Collaboratories and clubs

Posted on August 5, 2010 by Frank Norman

I first saw the word “collaboratory” in a special issue of Science magazine in 1993 that was devoted to scientific computing. This was relatively early Internet days when we still got excited about the numbers of computers hooked up to the Internet. I recall 1993 was just at the tipping point when the World Wide Web was starting to become useful, but usable ejournals were still a couple of years away.
One of the articles1 stated confidently that researchers would be linked into “electronic communities that will create new ways of collaborating and sharing information”. These were dubbed “collaboratories”, taking the term from a report by the (US) National Research Council that had recently been issued. This report in turn took inspiration from a 1989 NSF report by WA Wulf2 where he coined the term. Wulf wrote further about collaboratories in the Science special issue3. He stated that “the essence of the collaboratory … is the software that enables scholars to use remote libraries, collaborate with remote colleagues, interact with remote instruments, analyze data and test models”.
The word popped into my head again when I saw an announcement this week about CoLabScience – a new site that aims to facilitate scientific collaborations. It grew out of communities of physics and maths but its creators say they want to make it easy for all scientists to collaborate openly online:

Our new vision for CoLab is to enable scientific debate around any piece of scientific content. We want to make it stupid easy to center a discussion around protocols, data, plots, published papers, papers in progress, simulations, code, or any other component of scientific research. As an experimentalist, I should be able to import a lab protocol, raw data, or manipulable plots based on a live feed from that raw data and discuss it online with collaborators across the globe. As a computational scientist, I should be able to import code or live simulations and troubleshoot online with anyone in the world who might be able to help. As a member of a journal club, I should be able to import a published paper and collaboratively highlight and annotate in-line with colleagues, from those in the lab next door to those in another country. As a researcher ready to publish, I should be able to host a working version of my paper online, collaboratively edit with any of my colleagues, and submit a link directly to a journal, without being forced to download the paper and make finishing touches offline. In short, as a scientist, I should be able to easily and openly discuss any piece of my science with my entire scientific community.

The key word there is “openly”. The site was featured at the recent Open Science Summit in Berkeley and it is all about sharing information in an open way. This may prove harder to realise in the life sciences than in physics and maths, just as PubMedCentral has developed along very different lines to the physicists Arxiv repository.
CoLabScience is still just a shell, with around 100 registered users, including a number of familiar names from the Science 2.0 community. The cynic in me says it is just another blip on the web 2.0 landscape that will pop up and then disappear from view (Google Wave, anybody?). Maybe it has something useful to contribute but we will have to wait and see.
I was interested to see the mention of journal clubs in that CoLabScience piece. Journal clubs have been around for a long time – Wikipedia suggests that the first one was set up in the mid-19th century by Sir James Paget, at Barts Hospital in London. The Internet has facilitated the development of online discussions around journal articles but I wonder if they are ever really successful.
Email discussion lists and web-based discussion forums can be set up, though these may be subject to the normal problems of online discussion (flame wars, trolling, lack of participation). Some journals allow online commenting on an article, which occasionally generates interesting discussion but mostly readers do not comment. Tools like Friendfeed, with its Life Scientists’ room have some success in generating online discussion.
The Good Paper Journal Club here on Nature Network relied on the enthusiasm of a few members. Its activity seems to have dried up a bit recently, with more discussion about how to publish and how to improve writing skills than about scientific papers.
A newish site is The Third Reviewer – “a forum for scientists to share opinions about recently published research”. It started with neuroscience but has recently added a microbiology section. It can’t really be called a discussion site as most papers have just one or sometimes two comments.
Another approach is taken by JournalFire, recently reviewed by Martin Fenner. This again is a web-based tool, allowing for free public discussions around individual papers. It also allows you to set up private discussions, though if the group has more than four members you have to pay for these private groups.
Martin comments:

in the end, social tools for scientists are about critical mass. It will be interesting to see whether JournalFire can attract enough users in this very crowded market.

While writing this post I consulted the Wikipedia article mentioned above, and was interested to see a 2006 article it referenced that talked about open access and journal clubs. Essentially the article was a puff piece for a new website – www.JournalReview.org:

a website forum for open peer review and discussion/criticism of medical literature. Essentially an online journal club with free membership

Interestingly when I tried to follow the link the site came up as unavailable!

1 R Pool, Beyond databases and E-mail, Science 13 August 1993 261: 841-843).

2 Wulf, William A. 1989. “The National Collaboratory–A White Paper,” Appendix A in Towards a National Collaboratory, the unpublished report of an invitational workshop held at the Rockefeller University, March 17-18, 1989 (Joshua Lederberg and Keith Uncapher, co-chairs).

3 WA Wulf, The collaboratory opportunity, Science 13 August 1993 261: 854-855

Posted in Bibliographic management, Social networking | Comments Off on Collaboratories and clubs

Genomics poetry competition

Posted on August 4, 2010 by Frank Norman

I was delighted to see a new poetry competition announced. I must confess that I am not a big poetry afficionado, but I think on balance it is a good thing and deserves to be encouraged.
The Scottish Poetry Library have teamed up with the ESRC’s Genomic Forum to establish a genomics poetry competition. The Scottish Poetry Library’s blog gives brief details:

  • Write a poem of no more than 50 lines on the theme of ‘improving the human’.
  • First prize is £500, 2nd is £200 and 3rd is £100.
  • Entry is free!
  • The deadline for entries is 7 October 2010 (National Poetry Day)
  • The judges are Gwyneth Lewis (Wales’s National Poet 2005-06), Peggy Hughes at the Scottish Poetry Library, and Professor Steve Yearley, (director of the Genomics Forum).
  • Poems should not have been published or accepted for publication elsewhere.
  • Entrants can be of any nationality. Entrants can only submit one poem.

Full information and rules are on the Genomics Forum website.
I wonder how many poems they will receive that look like they were composed on Viktor Poor’s genetics keyboard .

Posted in Writing | Comments Off on Genomics poetry competition

Confusing icons

Posted on July 30, 2010 by Frank Norman

In the good old days of Windows 3.1 I used to just have one or two web pages open at a time – sometimes more if I was feeling daring. Now I seem to have about 20 tabs in my main web browser, and half a dozen more in various other web browsers. Hence the favicons that appear on the browser tabs are an invaluable guide when I am trying to find a web page I know I have open. The titles of the pages just don’t help when there are so many pages as each tab has only a small bit of real estate in which to display.
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More and more websites use these little icons now, and of course it gets harder for web managers to create a distinct icon for their site. Designing in 16 x 16 pixels is quite a challenge. Hence I keep getting different icons mixed up. I regularly get confused between Google and the Guardian:
favicon-google.jpg
My worst confusion is between Mendeley and Nature Network, with Seesmic more distinctive but bearing a vague similarity.
favicon-mendeley.jpg favicon-NN.jpg favicon-seesmic.jpg
What are your favourite look-alike favicons? Or is it only me?

Posted in Froth | 4 Comments

Publish and be jailed

Posted on July 27, 2010 by Frank Norman

I read an interesting account of the recent arrest of a research chemist in the USA. Chemical and Engineering News reports the case of Ke-xue Huang, a former Dow AgroSciences employee, who was arrested by the FBI for “theft of trade secrets to benefit a foreign government” and “foreign transportation of stolen property”. The bit that caught my eye was this:

the case centers on the disclosure of confidential Dow information on spinosyn insecticide biosynthesis in a review article first published online in late 2008 (Appl. Microbiol. Biotechnol. 2009, 82, 13).

and

In the process of writing the article, Huang is alleged to have passed along confidential information. “The grand jury found probable cause to believe that Defendant conveyed trade secret information to others in the People’s Republic of China,” U.S. attorneys wrote in a legal memorandum. They have requested that the court limit Huang’s access to the Internet and direct him not to contact certain possible codefendants or witnesses.

Obviously without knowing the details of the case it is difficult to comment much on this, but it seems a bit odd to me that a review article would disclose confidential information as it is presumably just reviewing information previously published elsewhere.
The article mentions that penalties include fines of up to $500,000 per offense and imprisonment for up to 15 years.
Perhaps this is an object lesson in the importance of intellectual property savvy – knowing what you can say (write) and when and to whom.
Most researchers will not end up in prison for getting it wrong, but failure to get a patent can be costly.

Posted in Copyright and IP | 3 Comments

Looking at an old funding decision

Posted on July 26, 2010 by Frank Norman

A historical article by Martin Johnson et al in Human Reproduction gives a fascinating insight into research funders’ thinking nearly 40 years ago.
In vitro fertilisation (IVF) is widespread these days but still manages to excite controversy in some quarters. Back in 1971, when Patrick Steptoe and Robert Edwards submitted a proposal to the MRC, many people had misgivings about IVF including eminent scientists such as Jim Watson. Johnson and co-authors have used archive material and interviews to examine the background and reasons for MRC’s refusal to fund their project. Johnson lists four key reasons for the rejection, and it is interesting to see how science, ethics and research strategy are all components of the decision.

  • A strategic error by Edwards and Steptoe when they declined an invitation from the MRC to join a new, directly funded Clinical Research Centre at Northwick Park Hospital, Harrow. They preferred to ask for long-term grant support at the University of Cambridge, but this meant they had to compete for funding with all the other research projects bidding for MRC support. This was also difficult for Cambridge, which lacked the back-up of an academic Department of Obstetrics and Gynaecology at that time.
  • Most of the MRC referees who were consulted on the proposal considered, in line with government policy, that it was more important to limit fertility and the growth of Britain’s population than to treat infertility. Treating infertility was seen as experimental research rather than as therapeutic.
  • Concerns about embryo quality (would babies be born with severe abnormalities?) and patient safety made the referees doubt the wisdom of funding embryo transfer without conducting studies in primates first.
  • Edwards’ and Steptoe’s high profile in the media antagonised the referees who strongly disapproved of this method of public discussion of the science and ethics of treating infertility.

Edwards and Steptoe vividly describe in their 1980 book1 the story of how they rose above this setback and successfully saw the first baby born following IVF. My favourite part of that book is Edwards’ description of his time at Mill Hill, in particular this bit:

First, I had to check the scientific literature to set the background. Upstairs in the Mill Hill Institute there is a very spacious, comprehensive library. I sat there amongst the polished tables reading the journals hour after hour. One morning in the quiet of that comfortable library, as I read one particular paper I stopped reading and said quietly, ‘Sod it’. I looked up. Nobody had heard me. Nobody in the library at that particular moment was aware of my sudden disappointment. For I had just learned that my discovery was not new.

Of course times have changed and as everyone now reads papers from the comfort of their desktop/iPhone/iPad, I no longer hear a chorus of ‘sod it’ and ‘Eureka!’ coming from the library.
A press release, plus coverage in The Independent give details if you can’t access the article itself2.

1 Robert Edwards & Patrick Steptoe, A matter of life, the story of a medical breakthrough, Hutchinson, 1980.

2 Martin H. Johnson, Sarah B. Franklin, Matthew Cottingham and Nick Hopwood. (2010) Why the Medical Research Council refused Robert Edwards and Patrick Steptoe support for research on human conception in 1971. Human Reproduction, epub ahead of print doi:10.1093/humrep/deq155.

Posted in Ethics, Research Councils, Research management | 5 Comments

Copyright, data and research

Posted on July 23, 2010 by Frank Norman

I have written on copyright before. It is one of those things that are important but very hard to raise much enthusiasm about. Praise is due therefore to the British Library for their latest effort.
They have just released a report on copyright and research – highlilghting its importance for researchers. It asks whether current copyright law is a help or a hindrance to UK research, and has one-page contributions from a range of people – researchers of various disciplines, intellectual property experts and journalists. They look at how the framework for intellectual property needs reviewing for the digital age. It is interesting to have such a broad range of opinion from academia.
Cameron Neylon is one of the contributors along with Jeremy Frey (Physical Chemistry, Univ Southampton), Dave Roberts and Vince Smith (both taxonomists at the Natural History Museum) all writing from a science perspective. Issues they highlight are the use of graphs and figures and access to the underlying data, text and data mining, and scientific publishing.
The report says it aims to

present the ‘grassroots view’ of the UK’s copyright framework and ideas on how it could be updated to work in this new and changing environment. There is a consensus that the laws on copyright and their interpretation must be redefined in the context of a modernising world and developing research techniques

It is just 20 pages long and worth a read or skim – just look at the three pages from a science perspective if you’re short of time.
Driving UK Research. Is copyright a help or a hindrance?)
Meanwhile, an article in Science by an intellectual property expert looks at current and changing practice around the release of scientific data.

Researchers must disclose their data in order to achieve recognition and to enable others to test, validate, and challenge their hypotheses. he traditional practice has been to contribute experimental and observational data to the commons when, or shortly after, the analysis of that data is published…Many traditional data-sharing practices were challenged, with significant and lasting effect, during the race to sequence the human genome.

He concludes that

The key to developing successful information commons is striking the appropriate balance among competing objectives. Commons weighted too heavily in favor of data users are not likely to attract sufficient contributions from data generators, whereas commons weighted too heavily in favor of data generators may not optimally advance the interests of science or the public.

Continue reading →

Posted in Copyright and IP, Research data | Comments Off on Copyright, data and research

Librarians and what we do – conference musings

Posted on July 21, 2010 by Frank Norman

I have just returned from the Health Libraries Group (HLG) Conference held at the Lowry Centre in Manchester Salford. I don’t often go to this biennial event, though I am a member of the Health Libraries Group. I am not really a health librarian so I have only a few shared interests with most members, who are concerned with the NHS and healthcare information. My concerns are focused on the MRC and biomedical science – “proper” research don’t-ya-know. Much of the conference passes over my head therefore, but I did find some papers of interest.
What is health information? asked Lyn Robinson from City University, refining this as “what is it about what we do that defines us as librarians?” She suggested that our distinguishing feature is our concern with the information communication chain from end to end, creation > dissemination > organization > indexing > retrieval > use. She characterized our interventions in the chain as domain analysis: historical studies, bibliographies, resource guides, information retrieval and bibliometrics all fall under this title.
She suggested that we are not tied to particular formats, which may come and go (microfiche, anyone?) or particular techniques (who remembers peek-a-boo cards? Apparently they were in use at MRC HO in the early 1980s). The thing that defines us, and that doesn’t go away, is this information communication chain. I would add that sometimes we do have to get into the nitty gritty of particular formats and techniques, and we need to cut through the Gordian knots that the chain can get itself into, to ensure that the information does keep on flowing. [Hmm, not sure that metaphor quite worked …]
The idea of domain analysis also intrigued me. My own minuscule contribution to the conference was a spot helping to publicise some bursaries that are being offered in memory of Leslie Morton – a great medical librarian bibliographer who was professionally active for an extraordinary 80 years until his death in 2004. He was my predecessor-but-one as librarian at NIMR, so I knew him a little. His interests were in medical librarianship, bibliography and medical history, so all fit into the category of domain analysis.
Andrew Booth looked further at this question of librarians’ expertise. Inspired by the premise of evidence-based medicine (viz that the competence of medical doctors decreases with years of experience), he decided to see what was known about the skills of expert versus novice librarians. Most of the studies he found concern expertise in searching, and quite a few of them compared librarians’ skills with those of novice or expert users (mostly clinicians, I think).
He commented that generally to be considered an expert you need ten or more years of experience in whatever it is you are expert in. But, surveying the 79 library skills studies he identified, it seems that it takes only between 4 and 8 searches to become expert. This is a bit of a blow to our self-esteem. Where expert librarians win out over novices is in their mental models of the information landscape, and their ability to structure, evaluate, select and filter. Also experienced librarians had better communication skills, helping them to better identify the information need. Andrew was presenting preliminary results but I will look forward to seeing his full analysis.
This stuff about age and experience seems relevant elsewhere too, as some suggest that scientists’ best work is done before they reach 40. I wondered too whether the Im-a-scientist project might reveal any age-related differences – that was about understanding questions and providing answers, a little like literature searching.
Another interesting presentation was from Tony Warne (Salford University) who took us on a journey through learning and thinking. He suggested that ‘not knowing’ is better than ‘knowing something that may be wrong’ (I’m not sure about that, as it suggests the possibility of absolute certainty about truth. Surely there is always the possibility that something you know is wrong?). He described learning as what happens when you are on the edge between knowing and unknowing. ‘Not knowing’ is more important than knowledge in enabling learning and you have to allow yourself into that ‘not knowing’ space as it leaves you room to develop insights.
This all sounds a bit hippy (he did have a pony tail and his website uses black backgrounds) but I think it makes sense. It chimed with something a later speaker said about the need for librarians to go outside their comfort zones in order to seek out new areas of work. Exploring things I don’t really know about but that seem linked to my work is something I have always believed in (hence why I am here on NN).
Tony Warne went on to describe his weekly blogging practice, looking back at the past week and thinking laterally, visualising and Googling to link his ideas into a trail of consciousness. He described Google as a tool to remind yourself of what you know but forgot that you know. It struck me forcibly that in this chain of communication there is little room for librarians to intervene or analyse any domains.
The final session to which I paid any attention (in one earlier session my notes just say (LOSING THE WILL TO LIVE) was one that I was chairing, so I was focused more on the number of minutes than on the content. I enjoyed a description of using Library Thing to create a curated list of recommended books, and a description of a four-person group blog on health informatics. I asked the latter speaker what he thought about the pros and cons of community blogging platforms, but it seems there are none of these in the library blogging world. Perhaps that is a good thing.
If you want to see more you can check out the conference tweets at #hlg2010 .

Posted in Education, Libraries and librarians | 5 Comments

Strength and grace

Posted on July 16, 2010 by Frank Norman

Tonight I have the privilege to take part in a performance of Mahler’s 8th Symphony at the Royal Albert Hall in London. I will be singing in the Crouch End Festival Chorus, joining the BBC Symphony Chorus, Sydney Philharmonic Choirs, a trio of boys’ choirs, the BBC Symphony Orchestra, 8 soloists and not forgetting the majestic Albert Hall organ, to perform this work on the first night of the Proms. The concert was sold out within a shore time of booking opening, but you can still attend if you are prepared to queue on the day, or you can catch it on BBC TV and radio.
I love this music. It is robust and emotional and uplifting. Some may dislike what they see as it’s gigantism – not for nothing is it nicknamed the Symphony of a Thousand. It is true that there are moments of unimaginable strength that blow your head off and dissolve your mind. But it is surprising how much of the music is for small scale forces that delight the ear – just a small group of singers with harmonium and harps, or a soloist with a few strings and mandolin. There is much grace in this music as well as strength.
We have had several large scale rehearsals. In a work on this scale, bringing together different groups to work together, there is an added challenge for the conductor. It’s not just rehearsing the music but making sure we all sing together the same way, despite our size. It needs an exceptional conductor to bring this off. Exceptional people taking on big challenges are not confined to music, as we have seen this week. I think that managing an institute of 1250 people will also entail managing small teams as successfully as the whole entity. Perhaps we should call UKCMRI the “Institute of 1200”?
But I digress. After a 6-hour rehearsal last Saturday, in a venue next door to the Wellcome Trust, some of us retired to a very fine pub called the Bree Louise. It used to be called The Jolly Gardeners and has connections for me.
In 1994 I gave a talk in the Wellcome building to a librarians’ workshop, about biomedical information on the Internet. I had been doing quite a bit of poking around on the Net and had amassed a goodly portfolio of useful sites. It was clear that this Internet thing was going to become significant for providers of information and i was keen to share this fact. The workshop organizer, John Cox, was one of the librarians at Wellcome and took me and four others to The Jolly Gardeners afterwards. Over a few beers the six of us agreed we should work together on a funding bid to create an online subject gateway to biomedical Internet resources. The bid was successful and the OMNI service operated for several years before ending up as part of Intute.
That was my first and only foray into external funding bids. I remember the great feeling on hearing that we had won the funding, followed by the realization that now we had to deliver what we had promised (and we had promised some things we were not sure we could deliver!). John Cox was the first project manager but he left for greater things after a year or so. His replacement was Sally Hernando, who I just learnt this week died from cancer in January. She was my age so it shook me a little.
Coming in as a new manager of an existing project is a tough call, but Sally was a tough lady. She was short in stature with fine facial features and a charming Yorkshire accent. She was also very astute and hard-headed, able to cut to the important issues and resolve them even if it meant telling some uncomfortable truths. I hope I learned something from her. I admired her courage back then and was grateful for her good humour. I think of her as a tower of strength but also a very gracious person.
Sally left Wellcome and moved into a strategic library role for NHS South West, where she made a very big impression. There are a couple of nice tributes to Sally from her colleagues – one free and one needs a subscription.
I shall think of Sally as I sing the closing section of Mahler 8 tonight. It sounds better in German, but here is a translation:
Everything perishable is merely an image
The unfulfillable – here it becomes actuality
The indescribable – here it is performed
The eternal essence of womanhood leads us aloft

Posted in Friends, Music | 4 Comments

Prizes and anniversaries

Posted on June 11, 2010 by Frank Norman

Yesterday I attended BioMedCentral’s 10th anniversary celebrations and research awards. Yes, it is a whole ten years ago that Vitek Tracz created his novel publishing business model of “author pays” open access, or “gold” open access as it is sometimes known. At the time it excited quite a bit of discussion (e.g. this message and others in the thread) and I suspect that many people thought it was a crazy idea. BMC has had a few ups and down since then – raising its prices and changing the way that its membership subscriptions worked, then being bought up by one of the big commercial publishers – but it has survived and appears to be moderately successful. So, I think congratulations are due to the BMC team. The model they pioneered has been successful and has been taken up by a wide variety of publishers, even our own dear NPG (though perhaps not as widely as some would want).
Congratulations are due to BMC not least for throwing rather a good party, at the top of the Gherkin building, giving me an excuse to post a few photos here. Sadly it was rather a gloomy, overcast evening so they are a bit grey.
roof.jpg
Roof of the Gherkin building
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View from the Gherkin
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Another view, showing Tower 42
The BMC research awards were also presented, with Matt Cockerill doing his best Jonathan Ross impersonation and a host of luminaries announcing the prizes: Tim Hunt, Richard Smith, Peter Murray-Rust, Cameron Neylon, to name a few. The list of prize-winners is on the BMC website. I didn’t receive a prize, in case you were wondering. Neither did another NN reprobate regular who was there:
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Graham Steel – looking scary
I don’t know how many other publishers award prizes for papers they publish, but it is a nice idea. PNAS have their Cozzarelli prize. The 2009 winners were announced recently. I’m not aware of any others.
Anyway, here’s to the 20th anniversary party in 2020. I’m putting the date in my Google calendar.

Posted in Open Access | 6 Comments

From Sci-Mate to Mendeley – a brief history of reference managers

Posted on June 8, 2010 by Frank Norman

This is an edited version of an article I wrote for the April issue of eLucidate, the UKEIG Newsletter.
The bibliographic reference is the foundation of scholarship. A reference is a surrogate for knowledge, a surrogate for research results that have been condensed into a journal article and then stored in the minds of scholars. Reference management therefore is all about knowledge, though we librarians sometimes forget that.
In the early days the main functions of personal bibliographic database programs were to provide a readily-accessible and searchable store of knowledge, and to act as an index to a reprint collection. Until the early 1990s [1, 2] these remained the main reasons for wanting to use such programs. Annotating and subject tagging references were important functions, but bibliography production was relatively unsophisticated. This was the era before end-user online searching so having access to your own personal database on your desktop was an advantage. The tools available at this time emphasised information storage and retrieval.
During the 1990s networked desktop access to major bibliographic databases became common and personal word processor packages were widely adopted. These two developments led to changes in personal bibliographic software usage. Facilitating the production of a bibliography in an appropriate format became the strongest reason for maintaining a personal database. Why bother creating your own comprehensive personal database to search when the whole of PubMed is available to search from your web browser? Hence, the knowledge component of reference management was pushed aside and we focused more on the notation of the reference – the arcane codes that we use to refer to documents – and on the mechanics of bibliography assembly and production, integrated with the process of writing a manuscript. A large number of programs competed in this market but two programs became dominant – Endnote and Reference Manager – both owned by the same company. In UK Higher Education site licences covering both products became available and we thought we had the situation covered. But nothing stands still, and a new trend emerged towards online bibliographic management tools.
Endnote produced a web-based version called Endnoteweb. It was originally a cutdown version of the main program, and is still less functional than the desktop version of Endnote. A new product called Refworks was designed from scratch as a standalone online tool. Endnoteweb and Refworks have been competing with each other in the last year or two, launching new versions at a frightening pace. Both are still primarily about bibliography assembly, I feel, but a new generation of bibliographic social bookmarking tools have put knowledge back at centre-stage, Bibliographic social bookmarking is the next wave of bibliographic management.
Eva Amsen a couple of years back pointed out how the adoption of bibliographic social bookmarking could work to the benefit of scientists, comparing it to the way that Flickr has become a large repository of images. Programs like CiteULike, Connotea, Mendeley and Zotero are at the heart of this trend. They vary in functionality but are all free and have grown into the bibliographic world from the web world, whereas the more established products (Endnote, RefWorks) have gone the other way. Connotea and CiteULike are both supported by major publishers; Zotero is an open-source product supported by a US university; Mendeley is a start-up company that has been successful in raising venture capital. These tools have many users now – Mendeley claims to have 8 million references shared, with 100,000 users.
These new tools have also been marketed at scientists and researchers directly, bypassing library support. Librarians need to become familiar with these tools, embrace them if they are useful, and ensure that the tools’ developers are aware of the role of libraries in providing institutional support for bibliographic management for researchers and students.
Libraries have started to take note of these tools. In 2008 in the USA the Northwestern University Library organsed a workshop called CiteFest to compare established tools like EndNote and RefWorks with newcomers such as Zotero, CiteULike and Connotea. Attendees worked through a series of exercises to test the functions of each product. Citefest declared Zotero the winner of their challenge. In 2009 Martin Fenner and I helped to organise a workshop held at University College London, Bibliographic Management meets Web 2.0. It focused on the needs of researchers, who are heavy users of these tools. Representatives from six of the online bibliographic management tools put their products through their paces and attendees had a chance to try some exercises (different from but inspired by the CiteFest exercises). Martin summarised the day on his blog, diplomatically suggesting that since “all the reference managers demonstrated were up to the challenge (though Connotea and CiteULike couldn’t put references into a Word document) it would be wrong to declare a winner”. My own feeling was that Mendeley made the best showing. Martin also pointed out that “the market is developing so fast, that a feature comparison will look very different in 12 months time”. Martin’s comparison chart shows the features of all the products (and others too) in a simple visual way.
Early in 2010 Innovations in Reference Management was held. This event, IRM10 for short, was organised by the TELSTAR project “to showcase and discuss innovative ideas and developments in the use of Reference/Bibliographic Management software.” This featured several of the same products again, but also included some usage case studies. The TELSTAR project is subtitled “Integrating References and Citations into Learning Environments” so it is mainly concerned with student needs. Recently TELSTAR released software that brings the functionality of RefWorks into the Moodle virtual learning environment
TELSTAR are running another event later this month, and Martin Fenner will speak at this, bringing a researcher’s perspective. He gives a taster of his talk in a recent blog post.
Portability is now a key requirement for bibliographic management tools, so we are all looking for online tools that are flexible and easy-to-use. We also want tools that support interaction with research collaborators. Easy sharing of references and the ability to tap into community knowledge is an interesting development but it has not yet become a ‘must-have’ feature. It may not be easy for the new generation of online tools to wean us away from existing tools, but since the new tools are mostly free-of-charge they come with a low barrier to adoption.
We like to use tools that save time and money. I have found that there is great interest in Mendeley at our Institute. People try it out and like it. Ten or fifteen years ago there was a steady drift from other reference tools towards Endnote. Endnote was the tool of choice for biologists. I think we are seeing the start of a similar drift away from Endnote towards Mendeley.

1 Thomas E. Wolff, (April 1992), Database, pp 34-39. Personal Bibliographic Databases: An Industrial Scientist’s Perspective.

2 JHRD Correia, (1990) CABIOS, 6(2), 126-7. Management of personal bibliographic reference using a simple database program

Posted in Bibliographic management | 5 Comments