Open Research London – Oct 2016 meeting

I was very relieved that the Open Research London (ORL) meeting on 19 October 2016 went well. Jon Tennant, Ross Mounce and Liz Ing-Simmons established ORL in Jan 2015 but it faded away after a couple of meetings.  I’d been thinking for some time that I should start up the group again, but was a bit wary of the work involved.  The group’s founders were happy for me to have a go at re-establishing it and I found a willing co-organiser here at the Crick in Martin Jones.

About 55 people turned up to the spectacular new Crick building to hear talks on two publishing innovations and a talk / interactive workshop on open science workflows.

Preprints – bioRxiv

John Inglis is the co-founder of bioRxiv, the preprint service for the life sciences based at Cold Spring Harbor Laboratory (CSHL).  He is also the founding Executive Director and Publisher of Cold Spring Harbor Laboratory Press in New York, a not-for-profit publisher of journals, books, and online media in molecular and cellular biology. He spoke about bioRxiv at three years old.

First a definition. John defined a preprint as “a complete but unpublished manuscript yet to be certified by peer review”. The definition is all about what it’s not (i.e. peer-reviewed) but the key to preprints is all about the speed of dissemination of research results.

Preprints are currently distributed under two models. In the first, a manuscript is submitted to a journal which makes it available as a reprint and then puts it into a peer review process.  The journal publishes those preprints that pass peer review.  The business model is that of the journal – i.e. it is funded by APCs (article processing charges). An example of this model is F1000Research. In the second model manuscripts are submitted to a service dedicated to preprints. There is no fee and no peer review as part of the service. The service is supported by institutions and foundations. An example of this model is arXiv, supported by Cornell University and others. It gets 100,000 submissions p.a.

John explained that CSHL is committed to science communication so bioRxiv was a natural extension to its activities.

Modelled on the arXiv, it is a dedicated, publisher-neutral service. The time seemed right to launch it in 2013 as there was a new enthusiasm for openness, a greater acceptance of digital resources and practices, and increased posting to the quantitative biology section on the arXiv showed that some biologists at least were ready for preprints.

In building bioRxiv the founders aimed for a simple, reliable submission system, and wanted to ensure that authors would have total control over their content (using a variety of licenses).

John Inglis is always careful to talk about bioRxiv  in terms of ‘posting’ and ‘distribution’ rather than publishing. There is no peer review component of the service.

Manuscripts submitted to biorXiv are allocated to one of 26 subject categories then checked for scope and format, and subjected to a plagiarism check. Some basic checks are made to confirm that the submission is scientific in nature, is a report of research (rather than just a hypothesis) and whether there are human health implications. In the latter case some further screening is needed.

If all checks are passed then a few hours later it will be posted on the website. The author can post revisions at any time. biorXiv gets information out there very quickly.

In its first three years bioRxiv has posted 6200 manuscripts.  Disappointingly not many of them are confirmatory or contradictory results.  25% of them have been revised at least once. There are more submissions in biology than in health.

Submissions come from 2900 institutions, across 82 countries. Submissions are increasing, currently standing at 450 per month.

Authors seem to like it. Transmission of research results is very rapid. They get useful feedback and their preprints are read. 11% of the preprints receive comments and there have been many blogposts and tweets about bioRxiv preprints – 93k tweets in the past 12 months.

Institutions and funders are starting to accept preprints as evidence of productivity. Both NIH and Wellcome are considering their policies on accepting preprints in grant applications. Rockefeller University has accepted preprints as part of a CV. EMBO accepts preprints on CVs for fellowship applications. Many journals will consider preprints for publication as papers, including Nature, Science and Cell.  PLOS Genetics has appointed editors specifically to search bioRxiv for potential manuscripts to publish in the journal.  CSHL has undertaken a good deal of advocacy with learned societies and publishers. Several publishers now offer a “submit your manuscript to bioRxiv” button as part of their submission process.

It’s time to start sending your manuscripts to bioRxiv!

Wellcome Open Research

Robert Kiley is Head of Digital Services at the Wellcome Library and is currently acting as Wellcome’s Open Research Development Lead, responsible for developing a new open research strategy for the Wellcome Trust. Over the past decade Robert has played a leading role in the implementation of the Trust’s open access policy and overseeing the development of the Europe PubMed Central repository. He is also the Trust’s point of contact for eLife. He spoke about the Trust’s latest publishing initiative: Wellcome Open Research.

Just as with bioRxiv, the purpose of WOR is to make research communication faster, and more transparent.

WOR is fast, inclusive (you can publish everything – not just standard research narratives), open, reproducible (data is published alongside the article), transparent (it uses open peer review), and easy (the costs are met directly by Wellcome). The only drawback is that it is only available for outputs from Wellcome-funded researchers.

In early submissions, they have seen a range of publication types and a range of researchers from senior to junior. Submissions have come from a range of institutions.

The open peer review process allows for one of three decisions from each reviewer: approved; approved with reservations; not approved. If a preprint gets two ‘approved’ decisions then it is indexed in PubMed and deposited in ePMC. The is the same process used by F1000Research, which provides publishing services for WOR.

Wellcome hope to attract a range of outputs from a range of researchers. They hope that other funders will in due course emulate their initiative.

Open science workflows

orl-oct16-1

Bianca Kramer and Jeroen Bosman are subject specialist librarians from Utrecht University who have considerable expertise in scholarly communication and research workflow tools. Together they led the global survey in Innovations in Scholarly Communication. Their talk, Open Science workflows: Tools and practices to make your research more open, reproducible and efficient promised us a glimpse of the future.

orl-oct16-2

One of the slides from Bianca Kramer and Jeroen Bosman’s talk

They started by showing some diagrams of research workflows – nice well-behaved cycles with boxes and arrows. But life is not so simple. To make the workflow more realistic Jeroen added cycles within cycles, put in some dead ends and some repeats. By the end it looked more like a game of snakes and ladders.

We then learnt a little about the survey of tools that Bianca and Jeroen had made, and how they had categorised different tools as either:

  • Traditional (same as print era)
  • Modern (internet era)
  • Innovative (social media, collaborative aspect)
  • Experimental (new tools, developing tools, startups)

Lest we become too focused on technology and tools though they emphasised that research workflows are less about tools and more about work practices and people.

Bianca and Jeroen are nothing if not practical and they are happiest when considering reality instead of abstractions.  The remainder of their presentation was in the form of a workshop, an endeavour to define a set of work practices that would constitute an open science workflow, and tools that would support it.

The scale of their ambition for the workshop, and the amount of preparation they had done, astounded me. There were three or stages to this exercise.

orl-oct16-3

The final result of Bianca Kramer and Jeroen Bosman’s workshop

Each seat had a small paper button with the name of a research tool on it.  We were first invited to review the tool on our own seat, consider its usage and application in open research, and then to discuss this with our neighbour. Around the periphery of the room a number of research practices had been arranged, grouped according to the different stages of the research cycle. We were next asked to affix our paper button to an appropriate research practice. Finally, we were each asked to move one of the research practices that we considered to be part of an open science workflow and place it in a new area at the back of the room, together with any tool we thought would help with the practice.  This back wall filled up with open research practices and tools.

As a participant it was quite challenging to grasp all of this, and a bit mind-boggling to assimilate everything that was on the back wall. I suspect that Bianca and Jeroen, who live and breathe this stuff, had a clearer picture than anyone else n the room. It certainly stimulated us to focus on the role that tools can play in open research practices, and on what an open research practice is. I liked the way too that the whole process of the workshop was open and transparent.  Everyone in the room had a sense of the task we’d been set and of how the solution to it was emerging – we could see it on the walls. This really was a great model for open research.

Bianca and Jeroen’s mixture of openness and outreach is a great combination.

You can read their own account of the workshop on their blog.

And that was Open Research London, Oct 2016. We’re planning the next one already – expect it to be Jan or Feb 2017. Hope to see you there! Find out more about Open Research London on the website or follow it on Twitter.

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Rapid or vapid?

Someone recently asked me what I thought about the open access journal Molecular Metabolism. I had just delivered a short talk to a group of researchers as a reminder about our open access policy and what my team could do to help them make sure their research was published open access.

Well, I didn’t think anything about Molecular Metabolism as I had never come across it before. In case you wondered, it’s been going since 2012 and has been published monthly for the past 2 years and more, so it seems to be reasonably well-established. Over that time it’s published about 350 articles, some of them having modest citation impact but nothing earth-shattering.  It’s not exciting in any way, but it seems an entirely worthy publishing venue. It is supported by the German Center for Diabetes Research (DZD) and the Helmholtz Diabetes Centre so it has roots in the diabetes and metabolism research community. And it’s published by Elsevier as a fully OA journal.

On the journal’s website it describes itself as

a platform reporting breakthroughs from all stages of the discovery and development of novel and improved personalized medicines for obesity, diabetes and associated diseases.

As well as being an OA journal it has adopted a rapid publication model.  Its peer review instructions require reviews to be delivered in 72 hours. Reviewers are asked only to accept, reject, or suggest minor revisions.

My enquirer outlined this rapid process and asked what I thought. It seemed a good model to me. It’s not a high grade journal, so long rounds of manuscript revision would be a waste of everyone’s time. The option to reject papers is still there.

My enquirer had been invited to review an article submitted to the journal. His response was that the journal must be a scam. He viewed their rapid review policy as an invitation to reviewers to accept substandard papers. My sense was that he was also implying a Bohannonian subtext of “and all OA journals must be rubbish, innit?”.  I suspect he has the same view about PLOS ONE.

This little exchange gave me more information about the person asking the question than about the journal he enquired of. It seems a shame that in some quarters OA, and the idea of the ‘sound science’ peer review is still regarded with such suspicion.

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Librarygeddon

The Library, the collection

When it’s done right it is a wonderful thing. The collection dedicated to meeting a specific need: carefully selected, sensibly arranged, appropriately indexed, comprehensive in its coverage and range of formats. It is precisely calibrated to meet a need. On its own it is a collection – worthy of celebration. But put the collection together with a community of users and a team of knowledgeable library staff and it turns into a Library – a boon to civilisation and scholarship.

To my way of thinking it is the community of users that comes first.  Perhaps this is librarianship’s chicken and egg situation – “Which comes first, the reader or the book?”.  Ranganathan answers the question by saying, in effect, “both”. His famous five laws of library science include these two:

Every reader their book
Every book its reader

Neil Gaiman has written thoughtfully about the value of public libraries as “cultural seed corn” and he hails the way that libraries encourage knowledge discovery:

there’s nothing quite like the glorious serendipity of finding a book you didn’t know you wanted to read. Anybody online can find a book they know they want to read, but it’s so much harder to find a book you didn’t know you want to read.

Public libraries are under great threat, even though they have many vocal defenders. Other kinds of libraries are equally under threat but don’t attract the same passionate advocates.

My career has been in special libraries, specifically what are sometimes called workplace libraries, where the raison d’etre for the library is the needs of a group of people in a workplace. In special libraries it is definitely the reader who comes before the collection.

Information needs are expressed by users, and captured by the librarian, who must take actions to meet those needs. The user needs define the shape and contents of the collection, and its organisation. In an engineering library you may find a small section of books on ‘medicine’, probably all lumped together under one classification mark. In a medical library those books would need to be classified in far more detail (dividing them into finer shades of topics), but any books on ‘engineering’ would be lumped into a single section. Thus, indexing and classification in the library must be determined by the needs of the users. Classification is relative, not absolute. A creative librarian will also develop services on top of the collection to meet particular needs of the community of users.

“I have always imagined that Paradise will be a kind of library.” – Jorge Luis Borges

The library when NIMR was at Hampstead, ca 1930

Growth

The library’s collection policy is an expression of its approach to managing the collection. It defines what to acquire, what to keep, and what to discard. It may aim for homeostasis (a fixed size) or it may attempt to keep hold of everything it has ever acquired (continual expansion).  Often libraries will make use of secondary storage space, where less-frequently required items are sent. (A bit like sending your old possessions up to the loft, or into the garage). A mature library collection, with a long historical overhang in secondary storage, can be seen as a record of the organisation’s interests and development. It reflects some of the parent organisation’s history.

A library devoted to a single subject for a long period of time, e.g. a learned society library like the Linnean Society Library, becomes an unrivalled repository of knowledge about the subject.

“To build up a library is to create a life. It’s never just a random collection of books” – Carlos María Domínguez

Over the years the library’s users and their needs may change, and this will impact on the collection and services too. Of course library staff may also change, and while they will strive for continuity there will inevitably be changes in emphasis as new staff replace old staff and make their mark with their own particular quirks.

Another of Ranagathan’s laws is:

The library is a growing organism

The library cannot stand still. Space limitations may mean that it cannot grow indefinitely large, but it still needs to live – to develop as user needs change and publishing trends change.  The library will discard (or relegate) no longer needed items as well as ingest new items. It must also exploit new developments in technology and the information industry, and adapt to changes in the broader environment.

“The only thing that you absolutely have to know, is the location of the library.” – Albert Einstein

The NIMR library at Mill Hill, 2011

Radical change

There should be a tight link between the collection, its users and the workplace, so that they change in harmony. But if an organisation undergoes a more radical change then the collection can come under threat. When organisations close, restructure, split, or suffer severe financial troubles, then there will be dire consequences for the library service and collection. This is the way of the world but, especially for longer-established collections, it can be a cause for some regret. Simon Barron has pointed out that sometimes there is a conflict between those who worship books regardless of use and the drive for efficient collection management. I saw a project advertised a couple of years back about the “non-economic benefits of culture“. I wonder whether it included a strand about the cultural value of libraries (of all kinds)?

A few years back I was the membership secretary for CHILL (a grouping of independent health-related libraries). These all count as special libraries, many of them relatively small. It was salutary to count up each year how many members had fallen by the wayside in the preceding 12 months. One member was a charity called Drugscope which had a fantastic information service on addiction, run by a dynamic information professional. But one year some of the charity’s key funding grants were not renewed, leaving a funding hole. There was no money to fund the information service. It just closed. Apparently it was not the only one. An editorial in Addiction in 2012 said: “Special libraries in the addiction field have been downsized or closed at an alarming rate during the past decade”.

The Royal College of Midwives also had an enviable collection and information services run by knowledgeable staff. Financial pressures led to closure. Happily the Library of the Royal College of Obstetrics and Gynaecology stepped in to rescue the collection in this case, or it would have been lost. Sadly the knowledgeable staff were lost. When the Royal Pharmaceutical Society of Great Britain was split, into a professional society and a regulatory body, this also occasioned a massive change for the library. Retaining a large historical collection was no longer economically feasible and a “lean and mean” approach was adopted instead. Large numbers of older items were disposed of.

Anecdotally I have heard that many Government department libraries have closed or drastically downsized in recent years, due to restructuring, merging or closure of departments.

Of course it’s important that libraries provide useful services in an efficient manner, but the inevitable consequence of rapid organisational change is the loss of many items of real historical interest.

This kind of loss is a global phenomenon. In 2014 it was reported that:

Scientists in Canada are up in arms over the recent closure of more than a dozen federal science libraries … Scientists fear that valuable archival information is being lost. Of most concern is the so-called grey literature — information such as conference proceedings and internal departmental reports.

We have a worldwide librarygeddon – loss or destruction of many specialist collections. Does it matter? Maybe, but probably not enough that we can do anything to change it.

Empty shelves in the NIMR Library gallery

They’re all empty now

NIMR Library heritage

My interest in this topic began in 2003, when I first learnt of plans for my Institute to be moved. The plans changed over time, but it has been blindingly evident to me right from 2003 that if the Institute moved from Mill Hill it would spell the end for our Library collections. I have got used to the idea and I can think of no valid argument why things should be any different, but I still regret that things have to be this way.

The NIMR library began in 1920 when the Institute moved into its Hampstead home. The aim of the library was to support scientific medical research at the Institute and to be a resource for the nation’s medical researchers. Work to assemble the collection had begun prior to 1920, collecting materials from around the world. Many items were received as donations, or through exchange programs. The MRC published Medical Science: abstracts and reviews and its highly-regarded Special Report Series, so it had valuable publications to offer in return for free journals and reports from other organisations. In those colonial days, reports (grey literature) were received from research organisations across the British Empire and the rest of the world.  We even used to receive The Lancet free of charge (though this changed when Elsevier bought the journal). As well as books, journals and reports, the Library has an extensive collection of pamphlets and reprints. The collection represents a unique period of British medical research, when Hampstead and later Mill Hill were at its centre.

The reprints were largely collected by individual scientists, I believe, and periodically deposited in the Library. They were all carefully catalogued and subject indexed – we have a vast rank of filing drawers filled with index cards. I think of the reprint collection as the intellectual encrustation of the Institute’s research, from the 1920s to the 1960s. Reprints have become unfashionable and few libraries are interested in taking large collections of reprints. But I think much of the value of the reprint collection is in the catalogue rather than the reprints themselves. It is a unique historical document of 20th century biomedical science.

It’s a strange thing, but when scientific records/publications become old they often have less value to science, but more value to the humanities, especially history. Just by keeping hold of our science literature collections as they aged so we acquired a history collection. The trouble was, we were not funded for historical research but for scientific research. Therein lies the problem I faced. Looking back, I can see many ways that I could have handled it better but I did as best as I could at the time.

It’s a big project

The simplest thing to do would have been to just throw everything away, and for a while I was afraid that was exactly what I would have to do. Happily, I gained approval (and resources) from on high to undertake a few projects to help ensure that those parts of the collection with most value could be dispersed responsibly.

There were about 3km of shelving filled with printed materials that needed to be disposed of. Printed journal volumes accounted for much of the shelf space.  The pace of digitisation of journals is such that it is very hard to find homes for printed journals. We did find homes in other libraries for a small quantity of journals, but most of the journals were sent for recycling.

Preliminary enquiries made it very clear that few libraries had an interest in more than a small proportion of the other items. That is not surprising – libraries can only collect what matches their strategic needs, and their collection policies (vide supra). The lists that we prepared of the most desirable groups of items – the pamphlets, reports and older books – have helped us to find homes for quite a few items. The 5,000 pamphlets in particular have gone as a single block to a major library. I tweeted pictures of quite a few of the books that have been transferred to other libraries, under the hashtag #nimrlibrarybyebye. A few hundred have found homes in libraries, mostly in London but some further afield.

A few hundred books have been retained to form a historical collection in the new institute – more of this in a later post. Some others have been retained by some of the labs for their use. And a few hundred have been transferred to members of staff as mementoes of NIMR. But several thousand items will go to the secondhand trade – I hope they will eventually make their way to collectors’ shelves.

I should emphasise that most items in the NIMR Library collection are not unique – probably not even rare by the standards of rare book collectors. And not really old either. Most of the collection was 20th century.

It is not so much the items themselves that I am mourning here, but the collection of all the items.  It’s the whole collection that is greater than the sum of its parts, the connections between all the different documents and the context of the Institute . This notion (value of the collection versus value of individual items) is a bit intangible, and unquantifiable; perhaps not a thing at all. That’s why when it is all gone (quite soon now), probably no-one will notice, or remember that it was there, apart from me.  I will remember.

You can look right through the empty shelves in our store

Empty stacks in the library store

There’s about 3km of empty shelves now

Posted in Books, Collections, Libraries and librarians | 2 Comments

Paradigm – the sculpture

Recently I attended the first public event at the Francis Crick Institute’s new building next to St Pancras.  Ironically the event was not about science but was a conversation with an artist, sculptor Conrad Shawcross. He created the enormous sculpture outside the new Crick building. The sculpture is called Paradigm, and was inspired by the thought of the ground-breaking, paradigm-shifting science that the Crick was created for.

In conversation with Ken Arnold, Creative Director at the Wellcome Trust, Conrad revealed something about his inspirations and reasons for creating Paradigm.  By the end of the evening we had learnt something about the artist and something about the sculpture. And possibly something about science as well.

Introduction

Katie Matthews, the Crick’s Director of Engagement, introduced the event and reminded us that the Crick is all about collaboration. Hence featuring a collaboration between a science institute and a sculptor is par for the course for Crick.

Ken Arnold continued by reminding us that we have now had 20 years of the sciart phenomenon.  Wellcome’s Sciart funding programme was launched in 1996 and concluded in 2006 but lives on in spirit. It was originally aimed “to fund visual arts projects which involved an artist and a scientist in collaboration to research, develop and produce work which explored contemporary biological and medical science”. Science and art are getting closer together again after a long separation.

Ken Arnold did a good job of leading the interview/conversation with Conrad Shawcross. He continually probed Conrad with questions, extracting interesting comments from the artist and generating new lines of thought. At intervals Ken opened up the floor to questions from the audience which ensured a varied pace and style of conversation and kept the flow of ideas going.

At the start Ken asked for a show of hands whether most people in the audience came to the event because they were primarily interested in science (a few) or primarily interested in art (a majority) or because they were equally interested in both (quite a few, including me). For completeness he also asked whether there was anyone not really interested in either art or science.  No-one put their hand up to that!

paradigm-night-2

The sculpture

Conrad Shawcross has worked with tetrahedral shapes before – experimenting with many wooden tetrahedra and exploring how they fit together. They do not tesselate (i.e. can’t stack neatly). Instead if you join them together they can become a bit chaotic or can form a 3-sided helix. He talks about this in a recent New Scientist article about another recent work of his.

This is the basis of Paradigm – a series of tetrahedra in which each succeeding one is 10% bigger than the one below so that although the base is only 80 centimetres across, the top spans 5 metres. It is a twisting helix that looks balanced, but only just. This precariousness is intended to be a metaphor for a scientific paradigm.  An idea in science may be accepted but it’s quite possible that a new idea will come along one day and topple the old one. Hopefully the Crick will upset a few paradigms in the future (but I think that Paradigm the sculpture will remain standing).

Conrad revealed that his original plan was for the sculpture to be just 8m high, and in stainless steel. But Paul Nurse suggested that maybe it should be bigger, and Conrad agreed. The only trouble was, it wasn’t possible to make it that high with stainless steel (for cost reasons, I think).  The solution was to use rusty iron instead, which allowed him to add some height to make it 14 metres high. Conrad also talked about the complexity of having to meet the brief of a commission such as this whilst also producing something artistically valuable that would work on a site in a very public space. He said that working within such constraints helps him to address problems that he wouldn’t otherwise have thought about.

The artist

Conrad Shawcross has been a sculptor for 15 years, since leaving art school.  He noted that he had attended Ruskin and Slade art schools, both situated within broad-based Universities not specialist art institutions. He had appreciated the mixing with medics, scientist etc, and he preferred to place himself within the history of ideas, rather than just in an art history milieu.

He has always been interested in machines, and had enjoyed taking apart and fixing his old Leyland van. He was in awe of the complexity of the motor, and also enjoyed the terminology:  pinion, crank, cam were all words that he found interesting.

He noted that one similarity between art and science was the way they help people to visualise things. Science lets you visualise, or create a representation of, things that are smaller than the wavelength of light – things you cannot see. Artists also visualise things that can’t be seen – things that are invisible or inconceivable.

And finally

My favourite quote from Conrad Shawcross came towards the end of the event. He said:

With any ‘good’ piece of art, the artist has to surrender control of its meaning

I like the humility of that statement, and the acknowledgement that the viewer of an artwork is an active player in the process.  It also struck me as having a further resonance with science – in a similar vein a piece of scientific research is sent out into the world to be understood and used in ways that the original researcher cannot control. Both artists and scientists have to relinquish control of their intellectual offspring and hope that they are not toppled by a shift of taste or paradigm.

I walk past Paradigm nearly every day now. I’m not sure what meaning I put on it, but as I left the building after the event I gazed up at the sculpture lit up against the night sky and saw a beauty and elegance that I hadn’t noticed before. I’ll keep my eye on it in future, searching out meanings.

Paradigm at night. Photo by Frank Norman

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The Lasker book prize

Well, not really.

The 2016 Lasker~Koshland Special Achievement Award in Medical Science has been given to Bruce M. Alberts for “Discoveries in DNA replication, and leadership in science and education”.

Bruce Alberts

The citation on the Lasker Foundation website says:

In his research, Bruce M. Alberts (University of California, San Francisco) devised powerful experimental tools that helped him understand the mechanism by which cells copy DNA, thereby establishing a new paradigm of molecular machines that perform crucial physiological functions.

There is a lovely interview with Alberts in PLOS Genetics, mentioning his early ambition to solve genetic code, and a meeting with Francis Crick.

MBoC

But I’m a librarian and when I see the name ‘Bruce Alberts’ I immediately visualise one of the most popular books on the biology shelves: Molecular Biology of the Cell (MBoC). At Mill Hill it was one of the few books that we bought multiple copies of for the library, and you can be sure that many of the labs there also had a copy on their shelves. Despite that it was rare to find a copy of the latest edition on the library shelves. Our copies were usually on loan – officially or unofficially.

The Award citation acknowledges the importance of this book:

Aiming to share not only what he knew about biochemistry, but to teach students how to think like scientists, he teamed up with a small group of colleagues to write an innovative cell biology textbook, now in its 6th edition, that has inspired countless individuals worldwide to find joy in experimentation, discovery, and logical reasoning.

The book’s fame and influence have secured it an entry in Wikipedia:

Molecular Biology of the Cell is a cellular and molecular biology textbook …The book was first published in 1983 and is now in its sixth edition.  Molecular Biology of the Cell has been described as “the most influential cell biology textbook of its time”.

I looked back at what reviewers said when the book first came out in 1983. Writing in Cell John Cairns observed presciently:

This is a marvelous book and is going to attract a lot of attention… it is enormous and covers a vast array of subjects.

He went on to say:

The pictures are excellent, the text is straightforward and readable, and about once every ten pages we are given a summary. Facts are laid out before us most lucidly…

Perhaps the sign of the coming of age for any subject, even procaryotic molecular biology, is that the successive waves of teachers and students should no longer have to hear about the details. Perhaps this book will be seen to have signalled the end of an era and, in its second half, to have given us a taste of what is to come.

Throughout its length, the book is written in an unobtrusively lucid style, which is the mark of much tender loving care.

The fourth edition came out in 2002, and was the first to include a CDROM accompaniment. Writing in Nature Angus Lamond said of this edition:

A generation of students have learned the basics of molecular cell biology thanks in no small part to courses based on the pioneering textbook Molecular Biology of the Cell…Through three editions it has established an enviable record for high-quality presentation, with the authors showing a remarkable ability to make both basic concepts and cutting-edge research topics accessible to readers.

The new edition is even larger than its predecessors, reflecting the vigorous activity of the field and the inexorable expansion of detailed information regarding cellular processes and molecular structures and interactions. …the punctilious attention to detail and effort devoted by the authors to covering this huge field in a lucid and easy-to-read style shines through on every page.

More recently the science historian Norberto Serpente wrote an affectionate  article to mark 30 years of MBoC, in which he cites a number of other reviews of the book.

He notes:

The pedagogical value of MBoC, as most reviewers agreed, was to be found in the design and quality of the illustrations, which condensed complex ideas into simple schematics, and in the clarity, consistency and emphasis on explanation achieved in its writing.

The Goodreads website page for MBoC is a rich source of ‘reviews’ of, or comments on, the book. Many of these are pithier than the above quotes, but still pretty overwhelmingly positive. Some of my favourite comments there were:

One of the most comprehensive cell biology books that served as a great reference for the start of my biology career.

Why read the bible if you could read this instead?

I learned a lot from this book. I give it a 5 because it is a great paper weight.

My biggest problem with this text is that it is really heavy. I actually dropped it and broke two toes.

Honouring great science books

The Lasker prize has form when it comes to celebrating great books. In 2012 the Lasker prize was awarded to Tom Maniatis.  The citation included this:

Maniatis created the quintessential Molecular Cloning manual—based on his own pioneering work—and thus spread revolutionary technologies into a multitude of laboratories across the world.

I wonder who should be next – what other scientists have combined great achievements in the lab with genuinely groundbreaking book publishing?

It’s interesting that the books by Maniatis and Alberts are both in the field of molecular biology. This field inspired a revolution in the way we approach biological problems and both books played their part in facilitating the spread of the revolution.

I’d like to nominate David Lipman for his work in developing the NCBI services, including PubMed. I’m not familiar with his work outside NCBI, but Wikipedia tells me that:

He is most well known for his work on a series of sequence similarity algorithm, starting from the Wilbur-Lipman algorithm in 1983, FASTA search search in 1985, BLAST in 1990, and Gapped BLAST and PSI-BLAST in 1997

Who would you nominate?

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Changing horizons

Much years. So change. Sniff. 

I have left the place where I worked for the past (almost) 27 years and I have started in a new place of work. It’s the same employer that I had before, but I’m in a new environment and a new building, with many new colleagues. I will return to the old place a few more times over the next three months but then that’s it.

I’ve never been in this position before, leaving a familiar place after so long. When I left home to go to University it was exciting with a little trepidation thrown in, but home was still going to be there to return to if I needed it. I left University with fond memories of the place and the life but I looked forward to entering the world of work.  I’ve moved job a couple more times, changing county and country, with the same mixture of regrets and excitement. But none of those previous moves felt as big a deal as this week’s uprooting from one place to another place.

In the end there were no tears, just an orderly frenzy of packing, tidying up, and making sure the ex-library space no longer looked like it was a library service. More sweat than tears.

Our crates being taken away.

My old office, emptied

I will lift mine eyes unto Mill Hill

I started at Mill Hill on 27 November 1989. My first ID card featured this old polaroid photo, taken on my first day at Mill Hill.

My photo ID in 1989

I remember that the Institute seemed full of strangeness and unfamiliar smells (particularly the pungent materials used to clean the cork floors). The Library environment was more familiar and I quickly found my feet.  On my very first day someone came along wanting an online literature search carried out (in 1989 this was a big part of my job). I was happy to find that the systems used in this Library were the same as I’d been used to in my previous job so the mechanics of getting online and carrying out a search were straightforward.  Less familiar was the subject matter – I’d been used to running searches for clinicians in a hospital and now here were researchers wanting molecular biology and immunology searches. It stretched me, but I found I could be quite elastic.

There was no internet. Email was a rarity (not to say an eccentricity). Journals were 100% printed. The online searching that I was responsible for was the most advanced service available, but CDROMs were soon to open the way to end-user searching. This led to me becoming a trainer – running search skills sessions. I quickly found my way to JANET, and new ways of connecting to people and information. A flood of new information was coming, from the internet. This was a fascinating new challenge, and kept me busy for a while.

The Library, on the fourth floor of the building, commanded fine views. On one side were green fields, on the other  suburbs and hills that just obscured most of central London. When I looked out of the window to the southeast I could see, peeping over the hill, the Post Office Tower and the NatWest building. To the southwest I could see the old Wembley stadium building. In between was the ridge of the North Downs, and on fine days you could see the Mole gap.

Today the new Wembley stadium building, with its big arch, is visible to the southwest, while several new towers are visible on the horizon to the southeast, evidence of London’s high-rise boom. The Mole gap is still there.

The Mole gap, where the River Mole cuts through the North Downs.

Natwest Tower, Gherkin, Walkie Talkie, and others

The Shard

Canary Wharf towers

But now, Lord, what do I look for? My hope is in Crick

My first day in the new building was 30 August 2016. There are no funny smells – everything is clean and the building is air-conditioned. My new photo ID leaves something to be desired, but at least there is no moustache this time.

My new photo. I look like I’ve been in the sun or had a few drinks.

After a welcome talk and obligatory safety and security talks I settled in to unpacking, putting stuff away, and sorting out IT and comms. The latter are more advanced than I’d been accustomed to and offer more possibilities for flexibility.

It didn’t take long to feel at home. My immediate colleagues have moved with me from Mill Hill, but we are now embedded within a much larger group of people.  I’ve met many of these new colleagues several times already, and have visited the building several times too (in various stages of completion). There’s no sudden change in my duties, so I have just picked up working on what I’d been doing the previous Friday. The open plan office design is different from what I’m used to, but I’m able to switch off from the surroundings and zone in to focus on what I need to.

Over lunch on the first day I met with two computational biologists – one I knew from Mill Hill, one I’d not met before was from the Lincoln’s Inn Fields site. We had an interesting chat about open access, ORCID, PubMedCentral and pseudo-repositories (e.g. ResearchGate). I look forward to more such conversations.

It will be a few more months before the Institute is complete – with all the research groups in the building and everything arranged as it should be. About two-thirds of my role is clear and defined but my challenge now is to define the remaining one-third. I need to reach up and see over the horizon again, to find the right direction for Information Services at the Crick.

 

Posted in Libraries and librarians | Comments Off on Changing horizons

Book sequences

You may have seen some of my #nimrlibrarybyebye tweets. These were a sequence of tweets showcasing books that we have been transferring to other libraries. Each tweet included a photo of a book or a handful of books. I will write a proper post about them sometime soon. The ‘byebye’ in the hashtag is to signify that nearly the whole of the library stock is being disposed of.  Transferring books to other collections means that part of our library will live on.

I’ve also been selecting things to keep (as mentioned in my recent Library day in the life post). I’ve focused quite a bit on science history – but that includes recent history such as the early days of the human genome project and bioinformatics. Related to that topic, two things in particular caught my eye down in our store.

Protein sequences – Dayhoff

Atlas of protein sequence and structure

One of these I’d seen before – it is an book of sequences. My memory told me that we had a small hard-bound book of Genbank sequences, but I must have imagined that.  The book is a softbound book of protein sequences, from 1967-68. However, I did remember the author correctly: Margaret O. Dayhoff.

Margaret O. Dayhoff was originally a physical chemist and was one of the founders in the field of bioinformatics. She created this first public comprehensive, computerised and publicly available listing of protein sequences, The Atlas of Protein Sequence and Structure. I think it started out in 1965. Read this biographical article for more details about her.

Dedication page

Mainly I’m tickled by the idea of printing sequences in a book!  I love this book because today the very idea of a book full of gene or protein sequences seems bizarre. It shows how naturally we use books to share information. There were more volumes and supplements published in this series in the next few years.

I like the image on the dedication page too – though I’m not quite sure what the origin of the sculpture depicted is.

The book later turned into the protein identification resource (PIR).

 

 

There is an interesting account in Nucleic Acids Research in 1981 of another of Dayhoff’s projects – a nucleotide sequence database which became the model for other databanks, such as GenBank.

On September 15. 1980, the Nucleic Acid Sequence Database Demonstration Project of the National Biomedical Research Foundation was made available to interested users through telephone access to our computer. Over two hundred user groups requested access during the ten months of the demonstration. …

We had been using the computer system ourselves for some time and had found that a computerized management system was essential to minimize the overall cost of collecting, updating, and critically reviewing the data.

Margaret Dayhoff was held in some esteem by her peers, and I discovered we also have a festschrift dedicated to her, a special issue of the Bulletin of Mathematical Biology.

Genbank online service – manual

 

 

 

While sorting out some old files in my office (I’m doing a lot of sorting out and throwing away these days!) I found a manual for the Genbank online service (GOS), 1992. I thought I must have thrown this away ages ago so was pleased to see it again.

I remember that the GOS was my first direct contact with Genbank. Back then I occasionally had people asking me about gene sequences. I discovered that I could search on Medline for a gene name and then identify the sequence accession number. This allowed them to retrieve the sequence from other sources. With GOS, accessed using telnet,  I was able to search GenBank directly in its most current format, and I could even get the sequence too. The interface was plain but no worse that what I was used to in other online systems.

Not long after this Gopher came along, followed swiftly by the WWW (as we called it then). These made it dead easy for everyone to find sequence information and my newly acquired skills with GOS became redundant. Information skills had a high churn rate even in 1992.

Martin Bishop’s 1994 book.  Guide to human genome computing / edited by Martin J. Bishop. London: Academic Press.

Some brave souls wrote books about sequence databases and manipulation – knowing that by the time the book appeared in print another dozen databases and software tools would have been developed. Martin Bishop, a scientist at the MRC Human Genome Mapping Project Resource Centre (HGMP-RC), was better placed than most to keep up-to-date and his was one of the first books on the subject I remember buying for the library .

Other classics were Russell Doolittle’s
Computer Methods for Macromolecular Sequence Analysis, part of the Methods in Enzymology series – vol. 266 in 1996.  And Andreas Baxevanis and Francis Ouellette’s Bioinformatics : a practical guide to the analysis of genes and proteins – part of the Methods of Biochemical Analysis series in  1998.  These days we have both of these online as ebooks.

Immunological sequences – Kabat

The other book that summoned up memories of the days when sequences were printed in book form was Kabat.  I remember the 1987 edition was an enormous book that received quite a bit of use when I first started here in the Library. I was excited when I spotted that there was a new edition in 1991 and went to some lengths to purchase a copy for the Library. That was the last edition of the book as it then turned into a database.  See this account by Martin in 1996:

“The chief drawback of this database has been that it has only been available in the form of a printed book. These data have recently become available on the global computer Internet, but no method of searching the data has, as yet, been provided. Here, the development of a specialized database program for accessing the antibody data is described. This database software has been made accessible over the World Wide Web, together with a program which allows a novel antibody sequence to be tested against the Kabat sequence database, to identify unusual features of an antibody sequence which may represent cloning artifacts or sequencing errors.”

I was pleased to see that we have a copy of each edition of Kabat, from 1979 through to 1991, on the shelves in the Library store.

Kabat – 5 different editions, 1979-1991

A longer history of Kabat appeared in 2000 in Nucleic Acids Research. This described a 30-year history, going back to 1970 when the data compilation first appeared as an article in J Exp. Med.

Elvin Kabat died in 2000, and the US National Academy of Sciences published a biographical memoir of him saying he:

was a founding father of modern quantitative immunochemistry together with Michael Heidelberger, his doctoral mentor…

The printed and subsequent Web version [of Kabat] was a pioneering effort that preceded the current GenBank database. Indeed, Kabat was also instrumental in urging the National Institutes of Health to support a national DNA sequence database and the development of sequence manipulation software.

It is salutary to think that the early 1990s were such a different world – no web, hardly any internet, email was just starting to be used.  And people thought nothing of publishing gene and protein sequences in paper format.

A page from the Atlas of protein sequences and structure

Nowadays the only reason for printing out sequences is to create a museum exhibit:

When the human genome is printed out in a series of books, the DNA sequence fills more than 100 books. Image Courtesy: Russ London’s photograph of the Human Genome in the “Medicine Now” room at the Wellcome Collection in London.

 


A couple of reviews delve more deeply into the history of bioinformatics and computational biology:

 

Posted in Books, Collections, History, Research data | 2 Comments

Library Day in the Life – July 2016

The Library day in the life project was a great way to let people know what librarians do. It was an excuse for us to document a day or week in our working life in excruciating detail and, in my case, to inflict those details on the reader(s) of this blog. I joined in the project in 2011 and 2012 but it stopped in 2012 having run its course.  I persisted and in 2013 wrote about another week of my activities. You can read my past Day in the Life posts.

Recently I was musing on changes in what I do at work, and the interesting times that I’m going through, and thought it would be good to try Library Day in the Life again. I made notes in two consecutive weeks in July and here they are. I admit there was a delay between the activities and the writing-up, so they may not feel as fresh as my accounts from previous years.

These two weeks turned out to be busy times. Getting ready to move an institute is quite a challenge.

I had several meetings with labs, helping them prepare to put old lab notebooks etc into off-site storage. I gave a couple of internal talks to key groups (management and influencers);  happily these went well. I’ve been busy dealing with printed books (selecting and disposing) and with a collection of scientific equipment. And there’s been a number of forward-looking activities, starting to move new developments forward.

My working day usually starts by me scanning an assortment of science policy and science news sources, to create the daily Research Buzz news channel for Institute staff. Most days there’s between 2 and 8 items, and sometimes items on women in science or scholarly communications (these go into separate channels). A quick summary of topics covered over the two weeks in July:

Brexit – 10 items
Other EU – 6
Careers/Life in science – 5
Stories about People/Awards – 4
Animals in research – 4
Diversity – 4
UK politics – 3
Research ethics/hygiene – 3
20 other items

Week 1. 18-22 July 2016

Mon 18 July
I read and sent a few emails about an old FACscan machine that is no longer needed. We are hoping to transfer it to the Science Museum. Some paperwork will be needed before we can confirm the transfer. The Museum is also interested in taking an old bioreactor – it’s quite a size so will be challenging.

I went along to two lab records meetings (with a PI and our Records Manager). One was very brief – the lab was relatively new so there was no paperwork needing to be stored. The other one took a bit longer, but things are under control. I received a couple of spreadsheets from labs with details of the contents of boxes they wanted to put into store. That’s my cue to start processing boxes to go into storage.

I was spurred to join a librarians’s group on Slack, after spotting an interesting-sounding tweet. I signed up to Slack a while ago but never did anything with it.  I’ll see how this group goes.

Later in the day I travelled downtown to attend a meeting of the SPOTON advisory group, helping to plan the next SPOTON conference (see their website for more details). It should be good – discussing the future of peer review.

While I was in the SPOTON meeting I checked my email and saw one about a possible OA deal with a publisher. The sender was requesting a meeting with me. Funnily enough I was in the same building, just a few rooms away from him at the time!

After the meeting I made my way to our other lab site to pick up a 30-year old lab notebook and a couple of protein models. The models are bound for our scientific equipment collection, and the lab notebook (with details of a Nobel-winning series of experiments) will be going, along with some others from the same person, to the Royal Society archives. These notebooks were nearly discarded but I managed to intervene in time to rescue them.

Tuesday 19 July
I went early to our downtown offices and worked there for an hour or two. Since I got a new laptop a couple of months back I’ve been surprised at the difference it makes. I can now easily work from any location.  I have a bit more to do to free myself from a desk full of papers, but I’m nearly there.

I am due to talk today to our Executive committee, to update them about library services. They were running a bit late on the agenda so I had plenty of time to run through what I was going to say. They seemed attentive and I was comfortable addressing them. There were one or two searching questions. “What do you fear most?” Hmmm. I suggested that my biggest fear was becoming irrelevant (so we need to work hard to counter that). Another worry was about how open access is going to play out (there is so much uncertainty still). “What about searching and data access?”  I needed more notice for such a big question but sketched some of the parameters. Later I followed up with the questioner by email – I think we might have more to talk about. Then came a surprise – it was decided that space would after all be provided in the new building for a modest collection of printed books, focused on science history/heritage and broader issues (ELSI).

After the meeting I hung around a bit longer as the Chair (the big boss) wanted to have a quick one-to-one talk.

After lunch I had a couple more lab records meetings, then met with colleagues from our Comms team to show them the scientific equipment collection.  They were making preparations to move the objects that had been conserved in Phase 1 of the project, and to appraise and select objects to be conserved in Phase 2. Then I had another lab records meeting. My working day has far more meetings than used to be the case.  Some of this is a temporary thing, concerning tasks related to the impending move, but partly it’s due to a change in my style of working.

While I was out of the office my library colleagues had been somewhat overrun by institute staff wanting to select books to take away. Today was the first day we had invited them to come and select 1 or 2 books for their personal use, as mementos of the old institute. I’d thought only a few people would come but it was pretty hectic. In one or two cases there were multiple people wanting the same book, so some mediation was needed.

In other news, someone asked why he couldn’t access an article from a particular journal. The answer was simple – we don’t subscribe to it, never have and I don’t expect that we ever will. We got hold of a copy of the article through ILL for him.

I also took one of our senior group leaders down to the Library store to help him look through some of the old parasitology and malaria books. He chose four items, including some old books on quinine (Chininum). There is still a load of fascinating material in that thar store, but it seems t’s not fascinating enough that any other library wants any of it. Quite a few libraries have visited and selected books they want, but many books remain.

Late in the day I received an email invitation to talk to our internal Science Leaders’ Meeting next week about Open Access. I’d been expecting this. They just want 10 minutes from me.

I went to the institute bar for a quick drink and to wind down after a very full day.
I got talking with someone about old books, and then about Google as a way to search for articles. I was surprised when he said that he found Google was better than PubMed. When I probed he was talking specifically about searching for known items – articles he knew existed but needed to locate. I suspect this is because Google indexes the full text of articles (I think I’m right saying that).

Wednesday 20 July

An unusual start to the day: I attended a special breakfast viewing of the John Dee exhibition at the Royal College of Physicians. It featured books from the library of John Dee, put on by the RCP Library. The viewing was targeted at librarians and included coffee and pastries, plus a talk from the curator who had assembled the exhibition. It gave me much food for thought, about the benefits of putting on exhibitions, and the large amount of work involved. The story of John Dee’s library touched a nerve – the library of about 3,000 items was destroyed/sold while Dee was away travelling.  Only a few items remain.

Back at base I had a one-to-one meeting with one of my team members.  I try to do these one-to-ones weekly now and I’ve found it’s helpful.  All part of my new way of working.

I exchanged a few emails about the list of artefacts we hold (a mixture of sculptures, paintings, furniture). Decisions will soon be made about their fate.

I’m also catching up with some loose ends of subscriptions – one book series that we used to subscribe to in print only. Last time I asked the publisher, a few year ago, the volumes in the series weren’t available electronically except as part of a bigger package. Now they are available as a series, though the price is still not cheap. I was promised a ‘special price’ for the backfile but it didn’t look very special. After I pointed this out the publisher came back offering a 15% discount.

More good news – an abstract that I’d submitted to a conference on scientific archives has been accepted. That’ll be my first trip to Heidelberg; my first archives conference;  my first time to speak in public about archives; my first speaking engagement for a while.

Finally I went along to the Internal Mill Hill lecture – given by one of our neurophysiologists. I usually find that I can follow the first 10-25 minutes of these lectures but then comprehend less and less. This talk followed the usual pattern.

Thursday 21 July
I resolved a small dispute about which lab a particular book should be located in, and checked on the availability and cost of a couple of ebooks. It’s surprising how difficult it can be to arrange for access to some books in e-format.

I have another lab records meeting.  This lab is a dry lab so you’d think they’d have no paper to speak of. The complications came from the number of visiting workers they are hosting (mostly retired scientists from other parts of the institute) and records from past PIs in the lab.

Following Tuesday’s Exec decision about establishing a book collection, I am selecting books to go into the collection. I went down to our store to pick out interesting historical items.

Then I had a catch-up phone call with my boss. The job description for a new position is just about finalised, so the advert should be issued soon.

I’ve made some progress in planning an open access meeting in October.

Friday 22 July
I received some notification that some boxes of records are ready for collection.  There is going to be a regular flow of boxes over the next few months as labs move. It will be a challenge to keep up with them.

I received a spreadsheet from our other lab site with details of boxes to be collected.  I had to spend some time working through it to put it into the format required.

Then I spent another hour or two selecting books. I choose books with scientific relevance to our current programs, or with links to key figures from the past, or topics that seem worthy of current consideration. And some that pique one’s curiosity or seem too good to leave behind.

Week 2. 25-29 July 2016

Monday 25 July

I’ve been trying to set up an institutional account with one of our key publishers, to make it easier to process open access payments to them for papers we publish. After huge delays this is now almost done. I’m looking forward to some reduction in paperwork.

I had a brief email exchange with the questioner (about searching and data) from last week’s exec. It’s good to have someone interested in such issues, and aware of a broader vision of ‘library’. He even thinks that informationists are a good thing.

Much of my current focus is on paper records from labs, but going forward I will need to be actively involved with digital records from labs. One lab that is closing down (moving to California) hit me with a question about their digital lab records. A solution seems to be coming.

I responded to a question from a lab about how they can comply with open access requirements for a paper about to appear.

I was pleased to get a response from the UKSG about an idea I’d sent in for the 2017 conference. They agreed it was interesting, but want to defer it till 2018.

Tuesday 26 July
Interested to see the Royal Society’s #Scienceisglobal campaign on Twitter. I gave it a bit of a push through our internal communication channels, hoping that some of our labs might join in. A couple of them did.

A few emails exchanged with a medium-size publisher to arrange to meet up soon and discuss some kind of deal. I’m very much take-it-it-leave it with some of these publishers, so if they don’t offer something imaginative (i.e. low-cost, low-commitment) I will not be biting.

The big event for today was a meeting of the NIMR Archives Project Committee. This was set up by the MRC to examine NIMR archive collections and discuss their fate. A Project Archivist has been appraising and listing the collections, and it is her recommendations that the committee considers. We’ve had four meetings already and have already dealt with the main collections. Today we examined several smaller bits and pieces. IN most cases t was agreed to transfer them to other archive collections, but some things will be disposed of. For me it’s always painful to agree to dispose of things. There is always some value in these documents, but sometimes it would need too much effort to extract that value. We then went down to the store, to see other personal archives in situ. These were mostly things in filing cabinets. The Ita Askonas material was particularly impressive – very detailed and neat records of experiments undertaken.

Later in the day I uncovered another drawerful of archive files. I hadn’t realised they were there.  The archivist was not best pleased.

One of our staff (who used to be the institute web manager) had selected an old book about the internet (The Whole Internet Catalog) from about 1992. She found it fascinating. I remembered that somewhere I had a copy of Brendan Kehoe’s book Zen and the Art of the Internet also from 1992. This was a free book – I remember that I’d downloaded it as a postscript file and managed to print it. I was pleased with the result and had it bound. It was a great introduction for those days when few people were excited about the Internet. I thought I’d lost it but miraculously it turned up when I was sorting through my old drawers.  I gave it to our ex-web manager and she said “This is a fabulous book! I love the quotes”.

I’m starting to think about the practicalities of having a book collection in the new building. Of course we will need some shelving, but we’ll also need some kind of classification scheme, or categorisation scheme. I think we should also give the books from the store a good clean too. And I need to think about security for the books and a lending system.

I finished preparing my talk about OA for Friday. I will focus on what Group Leaders need to do.

Wednesday 27 July

I’ve now booked my induction for the new building. I’m not 100% sure when I will move yet, but it should be just weeks away. I have to attend a building induction session before I can move in.

I spent some time processing boxes of records from the labs – barcoding them and adding the barcodes to the spreadsheets. Once you get into a routine it’s OK, but it does get a bit tedious.

I received a notification about a forthcoming paper from one of the labs.  I get these primarily so that we can advise on the open access arrangements, but I also feed anything that looks interesting through to our press office.  This one did look interesting so I forwarded it. This part of my work has massively decreased in the past 18 months. I used to do much more of this, but another department now takes the lead in publicising new research.

A member of staff is retiring on Friday after many years and there will be a bit of a do. I was asked to dig out some information about exactly who he’d worked for and in which labs during his time at the institute.

I went along to another internal Mill Hill Lecture, by one of our developmental biologists. This subject usually involves a long cast-list of genes and proteins and this talk was no exception. I struggled valiantly to stay focused.

After the talk I went along to say farewell to our Project Archivist who has found a permanent job and so leaves us today. The Project is nearly complete so she can be satisfied she has done a great job with it.

Thursday 28 July
We have started integrating our work into that of the IT helpdesk.  So when we get requests for assistance we now respond to them via the helpdesk software. It had a little glitch today and our requests were coming through miscategorised. We got that sorted out.  I think it’s good in the long run to be integrated with the helpdesk, but I can’t help having slight doubts about it, and I fear my colleagues may also see it as a nuisance. hence I try to make sure it works as smoothly as it can.

I received an email from a publisher telling about their 2017 journal collection 2017, and announcing pricing for 2017. The summer is far from over and yet here we are starting to think about 2017 journal subscription renewals already.

Another lab record meeting, and another one-to-one session with a colleague.

Friday 29 July
The next phase of the scientific equipment project started today – all the conserved objects from Phase one (150 of them) were collected for transfer to the new building. That’s a great conclusion for these historical items. Many of them have been saved from destruction several times, and without the intervention of several people (including myself) they might have ended up in the bin. Another 100+ objects are now being considered for preservation or disposal.

I had another meeting with a group leader about lab records. This lab has been around for 25 years or more, so there could be a large amount of paper. The lab head has quite a robust approach though and will only be keeping a modest amount of paper.

I have finally agreed with our off-site storage company on the format I should use for the spreadsheets giving details of boxes we are sending them for storage. Soon I will be able to arrange for collection of the first batch of boxes.

After lunch I went downtown to attend part of the Science Leaders’ meeting, and give my short open access talk. That seemed to go OK, though there was one slightly crazy question at the end from someone with a beef against open access journals. Afterwards I talked to a few people (including an interesting discussion about Otto Warburg).

Then I headed back to the institute to attend the retirement party – this person has worked there for 45 years, so it was quite a party. It also served as an end-of-term party, an end-of-the-old-institute party, an it’ll-never-be-the-same-again party.

Posted in Libraries and librarians | Tagged | 3 Comments

ReCon 2016 – my favourite small conference

ReCon has become my favourite small conference about publishing and research. It’s held each June in Edinburgh. I attended it in 2015 and really enjoyed it. There were stimulating presentations on non-trivial topics, and plenty of interesting conversations over coffee and lunch. So I went again this year with high expectations that were not disappointed.

A few librarians attend, plus many researchers (mostly early career), some publishing people and information industry people. It is more research-focused than the UKSG or R2R conferences, and (to my mind) is more focused on cutting-edge topics.  There is also a Hackday on the day after the conference but sadly I wasn’t able to attend that this year. Last year I learnt a lot from the Hackday.

Here is some of what I found most interesting about the conference. You can watch videos of the talks on the ReCon website.

Citation

Geoff Bilder (from CrossRef) is one of those people who is physiologically unable to give a boring talk. He promised us a rant but his talk, while vivid, seemed too carefully argued and well-worded to be designated a rant. He called it “The citation fetish”.  He reminded the audience that citations can be inaccurate and distorted, leading to excessive concern with impact factors, h-indexes and the like. Then he complained that these metrics have gained too much influence on decisions about research careers. So far, so familiar.

Then Geoff surprised us by pointing out that we use the wrong words in connection with citations.  When we talk about citations, we are talking about the inclusion of an article in a reference list. This is wrong we shouldn’t use ‘citation’ to denote the number of times an article is listed in a reference list. These are just references. Rather, when counting citations we should count each time an article is cited in the citing article. A cited article may be referred to several times in a citing article – but will only appear once in the reference list. This may seem a nit-picking point (I admit to thinking this) but Geoff suggested it is symptomatic of a problem with our citation habits – a concern with credit over reproducibility.

He also drew attention to ‘citation’ practice in the more informal world of blogposts. Typically a blogpost may include a link (just a hyperlink rather than a formal citation) to another web page (blogpost or something else). Sometimes a blog post may link to something which is in fact a DOI, i.e. a part of the world of formal literature. Sometimes blogposts may have more formal list of references at the end, with in-text citations. Some may include footnotes with links in.  In blogs all of these different styles of citing and linking are intertwingled (I’d not heard this word before, but apparently it was coined by Ted Nelson). As bloggers we’re not thinking that hard about how we cite/link.  We all do it, mixed up-wise.

Now Geoff got serious. He highlighted the Force11 data citation principles. The first three of these are: importance, credit/attribution, evidence. Geoff stated that the principles put too much emphasis on credit/attribution rather than on evidence (reproducibility), putting the cart before the horse.

I think this was the main point of his talk: citation practice should be at the service of reproducibility. Citing should be a way to help readers/researchers to follow through the arguments in a paper, and the execution of the research reported.

Focusing too much on credit/attribution harms this link. It occurs to me that there is a kind of diachronous Heisenberg uncertainty principle at work when we start to measure citations – the act of measuring affects future citation practice and thus deems all future measurements suspect.

Geoff enjoined us not to think magically about citations but to think critically and to doubt everything we think about citations.

After his talk I felt that we could quite profitably have sat around discussing what he said for the rest of the day. But sadly there were more talks to listen to. Luckily they were also thought-provoking.

Research data

Mike Jones (from Mendeley) had the difficult task of persuading us that we should be happy to trust his company (owned by Elsevier) with our research data.

I must confess I had missed the announcement that Mendeley now offered a data repository service.

It seems to have been around for about a year, though it was in beta for much of that time. Mendeley data is setting up as a competitor to broad repositories such as Figshare and Dryad, and will also work with Hivebench, recently acquired by Elsevier. Clearly Elsevier are putting together their own data ecosystem.

Mike rehearsed the well-known reasons underlying the current surge of interest in data sharing and data repositories. I liked his listing of the phases of data curation:

Storage (rescue) – Shared (needs incentives) – Discoverable (metadata) – Comprehensible (well-described/structured) – Valid (curation, review).

Finally, Mike mentioned that  they are developing a search engine called Data Search which will search across multiple data repositories. Jim Procter on Twitter pointed out  that its effectiveness will depend on the metadata.

I think it is useful to have another service in this general data repository space, but I think Elsevier will have an uphill battle to secure the trust of the research community. One of the questions from the audience highlighted this aspect.

Data viz

A major theme of the conference was data visualisation and there was a group of talks about this. Clearly it’s an on-trend topic as Nature also had a feature about it recently.   http://www.nature.com/news/the-visualizations-transforming-biology-1.20201

Jo Young gave an introduction to the topic, taking us rapidly through the history of data visualisation from 1786. William Playfair  invented several ways of visualising data. John Snow, with his famous map showing cholera hotspots grouped around a water-pump, was another pioneer, along with Florence Nightingale and Edward Tufte.

Jo gave us quite a broad definition of data visualisation, noting that IKEA self-assembly instructions can be categorised as such (personally I’d say they were fiction).  Others include: Barplots, Boxplots, Network diagrams, Choropleths,  Videos, Images / photos, Tables. I realised I am quite ignorant about this subject as I’d never heard of a ‘chloropleth’.

I’d never heard of Anscombe’s quartet either but Jo explained that it is a set of four small datasets having the same statistical features. However when visualised the datasets are revealed as being quite different. This provides a really persuasive example of the value of using dataviz.

Jo finished by giving some simple guidelines for designing data visualisations. She said that we are better at distinguishing different heights than different angles, so pie charts are not always the best choice for displaying data.  Other advice included:

  • consider your audience
  • focus on the substance of the data
  • pay attention to proportions and scales
  • avoid 3D, avoid colour if it’s unnecessary
  • don’t distort
  • don’t add irrelevant data
  • don’t prioritise design over data

Thus instructed in the basics, we then heard  Pawel Jancz from NumberTelling extolling the advantages of the Tableau system. It allows you to interact with your data, link to sources, publish it online. Tableau public is worth a look.

Pawel then gave some more guidelines on constructing visualisations. If interested, I would advise watching the video of this talk as it was quite visual and I can’t do it justice in words.

Next up, Ian Calvert from Digital Science told us to ignore all the guidelines we’d just heard about. We should just get on with generating visualisations. He explained that dataviz can be a tool for researchers to understand and improve their data. I’d not considered this use case before but it makes a good deal of sense.

Ian explained that visualisation can be a path to clean data i.e. to data with fewer errors, that is easy to process automatically, and easy to link with other datasets

He showed us a real example, using data about published journal articles from 1500 to present and highlighting how dataviz can make errors and anomalies obvious.

Innovations in scholarly communication

Next followed the highpoint of the conference – a detailed presentation about research software tools from a pair of Dutch info-wizards:

Jeroen Bosman and Bianca Kramer

They have been looking at tools used by researchers at different stages in the research cycle.  At first their project was called 101 innovations in scholarly communication – you may have seen the diagram they produced:

101 Innovations in Scholarly Communication

101 Innovations in Scholarly Communication: How researchers are getting to grip with the myriad of new tools. Image produced by Bianca Kramer and Jeroen Bosman.

Then the list of tools grew to 400, and now it is over 800. They have categorised each tool as either traditional, modern, innovative, or experimental and then examined whether you can characterise researchers by looking at the tools they use.

Another useful categorisation, aligned to the goals of scholarship, was their enumeration of tools as efficient, open or ‘good’ (or ‘ethical).

  • Efficient – connected tools, publish neg results, speed of publishing, standards, IDs, semantic discovery (text mining), etc
  • Open – peer review, lab notes, language (plain), open drafting, open access, CC-0/BY
  • Good – declaring competing interests, replication, reproducibility, quality checks, credit where due, no fraud

Each tool is associated with one or more stages of the research cycle, divided into 6 or 7 main stages and further divided into 30 sub-stages.

I’d seen this diagram and thought it interesting but not especially useful. Silly me. Their next step was to launch a worldwide survey of researchers (translated into 6 languages apart from English). The survey gained over 20,000 respondents, showing which tools people use.

Their data is in Zenodo and their is a data note in F1000research. Their scripts for analysing the data are also shared.

A rather cool dashboard allows you to interact with the data (though it can be a little slow).

Now they can say how many tools a typical researcher uses: the median is 22, but the distribution follows a typical bell curve, slightly skewed to a higher number.

The number of survey responses to each sub-area also shows which are the busiest in terms of tool development and use – search and write win out, peer review is least busy.

They are now starting to work on a heatmap analysis to find out which tools co-occur.

This talk started all kinds of hares racing in my mind and I advise you to read some of their material, or look at the video of the talk. They will also be presenting at Internet Librarian International in October in London.  I’m hoping to see them again at that time.

I recommend any librarian involved in publishing or research support to check out ReCon 2017 (no details yet but follow ReCon on twitter). See you there next year.

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

Important conversations and confusing journals

A few weeks back I was a roomful of senior librarians, having Important Conversations about Publishers (ICP). More recently I sat and listened to a number of ICPs at the UKSG Conference – bookended by talks from Ann Rossiter and Cameron Neylon, each with important things to say to publishers.  So far so momentous: the tectonic plates of scholarly communication are shifting and no-one is quite sure what the end result will be.

It is surprising to reflect that ICPs are a relatively recent phenomenon. Until about twenty years ago libraries’ key relationship was with their serials agent rather than with any publisher. I remember in about 1987 I had a visit from the rep for a major publisher and I didn’t really have much to say to him, certainly nothing in the ICP mold. Librarians back then did talk amongst themselves about publishers – mostly complaining about the daft things that publishers did to make librarians’ lives difficult. Generally the daft things relate to changes made to journals.

Journals can be confusing things. They differ from each other in myriad ways. They may be published monthly, weekly, semi-monthly, biweekly, quarterly, bimonthly, or at some irregular frequency (my favourite is sesqui-monthly). There may be split issues, combined issues; there may be volume numbers or not; there may be cover dates or not; the cover date may or may not correspond with the actual date of issue. We get used to all these things. And of course every journal needs its own title.

Changes can cause particular headaches for librarians, and for readers. Some changes are not too disruptive: a change in the frequency is only mildly confusing. Minor changes in title (adding a word or two) are not too troublesome, but major changes can mean that  readers fail to find the journal unless clear signposts are in place to redirect from the old title to the new title (and vice versa). In the days of print libraries could put signposts in their catalogues and lists, and even on the shelves themselves. Now we rely more on publishers to put the signposts in their websites. It gets worse when journals merge or split.

Some journals create confusion by having multiple sections, almost amounting to separate titles. One prominent example is Biochimica et Biophysica Acta (BBA). Currently it has ten separate sections, but over the years other sections came and went. On ScienceDirect about 20 different sections (past and present) are listed in total.

The confusing thing about BBA is that there is a single sequence of volume numbers through all the sections. So volume 1804 might be in one section, volume 1805 in a different section and volume 1806 in a different section again. Elsevier, the publisher of BBA, had a number of journals with this kind of structure; Mutation Research springs to mind as another prominent one.

This complex structure created challenges back in the days when we handled print issues of journals. We needed to know which issues to expect and in which sections they would fall; we had to decide how to shelve the issues (by title or by volume number); we had to decide how to bind them (different colours for each section?). All this is pretty much a non-problem now, in the days of online journals. But, as noted already, we rely on publishers websites to provide easy navigation.

This week a confused reader came seeking assistance in tracking down an article in a Wiley journal, Biopolymers. The article was in Biopolymers volume 94. Someone sent him the reference in an email, so he went to the Biopolymers website to find the article, but could not see volume 94 listed there, thus he sought my help.
bioplymer-issues

I wondered if it was perhaps a supplement volume, with conference abstracts, as these are sometimes published separately from regular journal issues. It wasn’t. As I inspected the listing of volume numbers on the website it struck me that only odd volume numbers were listed there, which seemed rather odd.

I was intrigued by this mystery. I searched PubMed and found the article listed there, then followed the link to the full-text and easily found the article on Wileys’ website.

So, I had the article but was still perplexed as to why I couldn’t see it (or any even-numbered volumes) on the Biopolymers web page.

Looking more carefully at the page for the article, I saw it had a large blue Biopolymers’ banner image at the top. But there was also a prominent red banner below it, showing the words Peptide Science prominently, and the word ‘Biopolymers’ in a smaller font running vertically up the red banner.
biopol-pepsci-banner
I looked up Peptide Science in Wileys’ alphabetical list of journals, followed the link and found all those even-numbered volumes listed, that were missing from the Biopolymers page.

peptide-sci-issues

In PubMed (and Scopus and Web of Science) all articles published in Peptide Science are listed as articles published in the journal Biopolymers. But on the publisher’s website, they are listed only under Peptide Science and the image of the cover clearly shows only the Peptide Science brand.
pept-sci-clue
That seems a bit unhelpful to me.

I see that Peptide Science is the official journal of the American Peptide Society, so perhaps that is the reason it holds fast to a separate identity. It might be better to separate from Biopolymers more completely but I guess there is some brand advantage in associating with it.

In the world where we only ever click on a link, or follow a DOI, maybe it doesn’t matter so much. But if someone emails you a reference, or you scribble down a journal reference, and then go about trying to find it you will fail.

Publishers love to claim that everything they do is for the good of the academic community.  But making it difficult to find articles, charging high prices for subscription journals, and putting barriers in the way of open access are all signs that this is an empty claim.

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