The Office of Scholarly Communication, jointly with Open Research Systems (Digital Initiatives) and Research Information team have developed a new preprint deposit service for University of Cambridge researchers, which will be available on the week commencing11th March 2024.
Why offer a preprint service?
Although researchers are generally well-served by existing subject repositories/preprint servers, we have identified an unmet need for those:
Who have no suitable subject repository/preprint server, or
Whose subject repositories/preprint server may be unable to offer long-term preservation, or
Who wish to use the University’s repository instead of existing subject repositories/preprint servers.
Why offer a preprint service now?
Following recent upgrades to both the University’s repository Apollo and Elements (the system that the University uses to hold and manage data on research activity), we are now in a position where we can offer a preprint deposit service.
What can be deposited?
Cambridge University researchers can deposit new (unpublished) preprints that have not been submitted to an external subject repository/preprint server.
Researchers can also deposit published preprints if they have concerns about its long-term preservation.
Can subsequent versions of a preprint be deposited?
New versions of a preprint can be added to an existing preprint record.
What happens once the preprint has been accepted for publication?
Researchers are asked to deposit the accepted manuscript as usual, via Elements. The Open Access Team will link the preprint record and accepted manuscript record in Apollo. The preprint and the accepted manuscript need to be separate records to ensure that the first deposit date of the accepted manuscript is not obscured, which is important for REF compliance purposes.
Dr Mandy Wigdorowitz, Open Research Community Manager, Cambridge University Libraries
On Friday 17 November 2023, participants from across Cambridge and beyond gathered for a hybrid meeting on Open Research from different perspectives. Hosted by Cambridge University Libraries at Downing College, ‘Open Research for Inclusion: Spotlighting Different Voices in Open Research at Cambridge‘ drew attention to different areas of Open Research that have been at the forefront of recent discussions in Cambridge by showcasing the scope and breadth of open practices in typically under-represented disciplines and contexts. These included the Arts, Humanities, and Social Sciences, the GLAM sector (Galleries, Libraries, Archives, and Museums), and research from and about the Global South. A total of 84 in-person and 75 online attendees participated in the day-long event consisting of a keynote address, two talks, two panels, and a workshop.
The conference opened with a welcome address from Professor Anne Ferguson-Smith CBE FRS FMedSci, Pro-Vice-Chancellor for Research and International Partnerships and the Arthur Balfour Professor of Genetics. Professor Ferguson-Smith emphasised the significance and timeliness of the conference and how it underscores the importance of the Open Research movement. She encouraged attendees to be open to new ideas, approaches, and perspectives that center around Open Research and to celebrate the richness of diversity in research.
Our keynote speaker, Dr Siddharth Soni, Isaac Newton Trust Fellow at Cambridge Digital Humanities and affiliated lecturer at the Faculty of English, then addressed the audience with a talk on Common Ground, Common Duty: Open Humanities and the Global South, providing an account of how to think against neoliberal conceptions of ‘open’ and to reimagine what openness might look like if the Global South was viewed as a common ground space for building an open and international university culture. Dr Soni’s address set the tone for a rich, multi-layered exploration of Open Research on the day, urging attendees to think of open humanities as a form of knowledge that seeks to alter the form and content of knowledge systems rather than just opening Euro-American knowledge systems to global publics.
Dr Siddharth Soni Common Ground, Common Duty: Open Humanities and the Global South
The next talk was from Dr Stefania Merlo from the McDonald Institute for Archaeological Research and Dr Rebecca Roberts from the McDonald Institute for Archaeological Research and Fitzwilliam Museum who further explored the theme of the Global South in their practical perspective on how they managed the curation of digital archives for heritage management from their work on the projects: Mapping Africa’s Endangered Archaeological Sites and Monuments (MAEASaM) and Mapping Archaeological Heritage in South Asia (MAHSA). They reflected on the opportunities and challenges relating to the production and dissemination of information about archaeological sites and monuments in projects across Africa and South Asia as well as their experience working with and learning from local communities.
Dr Stefania Merlo and Dr Rebecca Roberts Open Data for Open Research – Reflections on the Curation of Digital Archives for Heritage Management in the Global South
An Open Research panel session was next which featured panellists with diverse backgrounds and expertise who addressed registrants’ pre-submitted and live questions. Some questions included the meaning of Open Research, its advantages and challenges, how Open Research can be engaged with by researchers (and in particular, early career researchers), and how it can be rewarded and embedded into the culture of research practices. There was engaging insights and debate amongst the panellists, led by Bertrand Russell Professor of Philosophy, Professor Alexander Bird. He shared the platform with Philosophy of Science Professor, Professor Anna Alexandrova, Psychiatry PhD student Luisa Fassi, Cambridge University Libraries (CUL) Interim Head of Open Research Services Dr Sacha Jones, Cambridge University Press & Assessment’s Research Data Manager Dr Kiera McNeice, and Cambridge’s Head of Research Culture Liz Simmonds.
Open Research Panel
Following lunch, a second panel of scholars working across the GLAM sector (Galleries, Libraries, Archives and Museums) took place. The panel was chaired by CUL’s Scholarly Communication Specialist, Dr Samuel Moore, and brought together experts who showcased their diverse work in this sector, from software development and museum practices to infrastructure and archiving support. The panel included Dr Mary Chester-Kadwell, CUL’s Senior Software Developer and Lead Research Software Engineer at Cambridge Digital Humanities, Isaac Newton Trust Research Associate in Conservation Dr Ayesha Fuentes from the Museum of Archaeology and Anthropology, Dr Agustina Martinez-Garcia, CUL’s Head of Open Research Systems, and Dr Amelie Roper, CUL’s Head of Research. Each panellist presented on a specialist area, including Open Research code and data practices in digital humanities, collections research, teaching and learning collections care, and Open Research infrastructure. A lively discussion followed from the presentations.
GLAM panel
In a workshop session, Tim Fellows, Product Manager for Octopus, outlined how Octopus is a free and alternative publishing model that can practically foster Open Research. The platform, funded by UKRI, is designed for researchers to share ‘micro publications’ that more closely represent how research is conducted at each stage of a project. In a demonstration of the platform, Tim Fellows showed how Octopus works, it’s design, user interface, and application all with the aim of aiding reproducibility, facilitating new ways of sharing research, and removing barriers to both publishing and accessing research. An in-depth discussion followed which centered on the ways the platform can be used as well as its uptake and application across various disciplines.
Tim Fellows Octopus.ac: Alternative Publishing Model to Foster Open Research
The final talk of the day was on Open Research and the coloniality of knowledge presented by Professor Joanna Page, Director of CRASSH and Professor of Latin American Studies. She discussed the topic with a specific focus on the questions of possession and access by outlining projects by three Latin American artists who have engaged with Humboldt’s legacy and the coloniality of knowledge. Using videos and imagery, Professor Page encouraged the audience to consider how they might identify where the principles of Open Research conflict with those of inclusion and cognitive justice, and what might be done to reconcile those ambitions across diverse cultures and communities. An engaging discussion ensued.
Professor Joanna Page Open Research and the Coloniality of Knowledge
A drinks reception brought the event to a close, allowing attendees a chance to mingle, network and continue the discussions.
Special thanks to all speakers, attendees, and volunteers for making this event such a success. Stay tuned for information about our 2024 Open Research conference.
By Dr. Kim Clugston, Research Data Co-ordinator, Office of Scholarly Communication
Underlying all research data is always an effective and working method and this applies across all disciplines from STEMM to the Arts, Humanities and Social Sciences. Methods are a detailed description of the tools that are used in research and can come in many forms depending on the type of research. Methods are often overlooked rather than being seen as an integral research output in their own right. Traditionally, published journals include a materials and methods section, which is often a summary due to restrictions on word limits making it difficult for other researchers to reproduce the results or replicate the study. There can sometimes be an option to submit the method as “supplementary material”, but this is not always the case. There are specific journals that publish methods and may be peer-reviewed but not all are open access, rendering them hidden behind a paywall. The last decade has seen the creation of “protocol” repositories, some with the ability to comment, adapt and even insert videos. Researchers at the University of Cambridge, from all disciplines – arts, humanities, social sciences and STEMM fields – can now publish their method openly in Apollo, our institutional repository. In this blog, we discuss why it is important to publish methods openly and how the University’s researchers and students can do this in Apollo.
The protocol sharing repository, Protocols.io, was founded in 2012. Protocols can be uploaded to the platform or created within it; they can be shared privately with others or made public. The protocols can be dynamic and interactive (rather than a static document) and can be annotated, which is ideal for highlighting information that could be key to an experiment’s success. Collaboration, adaptation and reuse are possible by creating a fork (an editable clone of a version) that can be compared with any existing versions of the same protocol. Protocols.io currently hosts nearly 16,000 public protocols, showing that there is a support for this type of platform. In July this year it was announced that Protocols.io was acquired by Springer Nature. Their press statement aims to reassure that Protocols.io mission and vision will not change with the acquisition, despite Springer Nature already hosting the world’s largest collection of published protocols in the form of SpringerProtocols along with their own version of a free and open repository, Protocol Exchange. This begs the question of whether a major commercial publisher is monopolising the protocol space, and if they are, is this or will this be a problem? At the moment there do not appear to be any restrictions on exporting/transferring protocols from Protocols.io and hopefully this will continue. This is a problem often faced by researchers using proprietary Electronic Research Notebooks (ERNs), where it can be difficult to disengage from one platform and laborious to transfer notebooks to another, all while ensuring that data integrity is maintained. Because of this, researchers may feel locked into using a particular product. Time will tell how the partnership between Protocols.io and Springer Nature develops and whether the original mission and vision of Protocols.io will remain. Currently, their Open Research plan enables researchers to make an unlimited number of protocols public, with the number of private protocols limited to two (paid plans offer more options and features).
Bio-protocol exchange (under the umbrella of Bio-protocol Journal) is a platform for researchers to find, share and discuss life science protocols with protocol search and webinars. Protocols can be submitted either to Bio-protocol or as a preprint, researchers can ask authors questions, and fork to modify and share the protocol while crediting the original author. They also have an interesting ‘Request a Protocol’ (RaP) service that searches more than 6 million published research papers for protocols or allows you to request one if you are unable to find what you are looking for. A useful feature is that you can ask the community or the original authors of the protocol any question you may have about the protocol. Bio-protocol exchange published all protocols free of charge to their authors since their launch in 2011, with substantial financial backing of their founders. Unfortunately, it was announced that protocol articles submitted to Bio-protocol after March 1 2023 will be charged an Article Processing Charge (APC) of $1200. Researchers who do not want to pay the APC can still post a protocol for free in the Bio-protocol Preprint Repository where they will receive a DOI but will not have gone through the journal’s peer review process.
As methods are integral to successful research, it is a positive move to see the creation and growth of platforms supporting protocol development and sharing. Currently, these tend to cater for research in the sciences, and serve the important role of supporting research reproducibility. Yet, methods exist across all disciplines – arts, humanities, social sciences as well as STEMM – and we see the term ‘method’ rather than ‘protocol’ as more inclusive of all areas of research.
Apollo (Cambridge University’s repository) has now joined the growing appreciation within the research community of recognising the importance of detailing and sharing methodologies. Researchers at the University can now use their Symplectic Elements account to deposit a method into Apollo. Not only does this value the method as an output in its own right, it provides the researcher with a DOI and a publication that can be automatically updated to their ORCID profile (if ORCID is linked to their Elements account). In May this year, Apollo was awarded CoreTrustSeal certification, reinforcing the University’s commitment to preserving research outputs in the long-term and should give researchers confidence that they are depositing their work in a trustworthy digital repository.
The first method to be deposited into Apollo in this way was authored by Professor John Suckling and colleagues. Professor Suckling is Director of Research in Psychiatric Neuroimaging in the Department of Psychiatry. His published method relates to an interesting project combining art and science to create artwork that aims to represent hallucinatory experiences in individuals with diagnosed psychotic or neurodegenerative disorders. He is no stranger to depositing in Apollo; in fact, he has one of the most downloaded datasets in Apollo after depositing the Mammographic Image Analysis Society database in Apollo in 2015. This record contains the images of 322 digital mammograms from a database complied in 1992. Professor Suckling is an advocate of open research and was a speaker at the Open Research at Cambridge conference in 2021.
An interesting and exciting new platform which aims to change research culture and the way researchers are recognised is Octopus. Founded by University of Cambridge researcher Dr Alexandra Freeman, Octopus is free to use for all and is funded by UKRI and developed by Jisc. Researchers can publish instantly all research outputs without word limit constraints, which can often stifle the details. Research outputs are not restricted to articles but also include, for example, code, methods, data, videos and even ideas or short pieces of work. This serves to incentivise the importance of all research outputs. Octopus aims to level up the current skew toward publishing more sensationalist work and encourages publishing all work, such as negative findings, which are often of equal value to science but often get shelved in what is termed the ‘file drawer’ problem. A collaborative research community is encouraged to work together on pieces of a puzzle, with credit given to individual researchers rather than a long list of authors. The platform supports reproducibility, transparency, accountability and aims to allow research the best chance to advance more quickly. Through Octopus, authors retain copyright and apply a Creative Commons licence to their work; the only requirement is that published work is open access and allows derivatives. It is a breath of fresh air in the current rigid publishing structure.
Clear and transparent methods underpin research and are fundamental to the reliability, integrity and advancement of research. Is the research landscape beginning to change to allow open methods, freely published, to take centre stage and for methods to be duly recognised and rewarded as a standalone research output? We certainly hope so. The University of Cambridge is committed to supporting open research, and past and present members who have conducted research at the University can share these outputs openly in Apollo. If you would like to publish a method in Apollo, please submit it here or if you have any queries email us at info@data.cam.ac.uk.
