Tag Archives: reproducibility

Consider yourself disrupted – notes from RLUK2016

The 2016 Research Libraries UK conference was held at the British Library from 9-11 March on the theme of disruptive innovation. This blog pulls out some of the highlights personally gained from the conference:

  • If librarians are to be considered important – we as a community need to be strong in our grasp of understanding scholarly communication issues
  • We need to know the facts about our subscriptions to, usage of and contributions to scholarly publishing
  • We need high level support in institutions to back libraries in advocacy and negotiation with publishers
  • Scientists are rarely rewarded for being right, so the scientific record is being distorted by the scientific ecosystem
  • Society needs more open research to ensure reproducibility and robust research
  • The library of the future will have to be exponentially more customisable than the current offering
  • The information seeking behaviour of researchers is iterative and messy and does not match library search services
  • Libraries need to ‘create change to triumph’ – to be inventors rather than imitators
  • Management of open access issues need to be shared across institutions with positive outcomes when research offices and libraries collaborate.

I should note this is not a comprehensive overview of the conference, and I have blogged separately about my own contribution ‘The value of embracing unknown unknowns’. Some talks were looking at the broader picture, others specifically at library practice.

Stand your ground – tips for successful publisher negotiations

The opening keynote presentation was by Professor Gerard Meijer, President of Radboud University who conducted the recent Dutch negotiations with Elsevier.

The Dutch position has been articulated by Sander Dekker, the State Secretary  of Education who said while the way forward was gold Open Access, the government would not provide any extra money. Meijer noted this was sensible because every extra cent going into the system goes into the pocket of publishers – something that has been amply demonstrated in the UK.

All universities in the Netherlands are in top 200 universities in the world. This means all research is good quality – so even if it is only 2% of the world output, the Netherlands has some clout.

Meijer gave some salient advice about these types of negotiations. He said this work needs to be undertaken at the highest level at the universities. There are several reasons for this. He noted that 1.5 to 2 percent of university budget goes to subscriptions – and this is growing as budgets are being cut – so senior leadership in institutions should take an active position.

In addition if you are not willing to completely opt out of licencing their material then you can’t negotiate, and if you are going to opt out you will need the support of the researchers. To that end communication is crucial – during their negotiations, they would send a regular newsletter to researchers letting them know how things were going.

Meijer also stressed the importance of knowing the facts, and the need to communicate and inform the researchers about these facts and the numbers. He noted that most researchers don’t know how much subscriptions cost. They do know however about article processing charges – creating a misconception that Open Access is more expensive.

Institutions in the Netherlands spent €9.2 billion million on Elsevier publications in 2009, which rose to €11billion million* in 2014. Meijer noted that he was ‘not allowed’ to tell us this information due to confidentiality clauses. He drolly observed “It will be an interesting court case to be sued for telling the taxpayers how their money is being spent”. He also noted that because Elsevier is a public company their finances are available, and while their revenue goes up, their costs stay the same.

Apparently Wiley and Springer are willing to go into agreements. However Elsevier are saying that a global business model doesn’t match with a local business requirement. The Netherlands  has not yet signed the contract with Elsevier as they are working out the detail.

Broadly the deal is for three years, from 2016 to 2018. The plan is to grow the Open Access output from nothing to 10% in 2016, 20% in 2017, 30% in 2018 and want to do that without having to pay APCs. To achieve this they have to identify journals that we make Open Access , by defining domains where all journals in these domains we make open access.

Meijer concluded this was a big struggle – he would have liked to have seen more – but what we have is good for science. Dutch research will be open in fields where most Open Access is happening and researchers are paying APCs. Researchers can look at the long list of journals that are OA and then publish there.

*CORRECTION: Apologies for my mistyping.  Thanks to    @WvSchaik for pointing out this error on Twitter. The slide is captured in this tweet.

The future of the research library

Nancy Fried Foster from Ithaka S+R and Kornelia Tancheva from Cornell University Library spoke about research practices and the disruption of the research library. They started by noting that researchers work differently now, using different tools. The objective of their ‘A day in the life of a serious researcher’ work was exploring research practices to inform the vision of library of the future and identify improvements we could make now.

They developed a very fine-grained method of seeing what people do which focuses on what people really do in the workplace. This used a participatory design approach. Participants (who were mainly post graduates) were asked to map or log their movements in one single day where at least some of their time was engaged in research. The team then sat with the person the following day to ask them to narrate their day – and talk about seeking, finding and using information. There was no distinction between academic and non-academic activity.

The team looked at the things that people were doing and the things that the library could and will be. The analysis took a lot of time, organising into several big categories:

  • Seeking information
  • Academic activities
  • Library resources
  • Space, self management and
  • Circum-academic activities – activities allied to the researchers academic line but not central.

They also coded for ‘obstacles’ and ‘brainwork’.

The participants described their information seeking as fluid and constant – ‘you can just assume I am kind of checking my email all the time’. They also distinguished between search and research. One quote was ‘I know the library science is very systematic and organised and human behaviour is not like that’.

Information seeking is an iterative process, it is constant and not systematic. The search process is highly idiosyncratic – our subjects have developed ways of searching for information that worked for them. It doesn’t matter if it is efficient or not. They are self conscious that it is messy. ‘I feel like the librarians must be like “this is the worst thing I have ever heard”’.

Information evaluation is multi-tiered – eg: ‘If an article is talking about people I have heard of it is worth reading’. Researchers often use a mash up of systems that will work for that project. For example email is used as an information management tool.

Connectivity is important to researchers, it means you can work anywhere and switch rapidly between tasks. It has a big impact on collaboration – working with others was continuously mentioned in the context of writing. However sometimes researchers need to eliminate technology to focus.

Libraries have traditionally focused too much on search and not enough on brain work – this is a potential role for libraries. References to the library occurred throughout the process. Libraries are often thought of as a place for refuge – especially for the much needed brain work. The need for self management – enable them to manage their time prioritise the demands on their attention. Strategies depended on a complicated relationship with technology.

One of the major themes emerging from the work is search is idiosyncratic and not important, research has no closure, experts rule and research is collaboration. The implications for the future library are that the future library is a hub, not just focusing on a discovery system but connecting people with knowledge and technologies.

If we were building a library from scratch today what would it look like? There will need to be a huge amount of customisation to adjust tools to suit researchers personal preferences. The library of the future will have to be exponentially more customisable than the current offering. Libraries will have to make available their resources on customisable platforms. We need to shift from non-interoperable tools to customisation.

So if the future were here today we would think of future library – an academic hub (improving current library services) and an application store. We should take on even more of a social media aspect. Think of a virtual ‘app store’ – on an open source platform that provides the option for people to suggest short cuts – employ developers to develop these modules quickly. Take a leadership role in ensuring vendor platforms can be integrated. All library resources will speak easily to the systems our users are using. We need to provide individualised services rather than one size fits all.

Scientific Ecosystems and Research Reproducibility

The scientific reward structure determines the behaviour of researchers and that this has spawned the reproducibility crisis according to Marcus Munafo from the University of Bristol.

Marcus started by talking about the P value where the statistically significant value is 95% – that is, the chance of the hypothesis being wrong is less than five in 100. Generally, studies need to cross this threshold to get published, so there is evidence to show that original studies often suggest a large effect – however when attempted, these effects are not able to be replicated.

Scientists are supposed to be impartial observers, but in reality they need to get grants, and publish papers to get promoted to more ‘glamorous institutions’ (Marcus’ words). Scientists are rarely rewarded for being right, so the scientific record is being distorted by the scientific ecosystem.

Marcus noted it is common to overstate your data or error check your data if your first analysis doesn’t tell you what you are looking for. This ‘flexible analysis’ is quite commonplace, if we look at literature as a whole. Often there is not enough detail in the paper to allow the reproducibility of the work. There are nearly as many unique analysis pipelines as there were studies in the sample – so this flexibility in the joint analysis tool gets leveraged to get the result you want.

There is also evidence that journal impact factors are a very poor indicator of quality, indeed it is a stronger indicator of retraction than quality. The idea is that the whole science will self correct. But science won’t sort itself out in a reasonable timeframe. If you look at the literature you see that replication is the exception rather than the norm.

One study showed among 83 articles recommending effective interventions, 40 had not been replicated, and of those that had been replicated many showed the works had stronger findings in the first paper than in the replication, and some were contradicted in the replication.

Your personal investment in the field shapes your position – unconscious biases that affects all of us. If you come in as an early career scientist you get an impression that the field is more robust than it is in reality. There is hidden literature that is not citable – only by looking at this you have a balanced sense of how robust the literature is. There are many studies that make a claim in the abstract that is not supported by more impartial reading. Others are ‘optimistic’ in the abstract. The articles that describe bad news receive far fewer citations than would be expected. People don’t want to cite bad news. So is science self correcting?

We can introduce measures to help science self correct. In 2000 the requirement to register the outcome of clinical trials began. Once they had to pre-specify what the outcome would be then most of the findings were null. That is why it is a scientific ecosystem – the way we are incentivised has become distorted over the years.

Researchers are incentivised to produce a small number of papers that are eye catching.  It is understandable why you would want to focus on quality over quantity. We can give more weight to confirmatory studies and try to move away from the focus on publishing in certain types of studies. We shouldn’t be putting all our effort into high risk, high return.

What do we do about this? There can be top down measures, but individual groups can work in ways to improve the ways we work, such as adopting the open science way of working. This is not trivial – for example we can’t make data available without the consent of participants. Possible solutions include pre-registering all the plans, set up studies so the data can be made open, ensure publications are gold OA. These measures serve as a quality control method because everything gets checked because people know it is going to be made available. We come down hard on academics who make conscious mistakes – but we should be encouraging people to identify their own errors.

We need to introduce quality control methods implicitly into our daily practice. Open data is a very good step in that direction. There is evidence that researchers who know their data is going to be made open are more thorough in their checking of it. Maybe it is time for an update in the way we do science – we have statistical software that can run hundreds of analysis, and we can do text and data mining of lots of papers. We need to build in new processes and systems that refine science and think about new ways of rewarding science.

Marcus noted that these are not new problems, quoting from Reflections on the Decline of Science in England written by Babbage in 1830.

Marcus referred to many different studies and articles in his talk, some of which I have linked out to here:

Creating change to triumph: A view from Australia

The idea of creating change to triumph was the message of Jill Benn, the Librarian at the University of Western Australia. She discussed Cambietics, the science of managing change. This was a theory developed in 1985 by Barrett, with three stages:

  • Coping with change to survive
  • Capitalising on change
  • Creating change to triumph.

This last is the true challenge – to be an inventor rather than an imitator. Jill gave the Australian context. The country is 32 times bigger than UK, but has a third of the population, with 40 universities around the country. She noted that one of the reasons libraries in Australia have collaborated is the isolation.

Research from Australia counts for 4% of the world’s research output, it is the third largest export after energy, and out-performs tourism. The political landscape really affects higher education. There has been a series of five prime ministers in five years.

Australia has invested heavily in research infrastructure – mostly telescopes and boats. The Australian National Data Service was created and this has built the Research Data Australia interface – an amazing system full of data. The libraries have worked with researchers to populate the repository. There has been a large amount of capacity building. ANDS worked with libraries to build the capacities – the ’23 things’ training programme. You self register – on 1 March, 840 people had signed up for the programme.

The most recent element of the government’s agenda has been innovation. Prime Minister Turnbull has said he wanted to end the ‘publish or perish’ culture of research to increase the impact on community. There is a national innovation and science agenda and the government would not longer take into account publications for research. It is likely the next ERA (Australia’s equivalent of the REF) will involve impact in the community. The latest call is “innovation is the new black”.

There is financial pressure on the University sector – which pays in US dollars which is a problem. The emphasis on efficiency means the libraries have to show value and impact to the research sector.

Many well-developed services exist in university libraries to support research. Australian institutional repositories now have over 650K full text items, which are downloaded over 1 million times annually, there are data librarians and scholarly communication librarians. Some of the ways in which libraries have been asked to deliver capacity is CAUL and its Research Advisory Committee – to engage in the government’s agenda. There are three pillars – capacity building, engagement and advocacy, to promote the work of our libraries to bodies like Universities Australia.

Jill also mentioned the Australasian Open Access Strategy Group which has had a green rather than a gold approach. Australians are interested in open access. It is not yet clear what our role will be of institutional repositories into the future. In an environment where the government wants us to share our research.

How can we benchmark the Australian context? It is difficult. Look at our associations and about what data we might be able to share. Quote from Ross Wilkinson – yes there are individuals but the collective way Australia has managed data we are better able to engage internationally. Despite the investment into repositories in Australia – the UK outperforms Australia.

Australian libraries see themselves as genuine partners for research and we have a healthy self confidence (!). Libraries must demonstrate value and impact and provide leadership. Australian libraries have created change to triumph.

Open access mega-journals and the future of scholarly communication

This talk was given by Professor Stephen Pinfield from Sheffield University. He talked about the Open Access Mega Journal project he is working on with potentially disruptive open access journals (the Twitter handle is @oamj_project).

He began where it all began – with PLOS ONE, which is now the biggest journal in the world. Stephen noted that mega journals are full of controversy, listing comments ranging from them being the future of academic publishing, a disruptive innovation to the best possible future system.

However critics see them variously as a dumping ground, career suicide for early career researchers publishing in them and a cynical money making venture. However, Pinfield noted that despite considerable searching acknowledging what ‘people say’ is different from being able to provide attributed negative statements about mega-journals.

The open access and wide scope nature of mega-journals reverses the trend over past few years where journals have been further specialising, They are identifiable by their approach to quality control, with an emphasis on scientific soundness only rather than subjective assessments of novelty and also by their post publication metrics.

Pinfield noted that there are economies of scale for mega journals – this means that we have single set of processes and technologies. This enables a tiered scholarly publishing system. Mega-journals potentially allow highly selective journals to go open access (who often argue that they reject so much they couldn’t afford to go OA). Pinfield hypothesised that a business model could be where a layer of highly selective titles sits above a layer of moderately selective mega journals. The moderately selective journals provide the financial subsidy but the highly selective ones provide the reputational subsidy. PLOS is a good example of this symbiotic relationship.

The emphasis on ‘soundness’ in the quality control process reduces the subjectivity of judgements of novelty and importance and potentially shifts the role and the power of the gatekeepers. Traditionally the editors and editorial board members have been the arbiters of what is novel.

However this opens up some questions. If it is only a ‘soundness’ judgement then the question is whether power is shifted for good or ill? Also does the idea of ‘soundness’ translate to the Humanities? There is also the problem of an overreliance on metrics. Are the citation values of journals driven by the credibility or the visibility of the journals?

Pinfield emphasised the need for librarians to be informed and credible about their understanding of these topics. If librarians are to be considered important – we as a community need to be strong in our grasp of understanding these issues. There is an ongoing need to keep up to date and remain credible.

Working together to encourage researcher engagement and support

There were several talks about how institutions have been engaging researchers, and many of them emphasised the need to federate the workload across the institution. Chris Aware from the University of Hull discussed some work he was doing with Valerie McCutcheon on the current interaction between library and other parts of the institution in supporting OA, understand how OA is and could be embedded.

The survey revealed a desire for the management of Open Access to be more spread across the institution into the future. Libraries should be more involved in the management of the research information system and managing the REF. However Library involvement in getting Open Access into grant applications is lower – this is a research role, but it is worth asking how much this underpins subsequent activity.

As an aside Chris noted a way of demonstrating the value of something is to call it an ‘office’ – this is something the Americans do. (Indeed it is something Cambridge has done with the Office of Scholarly Communication).

Chris noted that if researchers don’t think about open access as part of the scholarly communications workflow then they won’t do it. Libraries play a key role in advocating and managing OA – so how can they work with other institutional stakeholders in supporting research?

Valerie later spoke about blurring and blending the borders between the Library and the Research Office. She noted that when she was working for Research and Enterprise (RSEO) she thought library people were nice, but she was not sure what the people do there. When she transferred to working in the Library, the perception back the other way was the same.

But the Research Office and the Library need to cooperate on shared strategic priorities. They are both looking out for changes in policy landscape they need to share information and collaborate on policy development and dissemination. They need better data quality in the research process to find solutions to create agile systems to support researchers.

At Glasgow the Library & RSEO were a good match because they had similar end uses and the same data. So this began a close collaboration between the two offices which worked together on the REF, used Enlighten. They also linked their systems (Enlighten and Research Systems) in 2010 where users can browse in the repository by the funder name. Glasgow has had a publications policy rather than an open access policy since 2008.

Valerie also noted that it was crucial to have high-level support and showed a video of Glasgow’s PVC-R singing the praises of the work the Library was doing.

The Glasgow Open Access model has been ‘Act on acceptance’ since 2013 – a simple message with minimal bureaucracy. A centralised service with ‘no fancy meetings’. Valerie also noted that when they put events on they don’t say it is a Library event, the sessions subject based not department based.

Torsten Reimer and Ruth Harrison discussed the support offered at Imperial College, where Torsten said he was originally employed for developing the College’s OA mandate but then the RCUK and the HEFCE policy came into place and changed everything. At Imperial, scholarly communications is seen as an overall concern for the College rather than specifically a Library issue.

Torsten noted the Library already had a good relationship with the departments. The Research Office is seen by researchers as a distraction from their research, but the Library is seen as helping research. However because the two areas have been able to approach everything with one single aim, this has allowed open access and scholarly support to happen across the institution and allowed the library to expand.

Imperial have one workflow and one system for open access which is all managed through Symplectic (there had been separate systems before). They have a simple workflow and form to fill in, then have a ticketing type customer workflow system plugged into Symplectic to pull information out at the back end. This system has replaced four workflows, lots of spreadsheets and much cut and pasting.

Sally Rumsey talked about how Oxford have successfully managed to engage their research community with their recently launched ‘Act on Acceptance’ communication programme.


This is a rundown of a few of the presentations that spoke to me. There were also excellent speed presentations, Lord David Willetts, the former Minister for Universities and Science spoke, we split up into workshops and there was a panel of library organisations around the world who discussed working together.

The personal outcomes from the conference include:

  • An invitation to give a talk at Cornell University
  • An invitation to collaborate with some people at CILIP about ensuring scholarly communication is included in some of the training offered
  • Discussion about forming some kind of learned society for Scholarly Communication
  • Discussion about setting up a couple of webinars – ‘how to start up an office of scholarly communication’ and ‘successful library training programmes’
  • Also lots of ideas about what to do next – the issue of language and the challenges we are facing in scholarly communication because of language deserves some investigation.

I look forward to next year.

Published 14 March 2016
Written by Dr Danny Kingsley
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Software Licensing and Open Access

As part of the Office of Scholarly Communication Open Access Week celebrations, we are uploading a blog a day written by members of the team. Wednesday is a piece by Dr Marta Teperek reporting on the Software Licensing Workshop held on 14 September 2015 at Cambridge.

Uncertainties about sharing and licensing of software

If the questions that the Research Data Service Team have been asked during data sharing information sessions with over 1000 researchers at the University of Cambridge are any indicator, then there is a great deal of confusion about sharing source code.

There have been a wide range of questions during the discussions in these sessions, and the Research Data Service Team has recorded these. We are systematically ensuring that the information we are providing to our research community is valid and accurate. To address the questions about source code we decided to call in expert help. Shoaib Sufi and Neil Chue Hong* from the Software Sustainability Institute agreed to lead a workshop on Software Licensing in September, at the Computer Lab in Cambridge. Shoaib’s slides are here, and Neil’s slides on Open Access policies and software sharing are here.

Malcolm Grimshaw and Chris Arnot from Cambridge Enterprise also came to the workshop to answer questions about Cambridge-specific guidance on software commercialisation.

We had over 50 researchers and several research data managers from other UK universities attending the Software Licensing workshop. The main questions we were trying to resolve was: Are researchers expected to share source code they used in their projects? And if so, under what conditions?

Is software considered as ‘research data’ and does it need to be shared?

The starting question in the discussion was whether software needed to be shared. Most public funders now require that research data underpinning publications is made available. What is the definition of research data? According to the EPSRC research data “is defined as recorded factual material commonly retained by and accepted in the scientific community as necessary to validate research findings”. Therefore, if software is needed to validate findings described in a publication, researchers are expected to make it available as widely as possible. There are some exceptions to this rule. For example, if there is an intention to commercialise the software there might not be a need to share it, but the default assumption is that the software should be shared.

The importance of putting a licence on software

It is important that before any software is shared, the creator considers what they would like others to be able to do with it. The way to indicate the intended reuse of the software is to place a licence on it. This governs the permission being granted to others with regards to source code by the copyright holder(s). A licence determines whether the person who wants to get hold of software is allowed to use, copy, resell, change, or distribute it. Additionally, a licence should also determine who is liable if something goes wrong with the software.

Therefore, a licence not only protects the intellectual property, but also helps others to use the software effectively. If people who are potentially interested in a given piece of software do not know what they are allowed to do with it, it is possible they will search for alternative solutions. As a consequence, researchers could lose important collaborators, buyers, or simply decrease the citation rate that could have been gained from people using and citing software in their publications.

Who owns the copyright?

The most difficult question when it comes to software licensing is determining who owns the copyright – who is allowed to license the software used in research? If this is software created by a particular researcher then it is likely that s/he will be the copyright owner. At the University of Cambridge researchers are the primary owners of intellectual property. This is however a very generous right – typically employers do not allow their employees to retain copyright ownership. Therefore, the issue of copyright ownership might get very complicated for researchers involved in multi-institutional collaborations. Additionally, sometimes funders of research will retain copyright ownership of research outputs.

Consequences of licensing

An additional complication with licensing software is that most licences cannot be revoked. Once something has been licensed to someone under a certain licence, it is not possible to take it back and change the licence. Moreover, if there is one licence for a set of software, it might not be possible to license a patch to the software under a different licence. The issue of licence compatibility sparked a lot of questions during the workshop, with no easy answers available. The overall conclusion was that whenever possible, mixing of licences should be avoided. If use of various licences is necessary, researchers are recommended to get advice from the Legal Services Office.

Good practice for software management

So what are the key recommendations for good practice for software management? Before the start of a research project, researchers should think about who the collaborators and funders are, and what the employer’s expectations are with regards to intellectual property. This will help to determine who will own the copyright over the software. Funders’ and institutional policies for research data sharing should be consulted for expectations about software sharing With this information it is possible to prepare a data management plan for the grant application.

During the project researchers need to ensure that their software is hosted in an appropriate code repository – for example, GitHub or Bitbucket. It is important to create (and keep updating!) metadata describing any generated data and software.

Finally, when writing a paper, researchers need to deposit all releases of data/software relevant to the publication in a suitable repository. It is best to choose a repository which provides persistent links e.g. Zenodo (which has a GitHub integration), or the University of Cambridge data repository (Apollo). It is important to ensure that software is licensed under an appropriate licence – in line with what others should be allowed to do with the software, and in agreement with any obligations there might be with any other third parties (for example, funders of the research). If there is a need to restrict the access to the software, metadata description should give reasons for this restriction and conditions that need to be met for the access to be granted.

Valuable resources to help make right decisions

Both Neil and Shoaib agreed that proper management and licensing of software might be sometimes complicated. Therefore, they recommended various resources and tools to provide guidance for researchers:

The workshop was organised in collaboration with Stephen Eglen from the Department of Applied Mathematics and Theoretical Physics (University of Cambridge) who chaired the meeting, and with Andrea Kells from the Computer Lab (University of Cambridge) who hosted the workshop.

The Research Data Service is also providing various other opportunities for our research community to pose questions directly of the funding bodies. We invited Ben Ryan from the EPSRC to come to speak to a group of researchers in May and the resulting validated FAQs are now published on our research data management website. Similarly, researchers met with Michael Ball from the BBSRC in August.

These opportunities are being embraced by our research community.

*About the speakers

Shoaib Sufi – Community Lead at the Software Sustainability Institute

Shoaib leads the Institute’s community engagement activities and strategies. Graduating in Computer Science from the University of Manchester in 1997, he has worked in the commercial sector as a systems programmer and then as software developer, metadata architect and eventually a project manager at the Science and Facilities Technologies Council (STFC).

Neil Chue Hong – Director at the Software Sustainability Institute

Neil is the founding Director of the Software Sustainability Institute. Graduating with an MPhys in Computational Physics from the University of Edinburgh, he began his career at EPCC, becoming Project Manager there in 2003. During this time he led the Data Access and Integration projects (OGSA-DAI and DAIT), and collaborated in many e-Science projects, including the EU FP6 NextGRID project.

Published 21 October 2015
Written by Dr Marta Teperek
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