Preprints in the news

I think Fiona Fox’s recent question about preprints and their impact on science news reporting deserves more consideration. She calls for more discussion of the issue and of possible solutions.

Preprints – good

I’ve invested quite a bit of time in supporting the idea that posting preprints should be a normal research practice in biomedical research. I admit that I was sceptical about preprints initially.  Sure it worked for Physics and Economics and people asked “Why can’t it work for biomedicine?”.  But the majority of reactions to Harold Varmus’ 1999 E-Biomed proposal showed that there was a good deal of disquiet among biomedical researchers about the idea of preprints. “Biomedical research is different from physics!” they said.

The growth of quantitative biology preprints in the q-bio section of arXiv showed that preprints could work in biology. In 2013 the founders of bioRxiv thought that preprints could be used more widely in biology, and their optimism has been borne out.  In 2015 Stephen Curry said that biologists should ‘Just do it‘ and they have been, in increasing numbers.

Contents of Prepubmed preprint search tool, June 2018. Jordan Anaya

A recent eLife webinar highlights the excitement about preprints in biology, and the need for more new initiatives. There is still a long way to go before all papers are posted as preprints, but we are seeing a steady increase year on year. Initiatives like ASAPbio highlight the benefits – speed of dissemination, increased feedback and visibility, establishing priority. It would be good to have more data about the benefits to back up the anecdotal accounts.

Infrastructure around preprints has evolved quickly, but I’m not sure it’s on a sustainable basis yet and there is still a need for standards development. I’m looking forward to seeing how bioRxiv develops following the CZI investment and what plans ASAPbio have.  It was good to see recently that Europe PubMedCentral is now indexing preprints.

I think things are moving in the right direction for preprints and expect that in ten years’ time we’ll see many beneficial effects resulting from their adoption.

Preprints – problematic?

I was intrigued therefore to see the blogpost about preprints from Fiona Fox on the Science Media Centre website. Fiona has a good deal of experience in science communication and her insights are always worth reading. Evidently many people people read her post about preprints as there was quite a backlash on Twitter. Her post made three main points about preprints:

  1. They seem to be beneficial for science
  2. They create a difficulty for science journalists
  3. They’re not peer-reviewed and therefore potentially dangerous when it comes to medicine

On the first point, very few will disagree. On the third point, I think many will partially agree too, but I rather thought this potential problem was well understood and on the way to being sorted. Philip Bourne et al’s ‘Ten simple rules to consider regarding preprint submission‘ include this:

This point about potential dangers has been discussed and discussed ad nauseam in the past.  It is being discussed again now as plans for medRxiv are developed and safeguards are being put in place. I don’t think it is an insuperable problem.

Slide from talk by John Inglis, ‘Preprints in Biology and Medicine’

News reporting, preprints, embargoes

For me the most interesting part of Fiona’s blogpost was her point about the difficulties that preprints pose for journalists trying to cover news of scientific advances.

Once an article is accepted by a journal for publication there is usually a period of time before it is published during which it can be sent to journalists ‘under embargo’.  This allows the journalists time to do some background work and prepare their news story. Supporters of the embargo system maintain that it is necessary to ensure high-quality reporting, and to ensure that science stories are seen as ‘newsworthy’.

Preprints currently are not subject to any embargo, but are posted online as soon as they have been through some basic checks. Hence journalists have no time to prepare. If they take the time to interview other researchers and gather opinions about the research in the preprint, then they run the risk that someone else gets into print sooner than them with a story, and their well-researched story might be discarded by a news editor hungry for hot news.

Embargoes divide opinion, but the Science Media Centre is a strong supporter of embargoes in practice. If you hate the embargo system then you might rejoice that preprints may hasten the end of that system.  If you accept that embargoes are good for science reporting, (and that science reporting is good for science) then we need to explore how preprints and good science reporting can work together.

Would it be feasible to have an option of a short embargo period for some preprints – those where press interest is expected / desired? Fiona suggests a number of other possible strategies at the end of her post, but these seem to have been overlooked in the rush to condemn her comments about the dangers of preprints. I think her call for discussion is timely and it’d be good to see proper engagement with it.

Surely we just need to adapt our current approaches to the new kid on the block?Maybe. But I still think we need to use this time to thrash out best practice and agree what the new rules should look like. 

Or is there something we have not thought of that could get us round these new realities with minimum adverse effects? 

The changes being made to a part of the system that was not working are set to have profound knock on effects on another part of the system that works and serves science well. The challenge here is to fix one end without losing the gains we have made in reporting findings to the public in an accurate and measured way.

Extracts from: Fiona Fox, 17 July 2018. The preprint dilemma: good for science, bad for the public? A discussion paper for the scientific community.

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Why open access makes sense

My colleagues in the Communications are looking pleased and exhausted today.  The Francis Crick Institute’s new website launched this morning. It’s had a complete overhaul of style, structure and content.  I’ve not been closely involved but I know enough to appreciate what a huge task this has been.

I too was pleased to see that our new website has launched, specifically as it has a brief piece about the Library & Information Services team (on this page), including a short profile of me. More importantly there is a page about the Crick’s open access approach, headed ‘Accessing our research‘. This explains the OA policy in brief, with links to the full OA policy and to the data policy, and also mentions the Crick’s signing of the Hague Declaration and DORA.  As our approach to open science develops I hope we can add more to this page.

The website now has a broader range of content – there are ‘features’ and ‘perspectives’.  One of the perspectives is about the new website itself, explaining the changes and calling the site ‘a new shopfront for the Crick‘.  Another perspective is about open access and was written by me, with useful input from my colleagues. It’s called ‘Why open access makes sense for the Crick‘ but I would suggest it applies just as well to most other research institutions.

Why OA makes sense at the Crick

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Elegy for a building

The building is still there, holding its head high, but it’s fatally wounded. It is plain to see that it won’t be with us for much longer. NIMR, Mill Hill – with its iconic copper green roof visible across north London; its 1930s art deco features; its massive presence on The Ridgeway NW7 – that building will very soon be flattened.

The main NIMR building on 14 June 2018. From some angles it looks almost untouched.

But in reality it is in tatters

I took one last stroll around there on a fine summer evening two weeks back. I walked along the roads and footpaths that allow you to circle the site. I enjoyed the green trees and the meadows, the birdsong and the flapping of birds in flight, the occasional sound of a car (reminding you that their sound is mostly absent from this green haven). I inhaled the desiccating smell of concrete dust and plaster, products of the demolition.

Fields behind the NIMR site

Fields and trees behind the site

Footpath leading from the back gate of the NIMR site.

Peering through the back gate into the NIMR site

Nearly all of the site is flattened now. There are mounds of rubble where buildings once were. I think I identified one pile where there used to be grad student houses. Large rollers are levelling some of the site.

A mound of rubble?

A roller


The oak trees along the Ridgeway

The oak trees at the front along The Ridgeway are still standing, and there are plenty more trees and green space to appreciate at the sides and back of the site. But even there one’s eye is inescapably drawn to the awful spectacle of Maxwell Ayrton’s grand 1930s building in a state of disarray.

View of NIMR from the fields at the back

View of NIMR building from the back, including sports pavilion.

Artists impression of the largest block to go up on the site, courtesy of Barratt Homes.

I’ll be happier when it’s all gone, and we can see the site alive with activity again, with 275 Barratt Homes raised up. One of the buildings will have a similar exterior appearance to the main NIMR building so it should look impressive once more.

Spot the shelves through the open windows

Insides laid bare, eviscerated

If you have good eyesight you can see the enquiry desk up there somewhere

Meanwhile it’s tantalising to see familiar parts of the interior laid bare and exposed to the elements. On the fourth floor, where the Library was, I could see some shelves (empty, of course) and the main enquiry desk.

I have already mourned the demise of NIMR. I have come to terms with the fact that my time in that particular job, in that particular environment, is over.  I have mourned the great historical resource that the NIMR Library collections constituted. There are some positives to set against the losses. I am lucky to have a (slightly altered) role in the Francis Crick Institute in its grand, brand new, building where I am gaining new experiences and developing new knowledge, and where many of my colleagues from Mill Hill now are.

After walking round the site I went into the Adam and Eve pub nearby to have something to eat. I saw a familiar face in there – an ex-NIMR employee – and said hello. While I was eating my dinner one of the songs that the live music trio played was “Nothing gonna change my world”, which seemed kind of ironic.

When I walked back to the bus stop I saw another familiar face – a past PhD student, with his parents who were visiting from China. He came to show them the place where he had worked/studied and was sorry to see the building in its current state.

My last view of NIMR

Some people have asked me whether it is ‘poignant’ or ‘weird’ to see the building reduced thus. I don’t think it is for me, surprisingly. My memories of 27 years going to work in that building are not located on the plot of land or in the building but are in my head, and they are still there. A little diminished perhaps by my fading powers of memory, but unaltered by bulldozers.

NIMR at night, ca 1950.

A Flickr album contains all the photos I took that evening.

Posted in History, Libraries and librarians | 7 Comments

Disruptive publishing

To build a successful career in scientific research you need to understand the scientific publishing system. It is going through a period of change and innovation but has remained largely intact. Recently I and a colleague ran some ‘Disruptive Publishing’ coffee break sessions to highlight some of the changes in science publishing to our researcher community. I produced a factsheet summarising interesting journal developments and my colleague created a colourful ‘snapper’ that gave us a way to open up conversations with unsuspecting researchers.


Wikipedia defines disruptive innovation as “innovation that creates a new market or value network and eventually disrupts an existing market and value network, displacing established market-leading firms, products, and alliances” and it notes that “disruptive innovations tend to be produced by outsiders rather existing players”.

Michael Clarke, in his 2010 Scholarly Kitchen blogpost, pointed out that Tim Berners-Lee created the Web in 1991 with the aim of “better facilitating scientific communication and the dissemination of scientific research … [it] was designed to disrupt scientific publishing”.

Clarke observed however that there had as yet been no significant disruption; change and innovation yes but not disruption. He was writing in 2010 but that is still true. The main players – the large multinational commercial publishing houses – still dominate science publishing.  The biggest open access publisher is one of the top four science journal publishers – SpringerNature.

Image source:


Clarke went on to list five different functions of the publishing system and suggested that the functions which are more ‘social’ – validation, filtration and designation – are less amenable to disruption than those that are more administrative – dissemination and registration.

We are starting to see more change in those areas. Validation (peer review) has been shaken by the advent of megajournals such as PLOS ONE and Scientific Reports. These journals are based on the idea that articles should be published if they are scientifically valid, leaving aside issues of novelty or newsworthiness. Notions of peer review are also being stretched by increasing posting of preprints (e.g. bioRxiv) and publishing platforms like Wellcome Open Research.

Filtration (deciding what is worth reading) is still heavily influenced by journal branding and thus by editorial selection, but altmetrics provide another tool while work on recommendation engines is proceeding in several companies. Machine learning approaches to search tools are also starting to appear.

Registration (research assessment) is perhaps the thorniest problem, and typically journal branding remains important when assessing a portfolio of research. Many institutions and funders have signed up to the principles of DORA but fewer have taken steps to put them into practice and practically problems remain. It is good to see DORA taking steps to engage more with the research community and spread good practice.

Looking further ahead, some believe that blockchain-like solutions may play a part in transforming scholarly publishing.

Coffee break sessions

We don’t have a revolution in publishing yet, but there is plenty of change and innovation and I think it’s hard for a busy researcher to be on top of everything that’s going on. Our coffee break sessions and the factsheet about Disruptive Publishing  were intended to brief researchers about some of the more interesting developments. During five separate sessions (one on each lab floor plus one on the ground floor) we talked to more than 50 people.  The topics that generated most interest were

  • the scooping policy of PLOS
  • preprints and bioRxiv
  • publishing different research outputs, not just articles
  • Frontiers for Young Minds – the science journal for school students.

The ‘snapper’ or ‘fortune teller’ that my colleague created provided a useful gambit to start conversations. We asked people to choose a number between one and eight and then talked about the issue corresponding to that number in the snapper.

The Disruptive Publishing snapper, created by Kate Beeby. @ka_be

It was definitely worth running these sessions but we learnt that the only way to make them work was to ‘ambush’ people while they were making a cup of coffee or washing their cup, or just walking along. They were nearly all interested to talk to us and to learn about what we had to tell them.


Journals started in 1665 with the Royal Society. The format of research articles changed little – fonts changed, different languages gained the ascendant, colour started to appear. But the outline of a journal article remained instantly recognisable. There was a big change in delivery in the 1990s when the internet came into play but not much underlying change. The growth of open access in the past decade and the advent of new online-only publishing ventures has accelerated the pace of change.

Pure OA journals

Journals like PLOS Biology, Nature Communications, eLife and … publish only fully open access articles. By publishing in these journals you can be sure that all OA obligations are met, and your research is as open as possible (but you still need to be sure to choose the CC BY licence). PLOS Biology will consider for publication manuscripts that confirm or extend a recently published study (“scooped” manuscripts, also referred to as complementary).


These journals typically have a wide subject scope and focus on ‘technical soundness’, rather than criteria such as ‘importance’ and ‘interest’. The two leading examples are PLOS ONE and Scientific Reports.  They are the two largest journals of any kind, each publishing over 20,000 articles p.a. Most other megajournals are somewhat smaller, but still focus on soundness as the main criterion for publication.

Peer review

Several journals have developed new systems to improve peer review. The Frontiers in journals have an initial independent review phase followed by a second phase in which reviewers and author interact. Reviewers’ names are published alongside the article. eLife delivers fast peer review decisions and consolidates all revision requests into one set of revisions. Post-review decisions and author responses for published papers are available for all to read. F1000Research publishes all submissions as preprints and then invites referees to judge the papers. Their reports and names are published alongside the article, together with the authors’ responses and comments from registered users. Wellcome Open Research follows a similar process. There is a Crick gateway on Wellcome Open Research.


bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences. Authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. Most funders now accept preprints in grant aplications. There is a Crick channel on bioRxiv highlighting our preprints.

Publishing different outputs

Wellcome Open Research accept a wide range of submissions, including software, data notes, study protocols, negative or null studies, replication and refutation studies. BMC Research Notes publishes scientifically valid research outputs that cannot be considered as full research or methodology articles.  The Research Ideas and Outcomes (RIO) journal  publishes all outputs of the research cycle, including: project proposals, data, methods, workflows, software and project reports. The Journal of Brief Ideas publishes citable ideas in fewer than 200 words. Science Matters publish single, validated observations – the fundamental unit of scientific progress.

Data journals

These journals publish data papers –papers that describe a particular online accessible published data set, or group of data sets. Examples include Scientific Data, Gigascience, Data in Brief.


The website allows you to create, copy, modify and evolve laboratory protocols, describing the critical details of experimental procedures that are often overlooked in articles Methods sections.

Young audiences

Frontiers for Young Minds is an open access science journal aimed at school students. It invites scientists to write about their research in language that is accessible for young readers. Articles are reviewed before publication by a board of kids and teens – with the help of a science mentor.

Impact factors

Some journals, notably eLife, ignore journal impact factors and do not use them in promotion. The San Francisco Declaration on Research Assessment (DORA) is developing and promoting best practice in the assessment of scholarly research, and argues against the use of journal-level metrics like the impact factor.

Posted in Journal publishing, Open Access | 1 Comment

The meaning of sixty

I recently celebrated my sixtieth birthday. I had a very nice birthday party in a local pub with several friends and family members. Having plied them with food and drink I thought I’d earned the right to give a short homily about being sixty.  Here it is. At the end are a few photos from the evening.

Sixty doesn’t mean what it used to mean. I’m not sure if that is because the world has changed its view of 60, or because I have gained a different perspective of the age now I am there. It’s probably a bit of both.

As a number, rather than an age, sixty has a certain attraction. I recall learning that it was the foundation of the Bablyonian number system. It seemed an awful big number to be that. I believe that’s why we have 60 seconds in a minute, and 60 minutes in an hour.

It’s clearly a largish number, though not as large as 100.

Old age

I was a late baby, the sixth and last child in the family, arriving when my parents were in their early forties.  Hence in my last year or so at home my parents were turning 60. I regarded 60 as quite old back then. The phrase ‘old age pensioner’ was common and since my father retired at 60 I guess that was what he was, officially. I looked at people who were 60-years old, like my parents, and I saw a huge gulf between my young age and their great age.


One of my best ever holidays was a trip to Pakistan, 17 years ago. I traveled to the Northern Areas, a mountainous region, and did a few guided treks up into the mountains. Rising at dawn and watching the morning sun light up the snowy peaks one by one was a magical experience. Having a cold shower with water piped straight from glacier melt was also memorable.


Eagles Nest Hunza, by @thehunza #GilgitBaltistan #pakistan #tripkar #beautifulpakistan #

When you’re at the bottom of a mountain you look up and it seems far off. When you get to the top your perspective is different. You’ve travelled a continuous route from the bottom to the top and perceive them as linked. You can look down at the route you travelled to get there, and you can gaze over a vast area – taking it all in in one view. It feels great to be there. It’s the same with age.


30 years ago I learnt some more about the age of 60. I took a holiday in Thailand and by coincidence I was there in Bangkok at the time of the King of Thailand’s 60th birthday – King Bhumibol who died last year. There were massive celebrations and crowds of people on the streets. I discovered that in Thai tradition 60 years is seen as a very significant age – the sexagesimal person has acquired wisdom and experience, survived the slings and arrows of 60 years, and still has plenty of life left in them. It is an age to be proud of and to celebrate. I thought – “That sounds good! I must try it one day”.


The Royal Palace in Bangkok, Thailand. 


Sixty is seen as significant because on that birthday you have been around the Chinese zodiac with its 12 animal years 5 times – one for each of the 5 elements. In Japan this birthday is called kanreki and to celebrate this special occasion, the 60-year-old person wears red clothes.  The tradition of wearing red on your sixtieth birthday is also a Chinese thing. A Chinese friend tells me I must wear red every day for 365 days from my 60th birthday. That’s the reason for the red theme tonight. By getting you all to wear red tonight I hope I can have a few days off.

Reaching 60

I have now been 60 for nearly 5 days. I don’t think it’s going away so I’d better make the most of it. I have picked up my first free prescription. I have registered for free travel on the tube etc. I will have a free eye test soon. I don’t feel all that different from before, but I feel a certain smug satisfaction at having got here, to the top of the mountain.  I am a bit surprised too – part of me feels I’m still 18, part of me feels like 30 or 40 (but not my knees). It does seem incredible that I am actually 60 but I don’t feel remotely like what the term ‘old age pensioner’ summons up.

They say that 60 is the new 40, but I’m not sure what that would mean for our timekeeping devices.  I’ll settle for being 60 but now having a better understanding that all ages are really the same in what really matters – enjoying life, expressing love, taking some control of life, using your talents well.

I wish all of us a long and happy life.





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Blog June

Apparently BlogJune is a thing. I’d not heard of it before – it’s a challenge to

blog every day in June – or as often as you can manage, or comment on someone else’s blog every day

The first part (‘every day’) really would be a challenge, but the qualification (‘or as often as you can’) sounds a lot easier. I’m not sure about commenting on someone else’s blog, as that could entail a great deal of reading before I found something that inspired me to comment sensibly.

One of my colleagues alerted me to this challenge last week. She has bravely risen to the challenge but I’m less brave. I only spotted her tweet about it at the end of the day on 1st June so a strict compliance with the challenge was not really on for me. But, hey, maybe I can rise to the lesser challenge. It might inspire me to post a bit more.

I see that Athene of this parish has written recently about writer’s block – a phenomenon where a normally prolific writer, such as she, has a dry patch. My experience is the inverse – most of the time I write nothing but occasionally I manage to finish a blogpost and get it online.

Maybe more regular posting during BlogJune will get me to the point where I can call my standard taciturnity a writer’s block?


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Digital skills – how do we …

The concept of digital skills is a bit slippery.  The term has changed its meaning as the digital universe has expanded. Jisc is currently doing some work in this area, led by Caroline Ingram.

I attended an interesting workshop recently to look into the challenges of developing researchers’ digital skills. Caroline led the workshop together with Rob Allen and David Hartland, both of whom have long experience in training in HE.

We considered what we meant by research support roles, what digital skills do researchers require, which organisations provide training, and what Jisc’s role should be (if any).


We agreed that it was not helpful to compile a long list of research support roles. These things change quickly and also vary across institutions. For instance, data scientist, data engineer, data librarian can all have distinct meanings, but they also overlap and may or may not each be necessary in a particular environment.

We discussed what we meant by ‘research support’.  Some workshop attendees considered that people in libraries and IT services who work with researchers  are also working in research and scholarship. Talking about ‘support’ has overtones of ‘Upstairs, Downstairs’ or Downton Abbey.  The term ‘Specialist Research Professional’ was preferred over ‘research support’.

Another helpful observation was that 95% of the time researchers have the skills to do what they need. They draw on their ‘foundational knowledge’ or will be able to figure out how to do something. The other 5% of the time they do need help, with hard problems.

Sometimes a Specialist Research Professional may become a member of a research team. This could be a part-time role as part of the research team or a full-time intra-team support role.


There are different ideas as to what ‘digital skills’ meant.I recall that 20 years ago we thought it meant knowing how to use Microsoft Office and being able to understand a Google search. Some at the workshop see digital skills as something close to information literacy, others see it as all about open access, others again see it mostly in terms of research data management. Most of the discussion focused on research data handling.

Skills training is not the whole story. Sometimes what’s needed is a more general awareness raising, for instance about copyright.

We agreed that the Jisc list of skills is a useful starting point.

Here’s a list of skills that we thought might be needed by researchers: personal information management, discovery (searching for data), appraisal of data, coding and data analysis, information governance, non-technical issues connected with digital skills (ethical, legal and social implications), reproducibility, productivity/workflow tools, managing collaborations. That last one is interesting – we don’t often talk about the skill required to manage digital participation and digital communities, though the AAAS are doing some work in this area.

Some more specific topics that I’d like to find training for include: data visualisation, mash ups (or are these out of fashion now?), text and data mining.

A more fine-grained approach needs to acknowledge that different individuals will have different depths of expertise in different areas. Also, depth of expertise depends on the context.  E.g. even someone knowledgeable about general research consent issues might look to the clinical trials team for more in-depth consent advice.

Who is doing what?

Current training providers include: Vitae,  Jisc, Digital Curation Centre,  ELIXIR,  EBI,  Emedlab, CODATA–DA.

Software Carpentry, Data Carpentry and various camps/unconferences were also enthusiastically endorsed by many at the workshop. MOOCs were mentioned, but it was noted that they were just about learning, not about creating a community.  That is where the carpentry events excel.

Other potential providers might be providers of specialist technical platforms – typically these churn out massive amounts of data and the staff of the platform will have skills in processing the data so would be well-placed to provide training. Software providers such as Matlab also provide training, and perhaps scientific instrument makers might.

Of course many individual institutions also provide training for their own researchers.

Jisc’s role

The following were suggested:

  • Help in accrediting courses
  • Collating a list of skills, that can be taught in 3-hr packages
  • Matching that list to existing providers
  • Identify good local sources of training and help them to go national
  • Adopt the carpentry approach of community-developed open training materials
  • Establish a ‘locum’ system for those who need to find short-term help with a project
  • Help to facilitate unconferences around digital skills
  • Extend the model of specialist data centres to specialist training centres


The results of the workshop will feed into a project report, some time later.

My conclusion was that it is very helpful to bring a disparate group of people together to discuss digital skills, and I think we learnt quite a bit from each other. Equally, it is very hard to say something about digital skills that applies across all areas of research without starting to sound bland. And, finally, it would be helpful if there were some agreed shared terminology about digital skills (but I suspect this is a forlorn hope).

Posted in Information skills, Research data, Uncategorized | Tagged , , | 1 Comment

Six questions about preprints

2017 is shaping up to be the year that preprints in biomedical sciences go mainstream.

At the beginning of the year MRC and Wellcome Trust both moved to accept preprints in grant applications and scientific reviews. Another major UK biomedical funder is likely to follow suit. In the USA the NIH has recently done the same. The ASAPbio initiative has issued its call for proposals for a central preprint service and it will be interesting to see what comes out of that. Meanwhile the Chan Zuckerberg Initiative has made a major commitment to support bioRxiv financially. Several new discipline-specific preprint servers have been launched. All this and there’s still nearly 8 months of 2017 to go!

The more I think about and learn about preprints, the more questions that seem to crop up. Maybe you can help me find some answers.

Last year’s SPOTON conference on the future of peer review featured a session on preprints and peer review which I chaired and introduced. The discussion was interesting although it felt inconclusive. The recently-issued report from the conference has a piece by me: “The history of peer review, and looking forward to preprints in biomedicine” – now available as a post on the BMC blog.  It’s nothing profound but I speculate slightly:

We may be moving to a world where some research is just published ‘as is’, and subject [only] to post-publication peer review, while other research goes through a more rigorous form of review including reproducibility checks. This [change] will be a gradual process, over a period of years. New tools … using artificial intelligence, will help by providing new ways to discover and filter the literature. A new set of research behaviours will emerge around reading, interpreting and responding to preprint literature. The corridors of science will resound with caveat lector and nullius in verba.

Whether / when to post?

Last week I gave a short talk about preprints to the postdocs at the MRC LMCB at UCL (here’s my slides). They were a lively group, already knowledgeable about preprints and open access but keen to learn more. I focused on a quick history of preprints and general stuff about them. The other speaker, Fiona Watts, provided real insight into the experience of a researcher who posts preprints, also drawing on her long experience as a senior editor on various top journals. She suggested that researchers should carefully consider which papers they preprint (is it a verb yet? I think it needs to be). Papers that have a heavy data component are appropriate for preprinting, but those with a high conceptual element might not be. I wonder if that is a generally-accepted notion, and whether there are other criteria that people use for deciding whether to post a preprint?

Scooping and citation

Related to this, the question of being scooped came up. Audience members shared their different experiences. Some believed it to be really uncommon, others reported having been scooped. In theory posting a preprint can give you priority over anything published subsequently. Some felt that would not be much comfort if someone else publishes a peer-reviewed paper before your preprint is published in a journal, particularly if the author of that paper fails to cite your preprint. Maybe peer reviewers need to be reminded that they should include preprints in their search for relevant literature?

There is some useful discussion of strategies about whether and when to post a preprint in a post on Niko Kriegeskorte’s blog.

One person at the LMCB meeting raised the question of preprint citeability. This had recently been discussed  on Twitter (it has been usefully summarised here on the Jabberwocky blog). Apparently NAR does not permit preprints to be cited.

Are there other journals that have a similar policy?

Clearly preprint citation is necessary if we are to give appropriate credit/priority to work posted as a preprint. But I can understand why some may be wary of allowing citation of work that’s not been peer-reviewed. I’m not altogether persuaded by the argument that because physicists do it it must be OK for biologists to do it. There are differences between disciplines and their cultures of knowledge-sharing.

I would like to know how much difference there is between a preprint version and a finally-published version of an article. (Indeed, I’d also like to know how much difference there is between a ‘green’ version of an article and the version of record, but that’s another story).

In the comments on the Jabberwocky blogpost mentioned above, Martin Jung suggests that the key issue is “how to support and improve scientific peer-review to better deal with grey literature and non-published sources” (such as preprints). We need to think harder about this.

Institutional servers

I’ve also been thinking about institutional policies around preprints. Judging by the ASAPbio page on University policies these are not yet widespread.

In talking to people about appropriate policies someone raised the idea of establishing an institutional preprint server. I can imagine a world where that would be a good idea, but I don’t think we are living in that world. I fear that an institutional server would be an irrelevant backwater, ignored by most in favour of the big disciplinary preprint servers. What do you think – is there much benefit to an institutional preprint server?

Two other useful things I read about preprints this week are a piece purporting to show increased citation rates for articles which started life as preprints, and a ten-point gospel highlighting the benefits and properties of preprints.

To recap my six questions:

  1. Is ‘preprint’ a verb yet?
  2. What criteria (if any) do you use for deciding whether to post a preprint?
  3. Should peer reviewers be told that they should include preprints in their search for relevant literature?
  4. Do you know of any journals which do not preprints to be cited as references?
  5. How much difference is there between a preprint version and a finally-published version of an article?
  6. Is there any benefit to an institutional preprint server?

Please give your answers in comments below, or on Twitter.

Posted in Open Access, Peer review, Preprints | 6 Comments

R2R – the Researcher to Reader conference

The R2R conference took place back in late February. It is an event more dominated than others (46%) by publishers – those on the business, strategy, and marketing side of the publishing industry. Smaller numbers come from libraries (15%), technology (12%) and consulting (10%). It attracts high-profile speakers (with interesting things to say) from publishing and elsewhere, and its workshops are interestingly different from those at other events. Ironically, researchers and readers were largely absent from the event. I attended it this year, for the second time. It’s a good event and I can recommend it if you’re interested in scholarly publishing.

Mark Allin, CEO of Wiley, gave the opening keynote talk and touched on some themes that would recur throughout the conference – the political situation and the piratical situation (if I may call it that).

Allinn was passionate about the need for scholarly publishers to support science and the drivers of science: debate, scepticism and liberal values. He referred to John Gibbons, a past presidential science advisor, and called for publishers to be partisan for science (this was an echo of Kent Anderson’s recent blogpost).

Allin said:

It’s tempting to keep our heads down. But we can’t afford to do that.   It’s a time for outreach, collaboration, partnership. A time to be bold.

Moving on to the researchers and readers, Allin put up a graph showing that Researchgate is distributing more articles than Sciencedirect, and SciHub is another substantial source. SciHub and Researchgate are easy to use and that’s what researchers want – ease of access. Allin stated that publishers can never stop piracy but they must instead compete with pirate sites by making legitimate access easier. Initiatives like the STM project RA21  aim to do this (more later on this).

Some other soundbites I noted from his talk were:

  • use the discontent of the customer to drive innovation
  • publishing needs to experiment more, do more, fail more
  • publishers need to commit to open source and open standards
  • publishers need to embrace the values of their customers – researchers and librarians; they should become more open, collaborative, experimental, disinterested
  • article submission is a pain point; preprints have a role to play in reducing the pain

He also recommended we read a recent book by Harvard Business School professor Bharat Anand – The content trap. The book reveals the need to make useful connections – e.g. between content and users, or users and other users. I first heard this articulated by Andy Powell about 10 years ago and it seemed persuasive then too.

Rick Anderson, from University of Utah Library (and a regular contributor to the Scholarly Kitchen blog) shone a light on a conundrum, looking at open access, library subscriptions and budgets.

He noted that many libraries are very short of funds and badly need to find cost savings. While it’s true that big deals deliver better value, they do not lower the cost. And big deals also make cancellation more difficult, reducing libraries’ flexibility.

New gold OA journals do provide a way to make content available without subscription, but they do not substitute for the existing journals, so libraries still must subscribe to those. Only green OA can help us to save subscription costs, but incomplete and delayed OA will not allow us to cancel. Complete and immediate OA would, but if that does come about it will affect the vitality of subscription journals. A different kind of serials crisis would ensue.

I guess the conundrum is a result of two different motivations for open access: a) to create a corpus of research literature that is open and available for reuse b) to save on the costs of scholarly communications. For a) we need gold open access, but for b) it seems that green is more effective.

I recall a senior publishing figure (I think he was from Blackwells) many years ago saying that he was happy to be quite permissive regarding allowing authors to self-archive their manuscripts as this was still a marginal activity. If a high proportion of manuscripts were self-archived then, he suggested, publishers would change their policy and stop allowing it.

Anderson did not mention offsetting deals – whereby publishers offer discounts to take into account the total spend on subscriptions and gold APCs. This kind of deal offers an alternative way to resolve the need for savings.

Michael Jubb and Richard Fisher sketched out where we are with books and ebooks. Academic libraries these days are preferring to purchase ebooks rather than print books. Bookshops on the other hand are selling far more printed books than ebooks.

The world of ebooks is very messy still and discoverability is a huge issue. There is a clear reader preference for print books and publishers are selling more print than ebooks – many publishers have 90% of their sales in print books.

I am not sure whether the reader preference for printed books is just a reflection of how poor ebook technology is, or whether there is a fundamental aspect of human reading behaviour that means ebooks will always be inferior. I like to believe that one day someone will come up with a way to improve the ebook user experience such that perceived problems with ebooks will disappear.

We then had a chorus of short talks about CHORUS – this is a publisher-led initiative to help (mostly) US universities and institutions to manage their open access responsibilities. I found little of great interest in this session. Syun Tutiya exchoed Rick Anderson in saying that the green road to OA does not work. He hoped that by 2020 Gold OA will account for a much bigger proportion of papers but also suggested that 100% gold is far, far in the future, or never!

Stephen Curry, Imperial College (who is a researcher, as well as a prominent open access advocate) gave an entertaining talk, including many recommendations for interesting books that we should read. Clearly he is not just a researcher but also a reader of distinction! He asserted that the motivations to undertake research are a mixture of wanting to understand the world, and to change it; to earn a living, to be remembered. The practicalities of becoming a successful researcher mean you should publish in a high impact factor journal. This creates a conflict – the ‘how’ can interfere with the ‘why’. Stephen is known as an advocate of open access and an enemy of the over-metrication of academia – he said that the conflict he described is eased if publishing is open and evaluation is broadly based. He outlined some practical suggestions for moving towards this ideal world, including widespread adoption of preprints.

His slides are available if you want to check out his book recommendations.

Laura Montgomery (Taylor and Francis) and Graham Walton (Loughborough Univ library)

It seems that User Experience (UX) research is all the rage in libraries these days.  The publisher Taylor & Francis sponsored some work in Loughborough University library to explore UX with postgraduate students. An initial literature review by Valerie Spezi  indicated that there wasn’t much research specifically on postgraduate students.

They mapped the UX of ten research students over 18 months, looking at how the students find and manage info, and seeking to identify opportunities to enhance the postgraduate research library in Loughborough.

The first step was to hold a workshop on how to get published, then they recruited participants from the workshop. Each was asked to keep a monthly diary over 8 months. They were set thematic questions each month. Some of the responses were predictable, some were surprising.

  • One student, asked whether they preferred print or ejournals responded “I didn’t know what a print journal was so I had to Google it to answer the question.”
  • When searching, most start at Google or Google Scholar. Many went to the library catalogue. Publisher websites were right at the bottom.
  • 43% said that the physical library not important for them at all. 39% said that the virtual library was very important.
  • Students took advice on information management tools from their colleagues, supervisors and lecturers. Graham Walton suggested that there is a need to train the supervisors.
  • Lack of access is a major frustration.

In questions, Michael Jubb pointed out that there has been quite a bit of similar work looking at researchers’ information and library use.


The second day started with a panel discussion on copyright. This was informative and infuriating in equal measure.

Robert Harington (American Maths Society) stated the case for the publishers, basically in favour of the status quo. He touched on the difference between sciences and humanities, pointing out that scientific writing describes the intellectual stuff (ie patents are the real intellectual property), whereas in humanities the writing is the intellectual stuff. He emphasised the importance of the work publishers do in registering copyright, which is required in the USA if authors want to sue for copyright infringement. Registration is not required in the UK, so I was surprised to learn of this. (See Wikipedia for more on registering copyright).

Danny Kingsley (Cambridge Univ) gave an entertaining presentation making the case against how copyright currently works. She used a particularly egregious example from the music industry. But I didn’t think that such an extreme example made the case very well against copyright for research texts. She emphasised that copyright does not work and that publishers don’t need it – they just need a licence to publish the material.

Mark Thorley (NERC) made a strong case for changes in how copyright is applied to research outputs. He explained that research funders want research to be as widely and openly and readily available as possible, so that others can use and build on the research. He pointed out that research outputs should reach beyond research community.

Thorley said that the scholarly communication system must be made fit for a digital age. Barriers to access should be removed, so that any user can use research outputs for any purpose. We need to rethink how we apply copyright.

Summing up he said that copyright was not a benefit nor a detriment; it has not outlived its usefulness, but it needs amending to ensure fair exploitation in a digital world.

Alexander Ross is a lawyer specialising in publishing. He noted that copyright was introduced to deal with piracy of printed works, to protect the interests of creators.

Recently exceptions have been introduced to cater for research – for text and data mining and quotation. He said that it would be useful to have a fair dealing code for use in the academic sector.

He also noted that Creative Commons is a good attempt to standardise copyright for academic purposes.

In the general discussion session the speakers made further points:

  • Slicing and dicing rights is not helpful for research.
  • Copyright isn’t the barrier – its what the holder does with it.
  • Publishers requiring copyright transfer before they’ll publish research is the key problem.
  • Advice from publishers on why authors should assign copyright is confusing in the extreme (e.g. T&F).

Kent Anderson (CEO of Redlink and a regular contributor to the Scholarly Kitchen blog) spoke on his favourite subject, telling us about the marvellous work that publishers do.  His talk was based on a blog post of his that had been inspired by Clay Shirky saying that “publishing isn’t a job, it’s now a button”. I can see how that statement was a bit provocative and an oversimplification, though there’s a grain of truth in it. But Anderson pointed out that one key thing the publisher does it to shoulder the risks of publication, and another is to provide persistence, ensuring there are no broken links. I’m not persuaded that publishers are all that good at the persistence’ part.

Anderson then worked through a long list of everything else that publishers do, but I did not find many of them all that persuasive.  At one point he seemed to suggest that academic fields are defined by and only exist when there is a journal serving the field. Cart before the horse, much.

Tasha Mellins-Cohen (Highwire) spoke on access management. Some background to her talk is in a recent blogpost.

She noted that off-site access to subscribed content can be a problem, and that’s why people go to pirate sites. Publishers have an incentive to make off-site access work better therefore. Three publisher-led initiatives may help with this.

CASA: Campus activated subscriber access – more information about this will be coming in the next few months. It provides a way to record devices that have been authenticated by IP range. So when you use your device on the institutional wifi, and later use it off-campus the publisher website will still recognise you as an authenticated user.

SAMS Sigma – This is a roaming passport that does something similar to CASA but it can be a permanent link.

RA21 is a project of the STM publishers association. Mellins-Cohen said that while the principles of RA21 are excellent she worries that it might end up raising barriers to access rather than lowering them.



Other summaries of the R2R conference have been written by Jennifer Harris and Danny Kingsley.


Posted in Copyright and IP, Journal publishing, Open Access | Comments Off on R2R – the Researcher to Reader conference

Weird things from publishers part 94

Many of the things that publishers do are perplexing, frustrating or reek of exploitation (it’s arguable that even the act of selling us subscriptions falls into the latter category) . I wrote earlier this year about a perplexing and frustrating example. Here’s some more.

A two-faced article

This article, in the Journal of the American Society for Mass Spectrometry can’t decide whether it is OA or not. Heck, it can’t even decide who it’s published by. Its bibliographic record in PubMed has two different links to the full text – one to Elsevier, marked as Open Access, and the other to SpringerLink.

The Springer link takes me to an abstract of the article showing it as an article published by Springer. It looks like something you need to subscribe to, or pay to access but a further link from that page in fact allows me to view the full text PDF. The article is marked as copyright American Society for Mass Spectrometry but I cannot see any statement to say that it is open access nor any Creative Commons licence. At the bottom of the PDF page it says “Published by Elsevier”.

The Elsevier link takes me to an HTML version of the whole article, on a page marked “Open Archive”. It also says it is “Under an Elsevier user license”.  I learnt that

“Articles published under an Elsevier user license are protected by copyright. Users may access, download, copy, translate, text and data mine (but may not redistribute, display or adapt) the articles for non-commercial purposes”

with various further conditions. The article is not available in PubMedCentral, which seems to me evidence that it is not genuinely open access, despite the label on the PubMed link to Elsevier.

I suspect the problem is that the article is in a journal owned by a learned society but published by a commercial publisher.  This is not always a good combination. Presumably the journal changed publisher and this created further confusion. I wonder why both versions are still extant?

Paying and paying and paying

Someone asked me to get them an article in a new Cell Press journal, Cell Systems. (Cell Press is an imprint of Elsevier). We purchased a copy of the article for the requester who then told us that they really wanted to get the supplementary information (SI) as well. We took a look at the publisher website, hoping the SI might be free. But it wasn’t free – it was going to cost us $22 to download it. Or rather, it would cost $22 to download one file.  This article has 9 separate SI files and each of them (as far as I can tell) will cost $22. My investigative instinct did not extend to trying to download all 9 SI files to check the full price really would be 9 times $22 = $198.

This single article seems an excellent argument against putting SI on a publisher website.

There does seem to be an option (Read-it-Now) to  pay a single price for the article and its SI all together, but this is a short-term ‘rental’ option and is not suitable for someone who wants to save and reuse the SI data.

How much is your APC?

The EMBO Journal is a moderately well-thought of journal, but I wouldn’t put it at the top of the prestige pile. I was therefore surprised to learn that if you want to publish an article there with immediate open access it will cost you $5,200. That puts it in the same price league as Cell and Nature Communications, both of which have an APC of $5,000. At least, they did last time I looked. And that’s the thing – I’m not in the habit of checking journal websites regularly to see what their APCs are this week. When I looked back to see what we had to pay last time (in early 2016) someone wanted to publish an article in EMBO Journal I found that it was just $3,900 – still a bit above the average APC for a journal published by a commercial publisher (EMBO J is published by Wiley) but quite a bit less than their current price.

I looked into it further and found  that there had been a large hike in all Wiley APC prices at the beginning of 2016 when the publisher changed its pricing model for open access. Up to the end of 2015 they charged an open access fee plus page charges of $95 per page. From 1 Jan 2016 they stopped charging the page charge and raised the APC to make the lost fees.

Part of me wants to applaud this transparency – having page charges on top of APCs seems like triple-dipping and in these days of online journals page charges are an expensive anachronism. Not to say a rip-off. But loading the extra cost onto the APC is still a rip-off.

I poked around the wayback machine a little to check on some of the facts about past APCs. Wiley’s spreadsheet listing all their APCs seems to be updated quite frequently, so I guess there are quite a few increases. I think it would be interesting to do this more systematically to track changes to APCs. (But not quite interesting enough that I felt moved to do it myself).

Freedom APCs

I found that I had a new Twitter follower – the Director of Cogent OA.  I’d not encountered this publisher before but quickly found that it is owned by Taylor and Francis (one of the big four) and it has thus far published 200 OA articles in 15 broad journals with a total of 122 sections. I’m not a fan of setting up large numbers of empty journals/sections in the hope that they will attract articles.

Cogent charges an APC of $1250 but this is marked as a ‘recommended’ price. Cogent are pioneering the idea of “Freedom APCs”.

As the first multi-disciplinary publisher to introduce Freedom APCs – a “pay what you want“ model – across the entire portfolio, our authors can choose how much they contribute towards open-access publishing based on their funding and financial circumstances.

I wonder how free the author really is to decide what they want to pay? Once again, it would interesting to do some experiments to test this out.

Interesting times

The landscape of publishing and open access grows ever more complex and confusing.  TO be absolutely on top of everything is really a full-time job, but few of us (certainly not me) are able to spend all our time on mastering everything that is changing.

Posted in Journal publishing, Open Access | 1 Comment