Open access deposits to Europe PubMed Central – building skills

Blogpost by Kate Beeby and Frank Norman.

Our funders’ open access policies mandate deposit of all primary research articles into Europe PubMed Central (ePMC). We opt for the Gold (immediate Open Access) route when we can, but if the publisher offers no Gold option then we have to deposit the paper into ePMC with a 6-month embargo. In some cases, the publisher makes the deposit for us, in other cases it is down to the author.

At the Crick, the OA team offers to make the deposit on the authors’ behalf. They like this and most group leaders do take us up on this offer. This involves obtaining all relevant files, uploading them onto the ePMC site, and associating the correct grant details with the deposit.

A short while after the deposit has been made, it is necessary to check the accuracy of the marked-up XML version of the article that has been created on ePMC. Until the accuracy has been confirmed by the author or their nominee the article is not released for public view in ePMC. The XML version is checked for accuracy around stylistic details (e.g. italicised words, use of symbols), as well as reference formatting (e.g. in-text links to figures, numerical citations) in comparison to the original files that were deposited.

It is important to note that we are not reviewing the content of the manuscript, nor undertaking some of the other checks involved with proofreading (e.g. text formatting, grammatical errors). The main focus of the deposit check is to ensure that the ePMC-created version matches that of the original submitted document.

This task can be challenging and time-consuming for staff at first. The knowledge of how best to do these checks grows with practice – though we don’t have a high throughput of articles requiring manual deposit, so practice opportunities are limited.

It’s difficult to find relevant training in this niche. There are courses from the Society for Editors and Proofreaders  but these are aimed at people looking to start a career in proofreading/editing in the publishing industry. They are too detailed for what we need. There is a useful ebook about proofreading – it’s free but needs Flash installed. It has some helpful information, particularly about the structure of research articles and what to look out for in figures, tables etc. We also wonder whether the project to define the skills that new Scholarly Comms staff need covers these skills?

It would be interesting to learn how other libraries and institutions manage ePMC deposits where required by funders. Do dedicated staff make these deposits on behalf of researchers? Are researchers required to do this task themselves? Are there any tricks you have developed when checking the ePMC version of articles?

If you are making ePMC deposits on behalf of authors and checking them later, have you developed guidance for new staff undertaking this work?  Have you found any training helpful to build these skills?

Please share your thoughts and ideas below in the comments.


Kate Beeby (@ka_be) is Assistant Information Specialist in the Library & Information Services at the Francis Crick Institute.

Thanks also to Patti Biggs for comments on this post.

Frank Norman, Patti Biggs and Kate Beeby are all part of the Open Access Team at the Crick.

Posted in Libraries and librarians, Open Access | Tagged , , | Leave a comment

To fail is to learn

After leaving school I worked in a library for a year and was in the music and drama section for six months. Towards the end of that time I was trusted enough that they let me prepare some orders for new stock. We needed to buy the orchestral parts for the Requiem Mass by Gabriel Faure. I prepared a standard order – six first violin parts, six second violin parts, four violas, four cellos and two double basses, plus all the brass, woodwind and percussion. It duly arrived and was labelled up ready to be borrowed. As it happens a choir that I sang with was performing the Faure Requiem, and hired the orchestral parts  for the concert. So when it came time to have a rehearsal with the orchestra I went up to our chorus master to proudly let him know that I had supplied the orchestral parts from the library.

Then he told me that there was a bit of a mess up.  The Faure Requiem string orchestration is unusual. It has just one violin part but the violas are split into first and second, and the cellos are too. So my standard order resulted in 12 copies of the violin part, and only two copies of each of the various viola and cello parts! My mouth dried up and I didn’t say anything but slunk away. Next time I that I had to order some parts I made sure to check  the instrumentation of the piece first.

How do you handle failure? Is it something to feel ashamed of, something that  that threatens your sense of esteem? Is it something to be concealed at all costs, denied, or blamed on someone else? This is an instinctive response for many of us. Or do you regard it just as a fact – something to be noted and investigated? Something that you can learn from and that helps you to improve? I’ve just read Matthew Syed’s book Black box thinking. In it, he shows how damaging our instinctive response to failure is and how beneficial is the learning approach. The book tries to show how failure is something we must learn from, how it is a necessary part of improving.

Matthew Syed begins by contrasting how failure is treated in healthcare and in aviation. In healthcare there is a culture of blame whereby errors are concealed and seen as marks of shame. Anyone who admits to an error will take the blame. In aviation every error, failure, incident or near miss, is treated as an opportunity (nay, a necessity) to learn and improve. There is no culture of blame. In countless examples Syed shows the harm done by a working culture that does not see failure as an opportunity for improvement.

A teacher once told me that ignorance (specifically the recognition of one’s own ignorance) is the first step towards learning. If you know everything then obviously you can learn nothing more. In a similarly paradoxical way Syed insists that failure is a necessary stage on the way to success.

He explains how our need to conceal errors or to blame others for them is a form of cognitive dissonance. If I am a leading expert on heart surgery then I will struggle to face up to my role in a failed heart operation – it strikes at the core of my expertise, my self. Syed lists several extreme examples of the mental contortions that people go through to avoid having to admit error. His examples come from law enforcement, healthcare, politics, religious cults and pseudoscience. He explains how people can have a ‘closed loop’ way of thinking: “It’s right because it’s right”.

Failure can be useful in many scenarios. It is important for innovation. James Dyson tested more than 5,000 different prototypes before his vacuum cleaner was ready to market. He was initially driven to develop his novel design by the failure of the prevailing models of vacuum cleaners. Syed also describes how a washing machine manufacturer used an evolutionary development process to make improvements to a powder nozzle. They changed something, tested it, then accepted or rejected the change and repeated the process. After many iterations (and failures) this resulted in a much-improved nozzle.

In cycling, the Team Sky system of marginal gains relies on a similar system of trial and error. Across the business world randomised controlled trials have been adopted, for instance to improve response rates to letters and emails sent to customers. The colour, font and wording can be tweaked and the response rate from customers measured to see what works best.

Syed also draws on psychological research. He describes how people with a ‘growth mindset’ have been shown to be more open to learning and to attempting challenges beyond their experience, whereas people with a ‘fixed mindset’ almost fail before they try. A ‘fixed mindset’ leads people to believe they cannot learn new skills and to fear blame for failures.

I felt a bit bludgeoned by the book – the key points are made, vividly illustrated, made again, reinforced with further examples. I longed for an executive summary! But the book certainly drives its point home and it pierced my own closed-loop thinking.  It made me question  whether I embrace failure, or I rationalise failures out of existence. Do I blame colleagues for failures? How can I innovate better?

Syed asks:

“Do you fail in your judgements? Do you ever get access to the evidence that shows where you might be going wrong? Are your decisions ever challenged by objective data? If the answer to any of those questions is ‘no’ you are almost certainly not learning”.

The book’s emphasis on trying things out and responding to evidence puts me in mind a bit of the Library UX movement.  I’ve been to a couple of Library UX workshops and the strong message I took away is that it’s wrong to assume anything – we must question what we think we know and test reactions to our services.

Am I brave enough to share my failures here? I certainly do make mistakes, and fail to do things I meant to. I think I have ordered two copies of a book by mistake in the past – forgetting that I’d already ordered it. I failed to get a project off the ground as I had tried to do it all by myself and that just wasn’t feasible. When the internet was new I set up a gopher, then a website, then a better website etc etc, gradually approaching something worthwhile. I learnt something from that about incremental development. Each stage was useful in persuading more people it was a good idea.

I remember an error from much longer ago. When I was 16 I had a summer job working in a bank.  The branch manager asked me to refill the red inkwell on his desk, and told me not to overfill it.  The red ink was in an enormous bottle so I found pouring a small amount of ink into the well rather tricky. I thought I’d done it right but later that afternoon the manager was in a fury as a red stain spread through his handsome wooden desk. His resourceful secretary managed to sort things out and I laid low for a while. I learnt that ink bottles were not my friend.

It would be interesting to hear of any of your failures and lessons learnt, or improvements made through error.

Posted in Books, Management | Comments Off on To fail is to learn

What is open science?

The question

Wikipedia suggests that open science began in the 17th century, with the start of the academic journal. Some say that open science started in 1957 with the establishment of the World Data Center system, for International Geophysical Year. The system was established with agreement for “free and open exchange of [geophysical] data among nations”.  I’d assumed that open science started much later, but it all depends what you mean by ‘open science’.

Kendra Godwin wrote that “open science, while often discussed, is not well understood nor uniformly defined”. Jeroen Bosman and Bianca Kramer also observed that there is a great deal of variation in definitions of what open science is. They explain it thus:

Rather than see this as a problematic lack of focus, or as a sign that it is too early to define what open science is or not, we’d argue that the scope of open science and the variety of actors involved make it not realistic, and even counterproductive, to expect there to be, now or in the future, one definition of open science that fits all.

This has not stopped people from attempting to come up with definitions! Bosman and Kramer categorise five types of definitions, from high-level definitions and all-embracing definitions to practical definitions, plus personal and catchphrase definitions.

I started thinking about this when the Crick announced its ‘open science collaboration’ with pharmaceutical company GSK, three years ago. The press release noted that “research findings from the collaboration will be shared with the broader scientific community, via joint publication in peer-reviewed journals”. I felt uncomfortable with the designation of this as ‘open science’ as it seemed very different from what I understood by that term. One or two tweets at the time showed I was not alone. When I thought about it more I realised that there was no absolute level of openness. This initiative was certainly more open than GSK’s standard practice, but equally clearly less open than research at the Montreal Neurological Institute (the most open research institute I know of).

How can we judge at what point along the spectrum from ‘closed’ to ‘open’ does research qualify for the ‘open science’ badge? It’s a conundrum.

The answer

I thought it would be a good idea therefore to assemble a group of experts to shed more light on open science. A meeting of Open Research London on 3 October 2018 at the Francis Crick Institute will feature four top speakers who will give their thoughts on open science, in particular the relationship between open science and commercial activity:

  • Patrick Vallance
  • Jenny Molloy
  • Wen Hwa Lee
  • Tim Britton

More details are here and an Eventbrite page will go live on 30 August.

Definitions

To set the scene for the meeting I’ve been doing some reading and thought I’d inflict it on you. I looked at a few definitions of open science. Many of the definitions put sharing research outputs at the heart of open science, but they differ in the details of what is to be shared. Openness and reuse are also key to many, while several definitions refer to the use of digital technology and collaborative tools. Most of the sharing is targeted at the scientific community but some definitions target the broader population too – public engagement and citizen science. Some definitions were pithy: ‘Increased sharing among scientists‘  or inscrutable ‘To make scientific research [outputs] accessible to all levels of an inquiring society‘. One is almost a slogan: ‘Open science isn’t a movement, it’s just (good) science‘and one is far-reaching ‘Carrying out scientific research in a completely transparent manner, and making the results of that research available to everyone‘. A longer list of quotes from definitions is at the end of this post in Table 1.

Three extensive reports about open science have recently appeared. These are from the US National Academy of Sciences (NAS), from the League of European Research Universities (LERU) and an international group of open scholars, led by Jon Tennant.

The LERU document states that “Open Science is not about dogma; it is about greater efficiency and productivity, more transparency and a better response to interdisciplinary research needs”. It also refers to the eight pillars of Open Science identified by the European Commission: the future of scholarly publishing, FAIR data, the European Open Science Cloud, education and skills, rewards and incentives, next-generation metrics, research integrity, and citizen science. These pillars are more all-embracing than most of the definitions above, though more aimed at policy-makers than researchers. The NAS report states that “Openness and sharing of information are fundamental to the progress of science and to the effective functioning of the research enterprise”, raising the stakes to an existential level. Finally, Jon Tennant et al’s open strategy document avoids attempting any definition, saying “it is a holistic term that encompasses many disciplines, practices, and principles”.

What, why and how to share?

Most definitions talk about sharing papers and sharing data, but several also mention software code and methods, and a couple mention sharing of peer reviews too.

Many definitions omit to mention the purpose behind open science.  Typically these are to do with accelerating and improving science:

  • to boost collaborative progress and bring greater transparency
  • to transform the entire endeavour of science
  • boosting information flow can improve our collective cognition

If open science is about sharing, then to do it you must simply share your outputs, in some kind of repository. Some definitions put more emphasis on collaboration and on digital technology – which is kind of a given I’d have thought. (I don’t see much about open science sharing using stone tablets or parchment scrolls). Open licensing (Creative Commons etc) is also a key to effective sharing. Some definitions talk about sharing throughout the whole research life cycle.

Open and commercial – innovation

Some definitions of open science also refer to open innovation.  As noted above, the pharma company GSK has adopted a number of open innovation strategies. In the pharmaceutical industry, the concept of open innovation has received a fair amount of attention as a possible countermeasure to the general decline in R&D productivity. In a recent paper Bountra, Lee and Lezaun argue that ‘open science approaches represent the most promising path forward’ for drug discovery.

Open and commercial – infrastructure

Much attention has been given recently to the question of commercial infrastructure that supports open science and the conditions that may need to be imposed.  Do commercial companies have a positive role to play in the development of scholarly communications infrastructure? Mark Hahnel warns that universities should be encouraged to take help from outside of academia when developing open science infrastructure, but should be careful in these dealings. Opinion is divided between those like Hahnel who think that there is nothing about open access/open science as such that precludes for-profit provision and those who believe that the profit motive is absolutely misaligned with the core values of academic life (10).

Jefferson Pooley has observed that ‘much of the for-profit scholarly communication ecosystem sits on the value-extraction end of the continuum‘, not the value-adding end. Jon Tennant wrote in a typically hard-hitting opinion piece, about the ‘corrupting’ effect that Elsevier has on open science in Europe.

Discussion

It seems that no single definition of open science fits all circumstances. I think the concepts of ‘more open’ and ‘less open’ are easier to pin down than the absolute of ‘Open’ with a capital O.  I saw another definition mentioned on Twitter that is quite good, in a different way, but it doesn’t cover every aspect.

I hope that the Open Research London event on 3 October will give us some more ways of thinking about open science. See you there!

Sources linked to in text

  • https://datascience.nih.gov/WhatisOpenScience
  • https://im2punt0.wordpress.com/2017/03/27/defining-open-science-definitions/
  • https://about.hindawi.com/opinion/a-radically-open-approach-to-developing-infrastructure-for-open-science
  • http://blogs.lse.ac.uk/impactofsocialsciences/2017/10/11/open-source-commercial-non-profit-for-profit-what-power-have-you-got/
  • http://blogs.lse.ac.uk/impactofsocialsciences/2017/08/15/scholarly-communications-shouldnt-just-be-open-but-non-profit-too/
  • http://uk.gsk.com/en-gb/research/sharing-our-research/open-innovation/
  • https://www.theguardian.com/science/political-science/2018/jun/29/elsevier-are-corrupting-open-science-in-europe
  • https://www.future-science.com/doi/full/10.4155/fmc.15.122
  • https://www.leru.org/publications/open-science-and-its-role-in-universities-a-roadmap-for-cultural-change
  • https://zenodo.org/record/1323437#.W22mqNhKjOR
  • https://www.nap.edu/catalog/25116/open-science-by-design-realizing-a-vision-for-21st-century
  • https://en.wikipedia.org/wiki/International_Geophysical_Year#World_Data_Centers
  • https://www.crick.ac.uk/news/2015-07-14-gsk
  • http://science.sciencemag.org/content/351/6271/329
  • https://en.wikipedia.org/wiki/Open_science
  • https://www.oxfordmartin.ox.ac.uk/publications/view/2613

Table 1

Phrases used to describe open science Ref.
Increased sharing among scientists 1
Reinventing the way we work together in the context of the web 2
Open Science is open [research outputs] 2
A new approach to the scientific process 2
Cooperative work and new ways of diffusing knowledge by using digital technologies and new collaborative tools 2
To make scientific research [outputs] accessible to all levels of an inquiring society 2
Right to use, reuse, modify, redistribute scholarly knowledge 2
Open science isn’t a movement, it’s just (good) science 2
Open access to [research outputs], and other forms of multi-directional exchange between academic researchers themselves and with the public 3
Science is purposefully conducted with digital technologies and in collaboration with others… allows for and facilitates the intentional sharing and reuse of all generated products 4
Free availability of [research outputs]. 5
Carrying out scientific research in a completely transparent manner, and making the results of that research available to everyone 6
A system for scholarly communications that is built to maximize the dissemination and reuse of all research outputs throughout the research lifecycle 7
Sharing expertise, resources, intellectual property and know-how with external researchers and the scientific community 8
To boost collaborative progress and bring greater transparency 1
Will transform the entire endeavour of science 2
Boosting information flow can improve our collective cognition 2
Using web-based tools to facilitate scientific collaboration 9
Collaboration with people at different levels and in differing fields 4
A process rooted in and relying on digital technologies 4
Science conducted in a way that will allow for sharing and reuse 4
And involvement with any or all parts of the research life cycle 4
References in table

  1. http://blogs.plos.org/neuro/2018/01/31/open-science-sharing-is-caring-but-is-privacy-theft-by-david-mehler-and-kevin-weiner/
  2. https://im2punt0.wordpress.com/2017/03/27/defining-open-science-definitions/
  3. https://www.rand.org/blog/2017/10/can-open-science-help-to-make-research-more-accessible.html
  4. https://datascience.nih.gov/WhatisOpenScience
  5. http://www8.nationalacademies.org/onpinews/newsitem.aspx?RecordID=25116
  6. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0669-2
  7. https://about.hindawi.com/opinion/a-radically-open-approach-to-developing-infrastructure-for-open-science
  8. http://uk.gsk.com/en-gb/research/sharing-our-research/open-innovation/
  9. http://openscience.org/what-exactly-is-open-science/

Table 2

Research output No. of mentions
Papers 7
Data 7
Code 4
Methods 3
Peer reviews 2
Materials 1

 

 

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Cat Zero – book review

This lablit novel is set in a research institute in north London. The story is centred on a virology research lab and its work.

An old lady dies. A cat dies. More cats die – could it be suspicious? Artie is a young virologist who’s recently started her own lab and is looking to make (more of) a name for herself. An eccentric epidemiologist works just down the corridor from her lab. These are some of the ingredients of Jenny Rohn’s latest lablit novel, Cat Zero.

Cat Zero is an everyday story of virus research, set in a research institute in Mill Hill, north London. Its author, Jenny Rohn, leads a cell biology research lab at University College London.

The book is a great read – a really gripping and engaging novel. It’s a tale full of surprise and detailed plotting, with some characters who you will love and some who will repel you. All of them spring to life in the author’s hands. The setting for the story, a modern but slightly peculiar biological research institute, is less familiar than the backdrop for most novels. The institute is vividly drawn and is almost a character in its own right.

The story moves along at a very good pace and the pages keep turning – it’s difficult to stop reading. The plot takes some directions you might not predict, but is always believable. Perhaps there’s a little bit of what Graham Greene called his ‘entertainments’, where the combination of chance events make a great tale but stretch the bounds of likelihood.

As the setting is a research institute, the novel includes many insights into life and work in scientific research labs – the joys of discovery and the long hours of preparation involved. Its setting in Mill Hill suggests that the fictional institute may have a bit of NIMR (National Institute for Medical Research) in it. Jenny Rohn has previously worked at the London  Research Institute (LRI) so I suspect that it too has contributed some of the atmosphere. The novel is full of characters, oddities, minor politicking, misogyny and of course science. We are introduced to the pressures of a science career and the rewards, and the intense teamwork and collaboration that is inherent to modern research. The manner in which the science is introduced is matter-of-fact, not pedagogic. The story about the science progresses alongside the human relationship elements and the later thriller elements, never overshadowing them, but integral to them. Jenny Rohn skilfully shows that researchers have an element of the detective in them as they sift the evidence and weigh up the possibilities. Hence it has the flavour of a detective story at times, though there are no detectives in it.

I did have one or two pedantic quibbles of fact. On a number of occasions the characters make a journey from Mill Hill to Hampstead by train, as though this is a direct line.  Those two stations are on different branches of the Northern line, though it would indeed be lovely if they were directly connected. Some of the incidental talk about reading research papers seems rooted in a print-on-paper view of journals.  This seemed a bit out-of-date to me (speaking as a librarian). But these are small worries.

This book is a really enjoyable read – I loved it and I’ve spoken to colleagues at the Crick who’ve read and enjoyed the book. One of them tweeted that it is “a fun read with mathematical models playing a key role”. We have a copy of Cat Zero in our library collection and I hope other libraries serving researchers will also acquire copies. You can get it from Amazon.

Jenny Rohn

Jenny’s PhD was on the evolution of feline leukaemia virus, which plays a part in this novel, and since then she has worked in the biotech industry and in science publishing before returning to academic research and starting her own lab. She has written two previous novels, established the LabLit.com genre and website and Fiction Lab (a science book club). She is also a regular and popular blogger and speaker.

Disclaimer

Jenny is a friend and fellow blogger on the OT site. That certainly influenced me to read the book, but had no bearing on my enjoyment of it. If I hadn’t liked the book I would just have said nothing!

A version of this blogpost was initially posted on to Amazon as a review of the book.

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A new scientific archive – launch and reflections

The event

I recently attended the launch of the EMBL archives, in its new purpose-built facility at the heart of the EMBL Heidelberg campus.  Most of the audience were from EMBL but there a few scientific archivists there too, admiring what has been achieved.

At the launch event we had a chance to look round the new facility and see some documents and photos from the archive. Then we heard talks by Iain Mattaj (EMBL Director), Giulio Superti-Furga (EMBL alumnus and Scientific Director of CeMM) and Anne-Flore Laloe (EMBL archivist) . All three speakers emphasised that the archive is and will continue to be a community-driven effort. EMBL alumni from across the world have submitted material. The archive is all about the people.

Cutting the ribbon to launch the archive. The slide shows the building where the archive is located.

Celebrating in style with jelly/fruit/cake

The archive

The germ of the idea for an archive came from the EMBL Alumni organisation as they prepared to work on the 40th anniversary of EMBL in 2014. They enlisted Sydney Brenner to endorse the idea (he had written to Nature in 2007 about the need for historical archives of science ).  Iain Mattaj, the EMBL Director, backed the idea and EMBL management took action to implement it.  Anne-Flore Laloe was recruited in 2015 to be the archivist.

Rolling stacks provide about 600 linear metres of shelving

As well as documents there are old instruments

The director’s view

Iain Mattaj stressed that it is important to keep records and archives of important information on events which help to shape our science and our society. This new archive is primarily about EMBL and EMBO but, because of the major role those organisations have played in the last 40+ years, the archive is also important for European molecular biology more generally.

Iain thanked Jenny Haynes and Jenny Shaw from the Wellcome Library for their input and support, as well as many others who lent support or ideas to the project to create the archive. And, of course, he thanked the archivist Anne-Flore who has taken the ideas forward, developed them and made them a reality.

The alumnus view

Giulio Superti-Furga recalled that several decades ago a small group of physicists and geneticists coalesced around the new field of molecular biology. Now there is a huge community of people working in molecular biology who have built a massive scientific field. Giulio compared the field’s development to someone running up to the top of a hill and then, exhausted, pausing to ask ‘how did we get here? Can I remember? Where are we?’  He said that this is why we need an archive.  The paradox is that it is exactly when things are happening that we have no time to record them. Hence EMBL only thought to create an archive after 40 years of leading research.

Giulio said that the archive is a fantastic, major milestone which also has symbolic value – showing how the molecular biology community in Europe came of age. He hopes that it will inspire other organisations too.

Archive photo of the EMBL site

The archivist’s view

Anne Flore started in her new role at EMBL with a blank slate, but huge expectations. When she started she had one cardboard box of papers and records.

“Archiving for EMBL’s future”

In the early days she talked to as many people as possible and told us that reactions were mixed. One person said “I’ve never seen an archivist before.” Another said “I thought I was going to meet with the EMBL anarchist!”.  She also held talks with archivists in many other institutions as she turned the initial plans into realistic ambitions. She wrote terms of reference, a collecting policy. Procured a catalogue system. The setup of the archive needs to stand the test of time, be adaptable to future changes and reflect the spirit of EMBL.

She catalogued the first item in mid-2016. Some big themes of the archive thus far are: instrumentation, photos, training, bioinformatics, social aspects of the lab.

Now the need is to ensure that things are collected in a representative fashion. Capturing material across all fields and types, including things that are being worked on right now. Historians may be interested in documents related to publications (cf  Darwin’s notebooks; Newton’s letters). Researchers should consider what papers of theirs might be of interest. Anne-Flore has started doing oral interviews too.

Her longterm goal is that no scientists will question the need for and existence of science archives.

To learn more about her approach, see her 2017 EMBO Reports article, explaining how “Archives for molecular biology preserve the heritage of science beyond the published record for future scholars”.

Anne-Flore emphasized that the EMBL archive is an accessible resource. Anyone can come in. It is a contemporary archive of science and technology, part of the broader landscape of archives.

Further reflections from Giulio

Two years ago I heard Giulio talk about the EMBL archive and the role of a scientific archive, at the first scientific archives workshop. He had some interesting ideas about the responsibility that scientists bear to future generations and he developed some of these ideas again in his talk at the archive launch.

Giulio believes that scientists should start self-reflecting while they are doing their research.  He said that without historical knowledge, we easily forget how things happened. For example, it is startling to be reminded that until the early 1960s most scientists thought that protein was the carrier of heritable characteristics.

Giulio sees it as a duty for scientists to record the history of their own research. He started a habit over 20 years ago to document his research and his work in a daily journal. He uses black ink on acid-free paper. He has written about 7,000 pages into this journal over the past 20 years.

Giulio’s notebooks

Researchers now are being encouraged to adopt the tenets of ‘Responsible science and innovation’ (RRI) – a kind of extended research ethics framework. The EU defines RRI as covering ethics, societal engagement, gender equality, open access/science and science education. Giulio’s definition of RRI also includes “proper recording of work and intellectual contribution” – going beyond publishing papers to record the context of research.

He then outlined what he’d like to see become mainstream practice:

  • Training young scientists to understand the importance of being responsible and to understand the importance of accountability.
  • Training established scientists to manage their data / reagents / legacy wisely.
  • Foster the interface between natural sciences and humanities and create exposure of young natural scientists to social scientists and historians.
  • Have all major scientific projects and initiatives be accompanied by a social scientist (e.g. historian or sociologist).
  • Interview veterans and encourage them to save and contribute their personal archives.

My thoughts

The archives ‘catch-up’ model seen at EMBL (collecting archives 40 years after the organisation began) is similar to what happened at CERN (collecting archives 25 years after the organisation began).  At the EMBL event I talked to the Records Manager of a new research institute. She is considering how to make the case now for defining the approach to archives, and I am in the same situation. Young organisations can be too busy establishing themselves to spend time thinking about archives. It’s good in theory to start collecting materials from the beginning, but it is hard to persuade people to see current documents as part of history.

I love Giulio’s practice of keeping research notebooks, but I suspect few researchers will be tempted to follow suit. I think his idea for attaching a social scientist to major projects is good, but perhaps an ethnographer or anthropologist would be even better. I don’t expect this will become widespread, but even to see some projects adopt the idea would be interesting.

It’s good to see scientific archives becoming more visible – the second workshop on science archives will take place later this month. I’ll be interested to learn there about new ways to capture the record, the process, the history of science.

 

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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
Source: http://www.prepubmed.org/monthly_stats/

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’
Source: https://www.slideshare.net/BaltimoreNISO/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.

Posted in Communicating science, Preprints, Uncategorized | Comments Off on Preprints in the news

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.

Disruption

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: http://blogs.plos.org/plos/files/2018/04/Power-to-the-Preprint_blog-image-002.png

Publishing

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.


Factsheet

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).

Megajournals

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.

Preprints

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.

 Protocols

The protocols.io 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.

Mountains

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.

hunza-sunrise

Eagles Nest Hunza, by @thehunza #GilgitBaltistan #pakistan #tripkar #beautifulpakistan # sunrisepic.twitter.com/GlVc2LcZVR

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.

Thailand

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”.

royalpalace

The Royal Palace in Bangkok, Thailand. 

China

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.

party

party2

cake

cake2

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