Tag Archives: Open Research

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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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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“Become part of the research process” – observations from RLUK2017

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When is a librarian not a librarian? Rather than a bad joke, this was one of the underlying interesting discussions arising from the 2017 RLUK conference held earlier in March. The conference Twitter hashtag was #rluk17 and the videos are now available. The answer, it appears is when we start talking about partnerships with, rather than support of, our research community.

As always with my write-ups of conferences, these are simply the parts that have resonated with me, and the impression I walked away with. This write up will be very different from anyone else’s from the conference, such as this blog from Lesley Pitman, and the RLUK conference report.

I have also written a sister blog describing the workshop I co-presented on the topic of Text and Data Mining.

Libraries’ role in research

The role of libraries and the people who work in them was the theme of one session – with arguments that libraries should be central to the research process.

Masud Khokhar, the Head of Digital Innovation and Research Services at Lancaster University, gave a talk on the Role of research libraries in a technological future. He said we need to get out of the culture of researchers only coming to the library with research outputs/outcomes. Language matters, he said. Lancaster University has made a deliberate decision not to use the word ‘support’, because “we have bigger aims than that”. Partnership is the future for libraries rather than just collaboration. We need to be creative co-developers working with the research community if we are to be a research library.

We need to generate a culture of experimentation: “Be creative, experiment fast, succeed or fail fast and learn from both”. It is a good challenge for us librarians to be more creative and less passive. We should embed library in research questions and processes.

The issue of how we present information to our clients came up, with Khokhar saying consistency when searching should no longer be important – we should depend on the context of the searcher. “Content might be king, but context is the kingdom”, he said.

He also showed evidence of how data visualisation can lead to greater downloads of data, and it may be even more important to data use than good metadata. Indeed, Lancaster University Library has allowed 10TB of server space for analytics of library data alone, because this is a growing and important area to drive decision making.

This perspective was also put forward by Patrick McCann from the University of St Andrews Library. He talked about the new role of Research Software Engineers, which is a role which works with the research community to develop research solutions and research outputs. St Andrews has a senior librarian for digital humanities and research computing. He noted: “we are part of the research process”.

A comment was made during the conference that many speakers had identified themselves as ‘not a librarian’. There was a call for us to open the idea of what a librarian is. Masud Khokhar suggested he would consider himself to be an ‘honorary’ librarian.

But the ‘librarian or not’ debate is an interesting question. William Nixon from the University of Glasgow noted that their Research Data Management team are not librarians, saying “it is a skill set in itself”. Kokhar argued that we need to develop digital leaders for libraries. Are these people already in libraries who we train up, or are they people with these skill sets we bring in and introduce to library culture?

Libraries’ role in the Open Science agenda

Libraries are the central pivot point for the move to open research across the world, was the message from presentations about activities in Europe and Canada. This fits with the narrative that libraries should be driving the agenda rather than reacting to it.

Susan Reilly, the outgoing Executive Director of LIBER talked about re-imagining the library space in the context of open science as she presented the LIBER 2020 vision.

Open Science (a term used in Europe for ‘open research’) is on the European agenda, every single member state has signed up to develop the necessary skills, development of the open science cloud. There has been an 80 million Euro investment in this. Given LIBER is a group of libraries with a common mission to enable world-class research, the question is whether LIBER should make the whole strategy about open science?

Reilly noted that libraries have been ‘bold’ on open science for years and held back by faculty and publishers. She argued we must be resilient on this agenda. Libraries need to be taking a leadership role in all research. “Libraries need to get into the researchers’ lifecycle”, she argued. They should provide tools throughout the research lifecycle to ensure ‘open science’. To achieve this, we need digital skills, which underpin a more open and transparent research lifecycle.

The end goal, said Reilly, is world-class research, but open science facilitates that through facilitating collaboration and ensuring the sustainability of research. The 2020 vision is: “Libraries powering sustainable knowledge in the digital age”.

The proposal is that by 2022, open access will be the predominant form of publishing and research data is Findable Accessible Interoperable Reusable (F.A.I.R). Reilly noted that it is research data management “where we get the most pushback” – an experience reflected in many other institutions.

Libraries can provide platforms of innovative scholarly communications. They can facilitate open access to research publications, with services ranging from payment for APCs and becoming a publisher. Libraries also offer research data management, innovative metrics and innovative peer review.

This is an opportunity for libraries to disrupt scholarly communications system. In order for us to achieve this goal, we need research skills that underpin a more open and transparent research lifecycle – and so we need to equip researchers to do this.

Reilly noted that when LIBER went out to stakeholders – “they bought into the vision”. To achieve these goals, Reilly said it is important for libraries to have a strong relationship with institutional leadership. There needs to be transparency around the cost of publications.

We need to work on diversifying librarian’s skills and research skills. This is a matter of ‘compete or fail’ or Elsevier could take over what libraries do. We need to get into the research workflow.

LIBER’s outcomes from their consultation with stakeholders were:

  • Importance of libraries having a string relationship with institutional leadership
  • Transparency around the cost of publications
  • Working on diversifying librarians’ skills AND researchers skills
  • Be clear about what the role of libraries is/should be
  • Compete or fail
  • Get into the research workflow
  • Opportunity for libraries to disrupt scholarly communications system

It was interesting (for me) to note how similar these are to the Strategic Goals of the Office of Scholarly Communication:

The Open Scholarship theme was continued in a presentation by representatives of RLUK’s sister organisation, the Canadian Association of Research Libraries (CARL). This is a leadership organisation thinking of ways to enhance members capacity and leadership in this environment. Martha Whitehead, the President of CARL and Susan Haigh, the Executive Director presented the Canadian Roadmap for advancing Scholarly Communication.

There are issues with open access, they noted. Repositories need to improve in two major areas – we need to improve their functionality, and support and encourage the development of value added services such as peer review and tools.

There have been challenges in discussions with publishers about maximising openness which have become ‘somewhat fraught’. Libraries are working with Canadian journals to develop, assess and adopt sustainable open access funding models. The idea is that the model will be non-profit (where the money goes back in).  While it is not clear if the discussions will coalesce around anything new and bold, there is value in bringing together the communities.

The Canadians presented an initiative related to Research Data Management (RDM) called Portage. This is designed to help with RDM in the country. It has a director, and because it is an organisation with a facility, the library voice is well respected around the table. Experts are contributing their expertise to this. There is also a Federated Research Data Repository – a joint software development project with Compute Canada, and the Scholars Portal Dataverse offers data deposit and sharing at no charge to researchers.

New challenges for libraries

Torsten Reimer spoke about the new focus of the British Library on ‘everything accessible’. He discussed the implications for libraries as we move towards a more open access future. We need to change focus, he argued, with new skills and areas, and we should be working together with the research community.

As more material is available openly then what is the role of a national library? Reimer asked. Perhaps libraries need to provide infrastructure, we should focus on preservation & adding value. Given the majority of academics use software in the context of their projects, should libraries be supporting, integrating and preserving it?

The ‘just in case’ model is no longer feasible for libraries. The British Library is looking at partnerships in content creation, research & infrastructure. Examples include plans to expose the EThOS API to allow for machine consumption of data about theses. They are also looking to replace the current “hand knitted” preservation system with more robust scalable shareable solution

Collaborate or die?

The opening keynote was by John MacColl, the University Librarian & Director of Library Services, at St Andrews University (and outgoing president of RLUK). MacColl spoke about the ‘research commons’.

He referred to the ‘tragedy of the commons’ which was an argument put forward in 2003 that individuals cancelling subscriptions for the Big Deal had meant an increase of 129% in cost to access literature. Publishers are creating ‘artificial scarcity’ to the literature which means they can charge as they please. This is a ransack of the commons.

It is not just cost, these Big Deals have meant that most collections are becoming the same and we are losing access to other resources. MacColl also noted the lost need for bibliographers. But his call was that research libraries face a challenge in re-appropriating the responsibility for the preservation of key scholarly objects held on publisher servers and other vendors worldwide.

So, argued McColl, we need to work collectively to ‘find means of getting around being held ransom by publishers’. We need a ‘post-collective Big Deal world’. This is Plan B, where we take back control, find post cancellation access, arrange document delivery and green open access.

But this is not something we can do individually. MacColl asked: “When we are doing things in our own institutions, who are we letting down by not thinking of the wider community?” We need some sort of formal governance to make that happen. The challenge is Higher Education is a very conservative world. People will not take a step unless convinced this is a sensible step to take.

We need to focus on the global – where libraries collaborate on shared bibliographic data and create a ‘collective collection’. Plan B needs to be national.

So much more

This blog has glossed over many very interesting presentations and talks. I do, however wish to mention the last session of the event which broadened the discussion outside of the library to the issue of ‘inclusion’ in the Higher Education sector. Libraries, as a neutral ‘safe’ place on campus, of course have a big role to play in this. As has been the case in every meeting I have attended since November last year, the double threats of Brexit and Trump have never been far from the discussion, and never more so than in the context of inclusion.

Darren Lund, a ‘middle aged white guy from Canada’ spoke very entertainingly about his work on diversity, making the point that if you have privilege you should use it to make positive change.

The final talk was a sobering walk through some research into the racial diversity of universities with plenty of data proving that universities are not as liberal as they are perceived to be by us. Statistics such as 92% of professors in the UK are white, and the fact there are only three Vice Chancellors from the black and minority ethnic community in the UK, supported Professor Kalwant Bhopal’s argument that we need to actively address the issue of inclusion.

Summary

This blog began with a fairly provocative statement – that people do not identify themselves as librarians when we start talking about partnerships with, rather than support of, our research community. This is an interesting question. Many librarians feel that their role is to support, not lead. Yet others argue that unless we do take a leading role we will become redundant.

So what is the solution? Do we widen the definition of a library? Do we widen the definition of a librarian? Or are we happy with the ‘honorary librarian’ solution? These are some of the questions that need further teasing out. One thing is sure, the landscape is changing rapidly and we need to change with it.

Debbie Hansen and Danny Kingsley attended the conference thanks to the support of the Arcadia Fund, a charitable fund of Lisbet Rausing and Peter Baldwin.

Published 30 March 2017
Written by Dr Danny Kingsley
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