritise openness and collaboration in research to benefit the public and academic communities rather than profit-driven initiatives.
Poster of the International Open Access Week 2024
Read more about Open Access week and this year’s theme.
Tuesday 22 October (11:00am-2:00 pm) – Open Science and ARC Roadshow
As part of this year’s Open Access Week activities, we’re launching the first in a series of pilot roadshows, jointly organised by the UCL Office for Open Science & Scholarship and the Centre for Advanced Research Computing.
Come and find us outside the Academic Staff Common Room in the North Cloisters between 11:00 am and 2:00 pm, where our team will be on hand to answer all your questions about Open Access publishing, Research Data Management, Research IT, Data Stewardship, Citizen Science, and any other Open Science-related topics you’re curious about! Stop by to find out more—we might even have some goodies waiting for you!
No registration needed – find the event location on the webpage.
Tuesday 22 October (2:30-4:00 pm) – Copyright, Open Science & Creativity
One event we’re particularly excited about is happening on Tuesday, 22 October (2:30–4:00 pm). We’ll be hosting a brand-new card game designed by Christine Daouti, titled ‘Copyright, Open Science, and Creativity’. This engaging game provides a fun and interactive way to explore key topics like equity in open science, authors’ rights, and open access publishing. You’ll have the opportunity to debate various aspects of copyright with fellow participants and explore issues such as open licences, AI in research, rights retention, and the challenges of equity in open science.
Spaces are limited, so be sure to sign up early! For more details and registration information, visit the event page.
Wednesday 23 October (2:00–3:30 pm) – Annual Open Science & Scholarship Awards
We’re also really glad to invite you to our second Annual Open Science & Scholarship Awards! Join us in celebrating the incredible contributions of colleagues and students to the future of open research and scholarship. The event will feature short talks from the winners in each category, followed by the award presentations. Afterwards, stay for drinks, nibbles, and a chance to network with peers.
Register today via our Eventbrite page!
Thursday 24 October, 2.30 pm – 4 pm, drop-in session on Copyright, Licences and Open Science
Join the UCL Copyright team for an online drop-in session where they’ll be available to answer your questions about copyright, licensing, and how to share your research openly. This is a great opportunity to clarify any issues related to your research, thesis, publications, or data. Feel free to drop in on Teams between 2:30 and 3:50 pm or send your questions in advance to copyright@ucl.ac.uk.
To get you started, here are a few questions you might want to consider:
- Why do research funders prefer CC BY licences for journal articles and monographs?
- What copyright considerations should you keep in mind when making your data open and FAIR?
- Can you use someone else’s copyrighted materials in your own thesis or publication that you plan to make open access?
This session offers a chance to resolve these and other copyright and licensing concerns so you can better understand the open research landscape.
Visit the event page for more information and sign up now!
Stay connected!
While we prepare for the events coming up, make sure you stay informed about new articles, events, and projects by signing up for your mailing list to receive the next issue of our Open@UCL newsletter. Also, join in the conversation during #OAWeek by checking this blog page for daily updates, and following us on LinkedIn or our newly created BlueSky account.
See you there!
New academic year, new channels for UCL Open Science & Scholarship: we are expanding our social media presence!
By Rafael, on 19 September 2024
Open Source Software Design for Academia
By Kirsty, on 27 August 2024
Guest post by Julie Fabre, PhD candidate in Systems Neuroscience at UCL.
As a neuroscientist who has designed several open source software projects, I’ve experienced firsthand both the power and pitfalls of the process. Many researchers, myself included, have learned to code on the job, and there’s often a significant gap between writing functional code and designing robust software systems. This gap becomes especially apparent when developing tools for the scientific community, where reliability, usability, and maintainability are crucial.
My journey in open source software development has led to the creation of several tools that have gained traction in the neuroscience community. One such project is bombcell: a software designed to assess the quality of recorded neural units. This tool replaces what was once a laborious manual process and is now used in over 30 labs worldwide. Additionally, I’ve developed other smaller toolboxes for neuroscience:
- YAHT: Yet Another Histology Toolbox
- prettify_matlab: MATLAB Code Formatter
- brain_street_view: Interactive Brain Mapping
These efforts were recognized last year when I received an honourable mention in the UCL Open Science and Scholarship Awards.
In this post, I’ll share insights gained from these experiences. I’ll cover, with some simplified examples from my toolboxes:
- Core design principles
- Open source best practices for academia
Disclaimer: I am not claiming to be an expert. Don’t view this as a definitive guide, but rather as a conversation starter.
Follow Julie’s lead: Whether you’re directly involved in open source software development or any other aspect of open science and scholarship, or if you simply know someone who has made important contributions, consider applying yourself or nominating a colleague for this year’s UCL Open Science and Scholarship Awards to gain recognition for outstanding work!
Part 1: Core Design Principles
As researchers, we often focus on getting our code to work, but good software design goes beyond just functionality. In order to maintain and build upon your software, following a few principles from the get go will elevate software from “it works” to “it’s a joy to use, maintain and contribute to”.
1. Complexity is the enemy
A primary goal of good software design is to reduce complexity. One effective way to simplify complex functions with many parameters is to use configuration objects. This approach not only reduces parameter clutter but also makes functions more flexible and maintainable. Additionally, breaking down large functions into smaller, more manageable pieces can significantly reduce overall complexity.
Example: Simplifying a data analysis function
For instance, in bombcell we run many different quality metrics, and each quality metric is associated with several other parameters. In the main function, instead of inputting all the different parameters independently:
[qMetric, unitType] = runAllQualityMetrics(plotDetails, plotGlobal, verbose, reExtractRaw, saveAsTSV, removeDuplicateSpikes, duplicateSpikeWindow_s, detrendWaveform, nRawSpikesToExtract, spikeWidth, computeSpatialDecay, probeType, waveformBaselineNoiseWindow, tauR_values, tauC, computeTimeChunks, deltaTimeChunks, presenceRatioBinSize, driftBinSize, ephys_sample_rate, nChannelsIsoDist, normalizeSpDecay, (... many many more parameters ...), rawData, savePath);
they are all stored in a ‘param’ object that is passed onto the function:
[qMetric, unitType] = runAllQualityMetrics(param, rawData, savePath);
This approach reduces parameter clutter and makes the function more flexible and maintainable.
2. Design for change
Research software often needs to adapt to new hypotheses or methodologies. When writing a function, ask yourself “what additional functionalities might I need in the future?” and design your code accordingly. Implementing modular designs allows for easy modification and extension as research requirements evolve. Consider using dependency injection to make components more flexible and testable. This approach separates the creation of objects from their usage, making it easier to swap out implementations or add new features without affecting existing code.
Example: Modular design for a data processing pipeline
Instead of a monolithic script:
function runAllQualityMetrics(param, rawData, savePath)
% Hundreds of lines of code doing many different things
(...)
end
Create a modular pipeline that separates each quality metric into a different function:
function qMetric = runAllQualityMetrics(param, rawData, savePath)
nUnits = length(rawData);
for iUnit = 1:nUnits
% step 1: calculate percentage spikes missing
qMetric.percSpikesMissing(iUnit) = bc.qm.percSpikesMissing(param, rawData);
% step 2: calculate fraction refractory period violations
qMetric.fractionRPviolations(iUnit) = bc.qm.fractionRPviolations(param, rawData);
% step 3: calculate presence ratio
qMetric.presenceRatio(iUnit) = bc.qm.presenceRatio(param, rawData);
(...)
% step n: calculate distance metrics
qMetric.distanceMetric(iUnit) = bc.qm.getDistanceMetric(param, rawData);
end
bc.qm.saveQMetrics(qMetric, savePath)
end
This structure allows for easy modification of individual steps or addition of new steps without affecting the entire pipeline.
In addition, this structure allows us to define new parameters easily that can then modify the behavior of the subfunctions. For instance we can add different methods (such as adding the ‘gaussian’ option below) without changing how any of the functions are called!
param.percSpikesMissingMethod = 'gaussian';
qMetric.percSpikesMissing(iUnit) = bc.qm.percSpikesMissing(param, rawData);
and then, inside the function:
function percSpikesMissing = percSpikesMissing(param, rawData);
if param.percSpikesMissingMethod == 'gaussian'
(...)
else
(...)
end
end
3. Hide complexity
Expose only what’s necessary to use a module or function, hiding the complex implementation details. Use abstraction layers to separate interface from implementation, providing clear and concise public APIs while keeping complex logic private. This approach not only makes your software easier to use but also allows you to refactor and optimize internal implementations without affecting users of your code.
Example: Complex algorithm with a simple interface
For instance, in bombcell there are many parameters. When we run the main script that calls all quality metrics, we also want to ensure all parameters are present and are in a correct format.
function qMetric = runAllQualityMetrics(param, rawData, savePath)
% Complex input validation that is hidden to the user
param_complete = bc.qm.checkParameterFields(param);
% Core function that calcvulates all quality metrics
nUnits = length(rawData);
for iUnit = 1:nUnits
% steps 1 to n
(...)
end
end
Users of this function don’t need to know about the input validation or other complex calculations. They just need to provide input and options.
4. Write clear code
Clear code reduces the need for extensive documentation and makes your software more accessible to collaborators. Use descriptive and consistent variable names throughout your codebase. When dealing with specific quantities, consider adding units to variable names (e.g., ‘time_ms’ for milliseconds) to improve clarity. You can add comments to explain non-obvious logic and to add general outlines of the steps in your code. Following consistent coding style and formatting guidelines across your project also contributes to overall clarity.
Example: Improving clarity in a data processing function
Instead of an entirely mysterious function
function [ns, sr] = ns(st, t)
ns = numel(st);
sr = ns/t;
Add more descriptive variable and function names and add function headers:
function [nSpikes, spikeRate] = numberSpikes(theseSpikeTimes, totalTime_s)
% Count the number of spikes for the current unit
% ------
% Inputs
% ------
% theseSpikeTimes: [nSpikesforThisUnit × 1 double vector] of time in seconds of each of the unit's spikes.
% totalTime_s: [double] of the total recording time, in seconds.
% ------
% Outputs
% ------
% nSpikes: [double] number of spikes for current unit.
% spikeRate_s : [double] spiking rare for current unit, in seconds.
% ------
nSpikes = numel(theseSpikeTimes);
spikeRate_s = nSpikes/totalTime_s;
end
5. Design for testing
Incorporate testing into your design process from the beginning. This not only catches bugs early but also encourages modular, well-defined components.
Example: Testable design for a data analysis function
For the simple ‘numberSpikes’ function we define above, we can have a few tests to cover various scenarios and edge cases to ensure the function works correctly. For instance, we can test a normal case with a few spikes and an empty spike times input.
function testNormalCase(testCase)
theseSpikeTimes = [0.1, 0.2, 0.3, 0.4, 0.5]; totalTime_s = 1;
[nSpikes, spikeRate] = numberSpikes(theseSpikeTimes, totalTime_s);
verifyEqual(testCase, nSpikes, 5, 'Number of spikes should be 5');
verifyEqual(testCase, spikeRate, 5, 'Spike rate should be 5 Hz');
end
function testEmptySpikeTimes(testCase)
theseSpikeTimes = [];
totalTime_s = 1;
[nSpikes, spikeRate] = numberSpikes(theseSpikeTimes, totalTime_s);
verifyEqual(testCase, nSpikes, 0, 'Number of spikes should be 0 for empty input');
verifyEqual(testCase, spikeRate, 0, 'Spike rate should be 0 for empty input');
end
This design allows for easy unit testing of individual components of the analysis pipeline.
Part 2: Open Source Best Practices for Academia
While using version control and having a README, documentation, license, and contribution guidelines are essential, I have found that these practices have the most impact:
Example Scripts and Toy Data
I have found that the most useful thing you can provide with your software are example scripts, and even better, provide toy data that loads in your example script. Users can then quickly test your software and see how to use it on their own data — and are then more likely to adopt it. If possible, package the example scripts in Jupyter notebooks/MATLAB live scripts (or equivalent) demonstrating key use cases. In bombcell, we provide a small dataset (Bombcell Toy Data on GitHub) and a MATLAB live script that runs bombcell on this small toy dataset (Getting Started with Bombcell on GitHub).
Issue-Driven Improvement
To manage user feedback effectively, enforce the use of an issue tracker (like GitHub Issues) for all communications. This approach ensures that other users can benefit from conversations and reduces repetitive work. When addressing questions or bugs, consider if there are ways to improve documentation or add safeguards to prevent similar issues in the future. This iterative process leads to more robust and intuitive software.
Citing
Make your software citable quickly. Before (or instead) of publishing, you can generate a citable DOI using software like Zenodo. Consider also publishing in the Journal of Open Source Software (JOSS) for light peer review. Clearly outline how users should cite your software in their publications to ensure proper recognition of your work.
Conclusion
These practices can help create popular, user-friendly, and robust academic software. Remember that good software design is an iterative process, and continuously seeking feedback and improving your codebase (and sometimes entirely rewriting/refactoring parts) will lead to more robust code.
To go deeper into principles of software design, I highly recommend reading “A Philosophy of Software Design” by John Ousterhout or “The Good Research Code Handbook” by Patrick J. Mineault.
Get involved!
The UCL Office for Open Science and Scholarship invites you to contribute to the open science and scholarship movement. Join our mailing list, and follow us on X, formerly Twitter and LinkedIn, to stay connected for updates, events, and opportunities.
