Category Archives: Supporting Open Research

Methods getting their chance to shine – Apollo wants your methods!

Supporting Open Research,

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.

There will be an Octopus workshop at the Open Research for Inclusion: Spotlighting Different Voices in Open Research at Cambridge on Friday 17th November 2023 at Downing College.

Cambridge Open Research Conference 2023: The stage is set

Open Research at Cambridge Conference, Supporting Open Research

By Nicola Swann and Mandy Wigdorowitz, Office of Scholarly Communication, Cambridge University Libraries

The programme is ready, spaces are nearly full, and we are nearing Cambridge University Libraries’ annual conference on Open Research (OR), taking place at Downing College or online on Friday 17 November 2023. This year’s theme is Open Research for Inclusion: Spotlighting Different Voices in Open Research at Cambridge.

OR is designed to promote equity and inclusion by ensuring that research is accessible to all, regardless of research background, location, or affiliation. The conference will acknowledge that OR can look different in different areas, with the common goal of advancing knowledge and understanding. Giving a voice to OR from diverse perspectives can propel learning, collaboration, and allow us to learn from one another’s approaches to openness.

“The conference looks fantastic! It’s a really fabulous mix of papers and speakers, and really exciting in terms of moving Open Research conversations into different disciplinary practices. It is the first programme I’ve seen that truly integrates research and open into a joint conversation. It’s brilliant!”

Dr Jessica Gardner, University Librarian & Director of Library Services, Cambridge University Libraries

This blog post highlights the speakers who will be joining us on the day and the topics they will explore. We’re delighted to host OR experts who will show the value of open practices in typically under-represented disciplines and contexts. These include the Arts, Humanities, and Social Sciences, the GLAM sector (Galleries, Libraries, Archives, and Museums), and research from and about the Global South.

The day starts 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, who is a key proponent of OR – see her views about OR on the Office of Scholarly Communication’s (OSC) website. Our Keynote speaker, Dr Siddharth Soni, Isaac Newton Trust Fellow at Cambridge Digital Humanities and affiliated lecturer at the Faculty of English, will then addresses us 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 the ‘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 Stefania Merlo from the McDonald Institute for Archaeological Research and Dr Rebecca Roberts from the McDonald Institute for Archaeological Research and Fitzwilliam Museum will further explore 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).

We will then change pace with an OR panel session comprising panellists with diverse backgrounds and expertise who will address registrants’ pre-submitted questions. There will be engaging insights and debate amongst the panellists, led by Bertrand Russell Professor of Philosophy, Professor Alexander Bird. He will share 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.

The spotlight switches to the GLAM sector in the afternoon, with a second panel chaired by CUL’s Scholarly Communication Specialist Dr Samuel Moore. This panel brings together experts who will showcase their diverse work in the GLAM sector, from software development and museum practices to infrastructure and archiving support. The panel includes 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 OR Systems, and Dr Amelie Roper, CUL’s Head of Research. They will each expand on specialist areas, including OR code and data practices in digital humanities, collections research, teaching and learning collections care, and OR infrastructure. 

In a workshop session, Tim Fellows, Product Manager for Octopus, will outline how Octopus is an alternative publishing model that can foster OR. To round the day off, Professor Joanna Page, Director of CRASSH and Professor of Latin American Studies, will present on the considerations of OR and the coloniality of knowledge with a specific focus on the questions of possession and access.

In true Cambridge tradition, a drinks reception will bring the event to a close, allowing attendees a chance to mingle and continue the discussions.

Make sure to book your place so you don’t miss out. Take a look at the programme to register and join researchers, students, librarians, administrators, and publishers across the University of Cambridge at every career stage. Get in touch if you have any queries info@osc.cam.ac.uk.

Reflections from the Edinburgh Open Research Conference

Supporting Open Research,

Dr Mandy Wigdorowitz holds the position of Open Research Community Manager for Cambridge University Libraries where she is developing an open research community across Cambridge. She has a PhD in Theoretical and Applied Linguistics from the University of Cambridge and is a registered Research Psychologist with the Health Professions Council of South Africa. She also holds the position of Associate Editor for the Journal of Open Humanities Data.

The Edinburgh Open Research Conference 2023, offered by the University of Edinburgh Library Research Support Team and grassroots group Edinburgh ReproducibiliTea, provided a platform for the exchange of ideas and discussions about open research under the theme ‘Open Research as a Tool for Addressing Global Challenges’. Living up to its theme, the conference held numerous presentations focussing on the various ways in which open research practices can positively support efforts to address various challenges centring around open initiatives. The conference provided an opportunity for people from across the world to come together in a hybrid format to discuss how adopting the open research principles of open access, participation in research, transparency, and open data can ensure that the efforts of research are set up to help address global challenges, including in education, climate action, and global pandemics.

As a presenter and attendee, I reflect on the main take-homes from this event.  

With any conscientious and inclusive movement, clarification of terminology is important. The open research movement is no exception. Throughout the conference, many speakers acknowledged ‘open science’ as being an inclusive term, encompassing all areas of ‘openness’ or ‘open scholarship’, and one which extends beyond the ‘sciences’ to include all disciplines where knowledge synthesis and open research is considered. It was proposed that the phrase ‘open science’ is about intent and the larger goal of open research, and it should not be reduced to disciplines that fall under the ‘sciences’ umbrella per se. While the sentiment of this stance is reassuring and inclusive in intent, it is undeniable that there is weight behind the words we use. Instead, I would argue that it would be more inclusive to replace ‘science’ with ‘research’ when referring to the broad ‘open research’ movement. Doing so would safeguard against unintended misinterpretations about who may partake in and benefit from this movement.

A highlight from the conference was its celebration and acknowledgement of the growing impact of public engagement and citizen-led research. Case studies offered insight into how involving the public in data collection, analysis, and decision-making processes can enhance the relevance and societal impact of open research endeavours. For instance, UCL’s Institute for Global Prosperity aims to understand what prosperity means for people as informed by members of their respective communities. In addition, the Extreme Citizen Science: Analysis and Visualisation project employs the use of culturally appropriate geographical analyses and visualisation tools that can be used by varying communities with differing degrees of literacy to formulate research questions and collect relevant data. Attendees were encouraged to explore innovative ways of collaborating with non-academic communities to foster a culture of inclusivity, knowledge sharing, and insights that are driven from the communities under investigation, and to think about the value of smaller, local-scale projects in addition to large-scale projects.

Much attention was afforded to the dissemination avenues that prioritise FAIR principles (Findable, Accessible, Interoperable, and Reusable) and open practices, as well as who the contributors and accessors of such research outputs are. These efforts have largely been attributed to the increased availability of digital collections, the development of new data-intensive methods, increased pressure from funders, the requirement of data management plans for preservation purposes, the involvement and collaboration of research libraries, and the rollout of rights retention policies. Discussions centred around digital objects and data, including how these are produced, how and where they are openly and transparently shared, how they can be accessed and preserved, and what the potential of their reuse is. Such questions lead to the need for reputable sharing outlets that service people from all parts of the world and across all disciplines. Significant outlets that were mentioned included repositories, data dashboards, and data papers.

Data dashboards provide an overview of the various aspects associated with a research project, which allows for clear access to data insights when conducting large projects. An effective use of a data dashboard comes from DecodeME, the world’s largest study of ME/CFS (myalgic encephalomyelitis). Data papers are peer-reviewed publications that describe curated datasets. Data papers can be shared in traditional research journals as one subtype of article publication, or in data journals which are dedicated to the publication of data papers. This avenue of dissemination has been active in the STEM and Health disciplines, but it is being increasingly recognised and promoted within the Humanities and Social Sciences, largely driven by data journals in these areas, such as the Journal of Open Humanities Data. Overall, these discussions shed light on the challenges and potential solutions to ensure the quality and accessibility of open outputs derived from various research projects.

In addition to the many discussions about open software, which are ubiquitous in open research, open hardware was recognised as an emerging area in this arena. Open hardware can include, for instance, computing devices, scientific instrumentation, and remote sensing satellites that contribute to the conduction of research and discovery of knowledge. Typically, legal restrictions prohibit the investigation and modification of closed source hardware, resulting in a lack of reproducibility, duplication of effort, obsolescence, and financial burdens which ultimately reinforce global inequities. There have been recent efforts, however, to develop open-source hardware tools and devices to address global challenges particularly in under-resourced communities. Real-world case studies were presented that explore where and how open hardware has been used to address global challenges (e.g., in microscopy, space exploration, environmental monitoring) and make a difference in the lives of everyday people. The Gathering for Open Science Hardware was identified as a community whose mission is to promote open hardware and the practices ensuring its success. Open hardware presents an exciting opportunity for progress as its potential for solving global problems is far-reaching and scalable.

Education also emerged as key to the open research movement. The conference presented best practices in research data management and open educational resources for postgraduate students and educators from the perspective of a university lecturer. Training and mentoring programmes about open practices were mentioned, where people interested in applying open principles in their work and becoming ambassadors in their communities could sign up to Open Life Science to participate in an open research training course, and to Open Hardware Makers to support open hardware projects.

In sum, the Edinburgh Open Research Conference was successful in showcasing the advancement of open research with a focus on addressing global challenges. Open research is a fundamentally iterative process where we can all learn and build upon the accumulated work and knowledge that has been done before us. In this way, the event illustrated the remarkable progress that has been made in various domains and throughout the research lifecycle. By bringing together individuals from diverse backgrounds and contexts, this conference provided a platform for knowledge sharing and community-building at the forefront of open research.

You can find all the talks and slides from the conference here.