All posts by Office of Scholarly Communication

Reflections on Open Research – a PI’s perspective

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As part of the Open Research Pilot Project, Marta Teperek met with Dr David Savage and asked him several questions about his own views and motivations for Open Research. This led to a very inspiring conversation and great reflections on Open Research from the Principal Investigator’s perspective. The main points that came out of the discussion were:

  • Lack of reproducibility raises questions about scientific rigour, integrity and relevance of work in general
  • Being open is to work in a team and be collaborative
  • Open Research will benefit science as a whole, and not the careers of individuals
  • Peer review remains a critical aspect of the scientific process
  • Nowadays, global collaboration and information exchange is possible, making the data really robust
  • Funders should emphasise the importance of research integrity and scientific rigour

This conversation is reported below in the original interview format.

Motivations for doing Open Research

Marta: To start, could you tell me why you are keen on Open Research and why did you decide to get involved in the Open Research Pilot Project?

David: Sure, but before we start I wanted to stress that when I make comments about science, these are very general comments and they don’t apply to anyone in particular.

So my general feeling is that I am very concerned and disappointed about the lack of research reproducibility in science. Lack of reproducibility raises questions about scientific rigour, integrity and relevance of work in general. Therefore, I am really keen on exploring ways of addressing these failings of science and I want to make a contribution to solving these problems. Additionally, I am aware that I am not perfect either and I want to learn how I can improve my own practice.

Were there any particular experiences which made you realise the importance of Open Research?

This is just the general experience of reading and also reviewing far too many papers where I thought that the quality of underlying data was poor, or authors were exaggerating their claims without supporting evidence. There is too much hype around, and the general awareness about the number of papers published in high impact journals which cannot be reproduced makes the move to more transparent and open approaches necessary.

Do we need additional rewards for working openly?

How do you think Open Research could benefit academic careers?

I am not sure if Open Research could or should benefit academic careers – this should not be the goal of Open Research. The goal is to improve the quality of science and therefore the benefit of science to the public. Open Research will benefit science as a whole, and not the careers of individuals. Science has become very egotistical and badge –accumulating. We should be investigating things which we find interesting. We should not be motivated by the prize. We should be motivated by the questions.

In science we have far too many people who behave like bankers. Publishing seems to be the currency for them and thus they are sloppy and lack the necessary rigour just because they want to publish as fast as they can.

In my opinion it is the responsibility of every researcher to the profession to try to produce data which is robust. It is fine to make honest mistakes. But it is not acceptable to be sloppy or fraudulent, or not to read enough literature. These are simply not good enough excuses. I’m not claiming to be perfect. But I want to constantly improve myself and my research practice.

Barriers to greater openness in research

What obstacles may be preventing researchers from making their research openly available?

The obvious one is competition for funding, which creates the need to publish in high impact factor journals and consequently leads to the fear of being scooped. And that’s a difficult one to work around. That’s the reason why I do not make everything we do in my research group openly available. However, looking at this from society’s perspective, everything should be made openly available, and as soon as possible for the sake of greater benefit to mankind. So balance needs to be found.

Do you think that some researchers might want to make their research open, but might not know how to do it, or might not have the appropriate skills to do it?

Definitely. Researchers need to know about the best ways of making their research open. I am currently trying to work out how to make my own project’s website more open and accessible to others and what are the best ways of achieving this. So yes, awareness of tools and awareness of resources available is necessary, as well as training about working reproducibly and openly. In my opinion, Cambridge has a responsibility to be transparent and open about its processes.

Role of peer-review in improving the quality of research

What frustrates you most about the current scholarly communication systems?

Some people get frustrated with the business model of some of the major publishers. I do not have a problem with it, although I do support the idea of pre-print services, such as bioRxiv. Some researchers get frustrated about long peer-review process. I am used to the fact that peer-review is long, and I accept it because I do not want fraudulent papers to be published. However, flawed peer review, such as biased peer-review or lack of rigorous peer review, is not acceptable and it is a problem.

So how to improve the peer-review process?

I think that peer-reviewers need to have greater awareness of the need for greater rigour. I was recently asked to peer review an article. The journal had dedicated guidance for peer reviewers. However, the guidance did not contain any information about suitability to undertake the peer-reviewing work. Peer-reviewer guidance documents need to address questions like: Do you really know what the paper is about? Do you know the discipline well enough? Are there any conflicts of interest? Would you have the time to properly peer-review the work? Peer-review needs to be done properly.

What do you think about the idea of journals employing professional peer-reviewers, who could be experts in their respective fields and could perform unbiased, high quality peer-review?

This sounds very reasonable, as long as professional peer-reviewers stay up to date with science. Though this would of course cost money!

I suppose publishers have enough money to pay for this. Have you heard of open peer-review and what do you think about it?

I think it is fine, but it might be subject to cronyism. I suspect that most people will be more likely to agree for their reviews to be made open as long as they make a recommendation for the paper to be accepted.

I recently reviewed a paper of a senior person and I rejected it. But if I made my review open, it would pose a risk to me – what if the author of the paper I rejected was the reviewer of my future grant application? Would they still assess my grant application objectively? What if people start reviewing each other’s papers and start treating peer-review as a mechanism to exchange favours?

The future of Open Research is in your hands

Who or what inspires you and makes you optimistic about the future of Open Research?

In Cambridge and at the Wellcome Trust there are many researchers who care about the quality of science. These researchers inspire me. These are very clever people, who work hard and make important discoveries.

I am also inspired by teamwork and collaboration. In Big Data and in human genetics in particular, people are working collectively. Human genetics and epidemiology are excellent examples of disciplines where 10-20 years ago studies were too small to allow researchers to make significant and reproducible conclusions. Nowadays, global collaboration and information exchange is possible, making the data really robust. As a result, human genetics is delivering really important observations.

To me, part of being open is to work in a team and be collaborative.

If you had a magic wand and if you could get one thing changed to get more people share and open up their research, what would it be?

Not sure… I suppose I am still looking for it! Maybe I will find one during the Open Research Pilot Project. Seriously speaking, I do not believe that a single thing could make a difference. It is the little things that matter. For example, on my side I am trying to make my own lab and institute more aware of reproducibility issues and ensure that I can make a difference in my own environment.

So as a Group Leader, how do you ensure that researchers in your own group are rigorous in their approach?

First, I really make them aware of the importance of reproducible research and of scientific rigour. I am also making a lot of effort to ensure that my colleagues are up to date with literature. I ask them if they read important literature and if they are unable to answer I ask them to do their homework. I am also imposing rigorous standards for experiments. In my lab people repeat the key experiments, or those which are particularly surprising, in a blind fashion. It takes a lot of time and extra resources, but it is important not to be too quick and to validate findings before making claims.

I am also ensuring that my people are motivated. For example, even though everyone helps each other in my group, all PhD students have direct access to me and we have regular discussions about their work. It is important that your group is of a manageable size; otherwise, as a group leader, you will not know all your people and you will not be able to have regular discussions about their work.

How do you identify people who care about reproducible research when making hiring decisions?

I ask all prospective applicants to make a short presentation about their previous work. During their presentation I ask them to tell me exactly what their research question was and how confident they were about their discovery. I am looking for evidence of rigorous methodology, but also for honesty and for people who are not overselling their findings.

In addition, I ask about their career goals. If they tell me that their career goal is to publish in Nature, or have two papers in Science, I count this against them. Instead, I favour applicants who are question-driven, who want to make progress in understanding how things work.

Role of funding bodies in promoting Open Research

Do you think that funders could play a role in promoting Open Research?

Funders could definitely contribute to this. The Wellcome Trust is a particularly notable example of a funding body keen on Open Research. The Trust is currently looking into the best ways to make Open Research the norm. Through various projects such as the Open Research Pilot, the Trust helps researchers like myself to learn best practice on reproducible research,and also to understand the benefits of sharing expertise to improve skills across the research community.

Do you think funder policies to mandate more openness could help?

Potentially. However, policies on Open Access to publications are easy to mandate and relatively easy to interpret and implement. It is much more difficult for Open Research. What does Open Research mean exactly? The right scope and definitions would be key. What should be made open? How? The Wellcome Trust is already doing a lot of work on making important research results available, and human genomic data in particular. But making your proteomic and genomic data publicly available is slightly different from ensuring that your experiments are rigorous and your results honest. So in my opinion, funders should emphasise the importance of research integrity and scientific rigour.

To close our discussion, what do you hope to achieve through your participation in the Open Research Pilot Project?

I want to improve my own lab’s transparency. I want to make sure that we are rigorous and that our research is reproducible. So I want to learn. At the same time I wish to contribute to increased research integrity in science overall.

Acknowledgements

Marta Teperek would like to thank SPARC EUROPE and Dr Joyce Heckman for interviewing her for the Open Data Champions programme – many of the questions asked by Marta in the interview with Dr David Savage originate from inspiring, open questions prepared by SPARC EUROPE.

Published 22 June 2017
Written by Dr Marta Teperek

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Cambridge RCUK Block Grant spend for 2016-2017

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Much to our relief, last Friday we sent off our most recent report on our expenditure of the RCUK Block Grant fund. The report is available in our repository. Cambridge makes all of its information about spend on Open Access publicly available. This blog continues on from that describing our spend from 2009 – 2016, and from the blog on our open access spend in 2014.

Compliance

We are pleased to be able to report that we reached 80% compliance in this reporting period, up from 76% last year. The RCUK is expecting 75% compliance by the end of the transition period on 31 March 2018, so we are well over target.

According to our internal helpdesk system ZenDesk, our compliance is shared between 52% gold (publication in an Open Access journal or payment for hybrid Open Access), and 28% green (placement of the work into our institutional repository, Apollo). We do not have the breakdown of how many of the gold APC payments were for hybrid. In the past it we have had an overall 86.8% spend on hybrid.

Not only do we have an increase from 76% to 80% in our compliance rates overall, this is even more impressive when we consider that this is in the face of a 15% increase in the number of research outputs acknowledging RCUK funding. Web of Science indicated in a search for articles, reviews and proceedings papers that Cambridge published 2400 papers funded by RCUK in 2016. In 2015 Web of Science the same search counted 2080 RCUK funded research outputs.

Headline numbers

  • In total Cambridge spent £1.68 million of RCUK funds on APCs (this is up from £1.28 last year)
  • 1920 articles identified as being RCUK funded were submitted to the Open Access Service, of which 1248 required payment for RCUK*
  • The average article processing charge was £1850 – this is significantly less than the £2008 average last year, reflecting the value of the memberships we have (see below)

*Note these numbers will differ slightly from the report due to the difference in dates between the calendar and financial years (see below).

Non APC spend

In total Cambridge spent £1.94 million of RCUK funds in this reporting period, of which £1.68 million was on APCs.  Approximately 13% was spent on other costs,  primarily distributed between staffing, infrastructure and memberships.  The greatest proportion is staffing, with £95,000 spent on this cost. Memberships were the next largest category, mostly arrangements to reduce the cost of APCs, including:

  • £42,000 on the open access component of the Springer Compact
  • £22,000 on memberships to obtain discounts – there is a list of these on the OSC website
  • £18,000 on the University’s SCOAP3 subscription

The RCUK fund has also supported the infrastructure for Open Access at Cambridge, with £62,000 covering the cost of several upgrades of DSpace and general support for the repository. This has allowed us to implement new services such as the minting of DOIs and our hugely successful Request a Copy service which allows people to contact authors of embargoed material in the repository and ask them to send through the author’s accepted manuscript. This category also covers our license for our helpdesk system, ZenDesk, which helps the Open Access team manage the on-average  responses to 60 queries a day. We are also able to run most of our reporting out of ZenDesk.

There are some other smaller items in the non APC category, including £1500 on bank charges that for various reasons we have not been able to allocate to specific articles.

Are these deals good value?

Some are. The Springer Compact is shown as a single charge in the report with the articles listed individually. The RCUK Block Grant contributed £46,020 to the Springer Compact and 128 Cambridge papers were published by Springer that acknowledged RCUK funding. This gives us an average APC cost per paper to the RCUK fund* of £359.53 including VAT. This represents excellent value, given that the average APC for Springer is $3,000 (about £2,300).

*Note that in some instances the papers acknowledging RCUK may also have acknowledged COAF in which case the overall cost for the APC for those papers will be higher.

Cambridge has now completed a year having a prepayment arrangement with Wiley. Over this time we contributed £108,000 to the account and published 68 papers acknowledging RCUK. This works out that on average the Wiley APC cost was £1,588 per paper. Like Springer, the average APC is approximately £2,300 so this amount appears to be good value.

However the RCUK has contributed a higher proportion to the Wiley account than COAF because at the time the account was established we had run low on COAF funds. Because the University does not provide any of its own funds for Open Access, there was no option other than to use RCUK funds. We will need to do some calculations to ensure that the correct proportion of COAF and RCUK funds are supporting this account. It is a reflection of the challenges we are facing on a rolling basis when the dates are fluid (see below).

It appears we need to look very closely at our membership with Oxford University Press. We spent £44,000 of RCUK funds on this, and published 22 articles acknowledging RCUK funding. This works out to be an APC of £2000 per article, which is not dissimilar to an average OUP APC, and therefore does not represent any value at all. This is possibly because our allocation of the expense of the membership between COAF and RCUK might not reflect what has been published with OUP. We need to investigate further.

Caveat – the date problem

We manage Open Access funds that operate on different patterns. The COAF funds match the academic year, with the new grants starting on 1 October each year.  The RCUK works on a financial year, starting on 1 April each year. Many of our memberships and offset deals work on the calendar year.

To add to the confusion, the RCUK is behind in its payments, so for this current year which started on 1 April 2017, we will not receive our first part-payment until 1 June. That amount will not cover the commitments we had already made by the end of 2016, let alone those made between 1 April when this year started and the 1 June when the money is forthcoming. This means we will remain in the red. Cambridge is carrying half a million pounds in commitments at any given time. The situation makes it very difficult to balance the books.

Our recent RCUK report covers the period of 1 April 2016 – 31 March 2017 and refers only to invoices paid in this period. In the report the dates go beyond the 31 March 2017 because the reconciliation in the system sometimes takes longer, so items are logged as later dates even though the payment was made within the period. The publication dates for the articles these invoices relate to are wildly different, and many of these have not yet been published due to the delay between acceptance and publication which ranges from days to years.

This means working out averages is an inexact science. It is only possible to filter Web of Science by year, so we are only able to establish the number of papers published in a given calendar year. This set of papers is not the same set for which we have paid, but we can compare year on year and identify some trends that make sense.

Published 22 May 2017
Written by Dr Danny Kingsley

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Open at scale: sharing images in the Open Research Pilot

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Dr Ben Steventon is one of the participants in the Open Research Pilot. He is working with the Office of Scholarly Communication to make his research process more open and here reports on some of the major challenges he perceives at the beginning of the project.

The Steventon Group is a new group established last year which looks at embryonic development, in particular focusing on the zebrafish. To investigate problems in this area the group uses time-lapse imaging and tracks cells in 3D visualisations which presents many challenges when it comes to data sharing, which they hope to address through the Wellcome Trust Open Research Project. Whilst the difficulties that this group are facing are specific to a particular type of research, they highlight some common challenges across open research: sharing large files, dealing with proprietary software and joining up the different outputs of a group.

Sharing imaging data 

The data created by time-lapse imaging and cell tracking is frequently on a scale that presents a technical, as well as financial, challenge. The raw data consists of several terabytes of film which is then compressed for analysis into 500GB files. These compressed files are of a high enough quality that they can be used for analysis but they are still not small enough that they can be easily shared. In addition the group also generates spreadsheets of tracking data, which can be easily shared but are meaningless without the original imaging files and specific software to allow the two pieces of data to be connected. One solution which we are considering is the Image Data Resource, which is working to make imaging datasets in the life sciences, which have not previously been shareable due to their size, available to the scientific community to re-use.

Making it usable

The software used in this type of research is a major barrier to making the group’s work reproducible. The Imaris software the group uses costs thousands of pounds so anything shared in their proprietary formats are only accessible to an extremely small group of researchers at wealthier institutions, which is in direct opposition to the principles of Open Research. It is possible to use Fiji, an open source alternative, to recreate tracking with the imaging files and tracking spreadsheets; however, the data annotation originally performed in Imaris will be lost when the images are not saved in the proprietary formats.

An additional problem in such analyses is the sharing of protocols that detail the methodologies applied, from the preparation of the samples all the way through data generation and analysis. This is a common problem with standard peer-review journals that are often limited in the space available for the description of methods. The group are exploring new ways to communicate their research protocols and have created an article for the Journal of Visualised Experiments, but these are time consuming to create and so are not always possible. Open peer-review platforms potentially offer a solution to sharing detailed protocols in a more rapid manner, as do specialist platforms such as Wellcome Open Research and Protocols.io.

Increasing efficiency by increasing openness

Whilst the file size and proprietary software in this type of research presents some barriers to sharing, there are also opportunities through sharing to improve practice across the community. Currently there are several different software packages being used for visualisation and tracking. Therefore, sharing more imaging data would allow groups to try out different types of images on different tools and make better purchasing decisions with their grant money. Furthermore, there is a great frustration in this area that lots of people are working on different algorithms for different datasets, so greater sharing of these algorithms could reduce the amount of time wasted creating algorithms when it might be possible to adapt a pre-existing one.

Shifting models of scholarly communication

As we move towards a model of greater openness, research groups are facing a new difficulty in working out how best to present their myriad outputs. The Steventon group intends to publish data (in some form), protocols and a preprint at the same time as submitting their papers to a traditional journal. This will make their work more reproducible, and it also allows researchers who are interested in different aspects of their work to access the bits that interest them. These outputs will link to one another, through citations, but this relies on close reading of the different outputs and checking references. The Steventon group would like to make the links between the different aspects of their work more obvious and browsable, so the context is clear to anyone interest in the lab’s work. As the research of the group is so visual it would be appropriate to represent the different aspects of their work in a more appealing form than a list of links.
The Steventon lab is attempting to link and contextualise their work through their website, and it is possible to cross-reference resources in many repositories (including Cambridge’s Apollo), but they would like there to be a more sustainable solution. They work in areas with crossovers to other disciplines – some people may be interested in their methodologies, others the particular species they work on, and others still the particular developmental processes they are researching. There are opportunities here for openness to increase the discoverability of interdisciplinary research and we will be exploring this, as well as the issues around sharing images and proprietary software, as part of the Open Research Pilot.

Published 8 May 2017
Written by Rosie Higman and Dr Ben Steventon

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