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

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,, 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. 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 was acquired by Springer Nature. Their press statement aims to reassure that 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 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 and Springer Nature develops and whether the original mission and vision of 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

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.

Should the UK make a deal with Springer Nature?

This is a guest post by Prof. Stephen J. Eglen on the concurrent negotiations between the UK academic sector and the publisher Springer Nature. Prof. Eglen is a Fellow of Magdalene College and Professor of Computational Neuroscience in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge. This post does not necessarily reflect the view of Cambridge University Libraries.

The UK academic sector is currently in discussion with Springer Nature around a renewed ‘read and publish’ deal for journal content. I understand that most institutions are likely to reject the current deal, but wish to continue negotiations. My position is that further discussions with Springer Nature are futile; we should stop accepting ‘transformative deals’. The likely effect of this deal would be that more of Springer Nature’s content may be openly available to read, but with the ‘paywall’ shifted to the publish side. Here I list my key objections:

  1. There is still no justification for the high APCs (9500 EUR + taxes) for Nature tier journals. Accepting a deal, regardless of the level of discounts that could be achieved, is implicitly accepting their business model. Springer Nature declined to engage with the Journal Comparison Service run by cOAlition S that aims to help understand how costs are determined.
  2. Springer Nature’s view is that ‘gold OA’ is the only viable way to open access. Other models for open access are available, and show promise, including diamond OA journals and Subscribe to Open. However, Springer Nature assert that “they haven’t found a way of making them financially sustainable”.  If we accept a gold-only view of open access,  how can we objectively assess the sustainability of alternative models?
  3. A move to a ‘gold only’ OA world would shift the barrier from reading to publishing content. Springer Nature recently announced a waiver policy for researchers from about 70 lower income countries. This still excludes many researchers worldwide e.g. from Brazil and South Africa, perpetuating neo-colonial attitudes towards the creation of scholarly content and reinforcing existing institutional inequalities within countries. Any waiver programme for APCs should be “no-questions-asked” regardless of where researchers are based. This would need to be properly costed and part of the justification of the APC (point 1).
  4. As of January 2023, several UK institutions have rights retention policies in place, with more expected to follow in the coming months. Individual researchers can also use rights retention strategy by themselves. Rights retention statements allow researchers to meet UK funder’s requirement by depositing their author-accepted manuscript without embargo. I believe Springer Nature should publicly state that they will allow any author worldwide to maintain their rights on their own author-accepted manuscripts.
  5. Over half of Springer Nature’s hybrid journals failed to meet their 2021 targets for open access articles within hybrid journals.  Those hybrid journals that fail again this year to meet their targets will be removed from cOAlition S’s transformative journal program.  Having some journals ineligible for cOAlition S funding but part of a UK read-and-publish deal would further complicate an already confusing system.  It would also question Springer Nature’s commitment to open access.

A detailed public critique of the deal is not possible because of the confidential nature of the negotiations.  Finances aside, I feel there was one element that was simply unworkable and unethical due to it requiring scholars to keep one aspect confidential if the deal were accepted.

The UK is one of only a few countries with a  heavy reliance on transformative agreements.  Sweden has already decided that transformative agreements are not sustainable and the transition period should finish at the end of 2024. Coalition S has also confirmed it will end its support of hybrid journals by the end of 2024. I would like to see the UK move away from transformative agreements. We could instead work internationally to promote more ethical and sustainable alternatives that put scholars at the heart of scholarly communication. In particular, the APC model has been tried, and introduces as many headaches as it has tried to solve. 

It is time instead to try new approaches.  There are several interesting models being developed by forward-looking organizations that the UK could endorse.  For example, MIT press recently launched shift+OPEN as a way to flip subscription based journals to diamond open access model.  Another interesting approach is Subscribe to Open where journals drop their paywall if a threshold amount of subscriptions are received.  Money saved on dealing with legacy publishers like Springer Nature is better spent investing in our own infrastructure and new approaches.

Springer negotiations: what’s our plan B? 

The negotiations 

The UK universities sector is negotiating a read & publish deal with publisher Springer Nature. Reaching a transitional agreement is particularly important to make it easier for our authors to publish their work open access, as well as continuing to read all of Springer Nature’s content. The deal needs to be affordable for our sector, which is already under financial strain.  

The Jisc negotiating team and the University of Cambridge are committed to finding a deal that works well for us, that is our plan A. But we are aware that some previous negotiations between universities and publishers could not find enough mutual ground (for example UCLA and German universities). If a contract can’t be signed, what would that mean for our researchers? 

What would we keep access to? 

Our current deal with Springer Nature includes perpetual access to some of their catalogue. We would retain access to 69% of content we currently subscribe to, even if we have to walk away from negotiations without a deal. When clicking on these articles, you will be given automatic access if you are connected to a Cambridge network or VPN, or you would be able to gain access from elsewhere with your Raven credentials.  

Of course, we would only retain access to historic materials, not new publications. This means that the percentage of articles we have access to will slowly decline over time. The areas most impacted by the loss of access would be Physical Sciences, Biological Sciences and Clinical Medicine. But we have other plans to help people get access to the articles they require. 

How would we access other articles? 

If the University does not subscribe to an article you need to access, you would still be able to get hold of it, but the process is a little longer. The best thing to do is to install the Lean Library plugin on your device. Lean Library will look for open access content and allow you to access anything to which we retain post-cancellation access.  

If you can’t get access through Lean Library, Cambridge University Libraries will help you get the article through an inter-library loan or other routes. The exact process will depend on ongoing work, so look out for further communications about the details.  

How would we publish in Springer Nature journals?  

Open access publishing is a great way to ensure that everyone in the world can read and apply your work for free. Many funders now require open access as a condition for their funding. As an additional complication, funders including the UK research councils will not pay for open access in hybrid journals, which charge for both subscriptions and open access (what we sometimes call ‘double-dipping’), unless there are transitional read & publish deals in place, or the journal is a transformative journal.  

A read & publish deal would mean that the cost of open access publishing is covered by the libraries upstream, and researchers can publish at no additional cost. However, if a deal cannot be reached, many Springer Nature journals would remain hybrid journals. This means that many researchers would be required to publish open access, but have no access to central funds for this.  

The solution is the Rights Retention strategy. By signing a pilot agreement with the University and including a rights retention statement in their manuscript, authors will retain their rights to make the manuscript openly available immediately on our repository, Apollo. This way, they will fulfil their funder requirement without having to pay a penny.  

It should also be noted that some journals, such as Nature, have put into place specific provisions for researchers whose funders mandate open access.  

How will we find out more? 

The current contract runs until the end of December 2022 and we are assured of a grace period stretching to February 2023, during which access will continue if negotiations are ongoing.  

We will continue to update our website as more information becomes available. An announcement will be made by email across the University once the outcome of the negotiations is known. Please email or speak to your librarian if you have any questions.