Not another new open access journal

Posted on June 29, 2011 by Frank Norman

Or, rather, not just any other new open access journal. The Wellcome Trust, the Max Planck Society and the Howard Hughes Medical Institute have announced that they are to launch a new top-tier open access journal for biomedical and life sciences research. The first issue of the journal, whose name has yet to be decided, is expected to be published in the summer of 2012. The journal will accept submissions from any researcher, not just those funded by the three founding partners.

Some of the key features and innovations are:

  • editors will be highly regarded, experienced and actively practising scientists
  • fair, swift and transparent editorial decisions followed by rapid online publication
  • open and transparent peer review process – for transparency, reviewers’ comments will be published anonymously
  • papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments
  • an opportunity to create a journal and article format that will exploit the potential of new technologies to enable improved data presentation
  • the journal is considering whether to pay reviewers

One other big difference is that there will be no publication fees. No subscription costs, no publication charges, just supported by the three funders. That may change in the longer term but for the immediate and medium term there are no fees.

This is a surprising business model and has led some commentators, such as Declan Butler from Nature News, to question the rationale. Despite describing himself as an OA supporter, Butler has previous form as an outspoken critic of open access publishers, so his opposition to this development is not very surprising. Here is an excerpt from his recent post, in which he asked Mark Walport, Wellcome Trust supremo, about the new journal’s business model

“the PLoS model has shown that having a stable of journals provided the ultimate sustainability, and in the long term we will be looking to develop a sustainable model,” replied Walport. In the meantime, the three agencies would pay for everything — a non sustainable model — with no author charges at all being required. How much in dollars this support would amount to Walport wouldn’t say, only that they would “fund it sufficiently to do its job well.” So they are heftily subsidising it, but have so far committed only to cover the costs of launching the journal to ensure its a success. What happens after, who will pay, and what business model it will have remains unclear.

News about the development has been bubbling under the surface for the last twelve months or so. The Medical Research Council has no involvement, so far as I know, presumably because the new journal could be seen as unfair competition for commercial publishers and therefore not an appropriate way for a publicly-funded organisation to spend its money.

There was more of a welcome for the new initiative over at Science, which reported the news fairly dispassionately. They quote Michael Eisen, a PLoS co-founder and board member, saying that

there are a lot of things fantastic about this. The instinct here is that peer review needs to be shaken up.

Cameron Neylon, again unsurprisingly, comes out strongly in support of the new journal. On his blog he observes that the top of the journal pile has remained firmly in the grip of Nature, Science, and Cell and also comments drily that

scholarly publishing has never really had a viable business model, it has had a subsidy from funders. Part of the problem has been the multiple layers and channels that subsidy has gone through but essentially funders, through indirect funding of academic libraries, have been footing the bill.

Hence, he argues, this move makes a good deal of sense.

Government funders are mostly constrained in their freedom to act but the Wellcome Trust, HHMI, and Max Planck Society have the independence to take the logical step. They are already paying for publication, why not actively support the formation of a new journal, properly open access, and at the same time lend the prestige that their names can bring?

Posted in Journal publishing, Open Access | 4 Comments

Google: how to un-personalise your search

Posted on June 29, 2011 by Frank Norman

Google never stands still. It is forever seeking to improve the way it tries to match your search request to its database, and then to show you potentially useful websites. Mostly we are not aware of how it does this, or when it makes changes to its methods. Since the launch of Google instant last year, though, it has become more obvious that Google is doing something more than just searching – it tries to guess what you want to search for before you have finished typing in your search. It knows your mind better than you do yourself! This can be useful when it works but damned annoying when it doesn’t. It reminds me of Microsoft’s infamous helpful paperclip, the Office Assistant (except that was damned annoying 99.99% of the time, at a conservative estimate).

Another Google feature that can be a help or a hindrance is personalisation. In theory it sounds useful – it helps to ensure that the results you see from Google are tailored to your needs. But in practice there can be downsides, as blogger Cyrus Shepard has pointed out recently:

[personalisation] creates a real risk of limiting our worldview. Every new search result starts to look like the search before. Our ideas become isolated and homogenized, like exclusively watching only Fox News or MSNBC, while refusing to consider CNN. There are times when personalization and localization work well, such as when I’m looking for a pizza restaurant in Seattle. The maddening part is, what if I want to turn it off? There are times when I want unbiased results not based on my past search history, my location, or what my social circle has shared.

He goes on to share some tips on how to switch off the Google personalisation features. Worth a look.

[Added 1 Jul, 08:30. Oops – I forgot to include the link to Cyrus’ blog post.

Meanwhile, watch this space for more news about Google’s plans to take on social media giant Facebook.

Posted in Searching | Tagged , | 4 Comments

Elsevier and the executable paper

Posted on June 13, 2011 by Frank Norman

Have you ever wanted to make your paper come alive with data? The results of a recent competition may help that to become a reality.

Elsevier are fond of tapping into the scientific community’s ideas on the future of publishing. A few years back they issued a grand challenge on ‘Knowledge enhancement in the life sciences‘, and also had a contest about the article of the future, or ‘Article 2.0’ as they called it. They have another competition running right now to develop library and searching apps on their SciVerse platform. And they have just announced the winners of the Executable Paper Grand Challenge.

Now, I’m sure there are plenty of papers that should be executed, or made to disappear, but this challenge was not about those. The competition was intended to address the problem that computer science research results can be difficult to reproduce. Paper is a static medium and most current electronic journals reproduce that quality by relying on the PDF format. The Beyond the PDF project is looking to address this problem, and various publishers are trying things out too.

The first prize (US$10k plus an iPad) in Elsevier’s competition went to a Polish team, with a US collaborator, who developed a system (called the Collage Authoring Environment) which “allows researchers to create papers by combining narrative discussion with snippets of executable code”. Second prize went to a Dutch-German team that developed a “web portal for creating and sharing executable research papers”. Third prize went to a US team for their “universal identifier for computational results”. Papers describing the winning entries have been published in an Elsevier journal (see links on the competition home page).

Although the competition sounds at first to be just about publishing computer science, I was interested to see that the winning entry does address itself to the wider world of publishing scientific research and the question of research data accessibility. The introduction to their paper says

Furthermore, the actual data which is the result of (and frequently the basis for) published research is not preserved and made accessible in a coherent manner – thus, the reader of a scientific paper must often take the author’s word that the professed results and conclusions are, in fact, valid. Clearly, the scientific paper itself no longer conveys sufficient information to enable reviewers and other readers to judge it on its own merits.

The paper also includes a nice review of current trends in scientific publishing, including a poke at Web 2.0, noting tartly that

…naïve approaches to sharing and reusing are insufficient and inappropriate in the realm of science.

I do not know enough about other work going on this area to be able to judge whether Collage will be the system that finally makes it possible to combine narrative, data and processing all in one place, but I look forward to the day when this can happen.

Posted in Journal publishing, Research data | 2 Comments

The challenge of going beyond

Posted on May 17, 2011 by Frank Norman

Change is a natural part of life so resisting it has always seemed futile to me. My hair falls out and turns grey and I prefer to just accept that it has happened rather than to wear a wig or dye my hair. But sometimes change happens and we feel regret for what is lost in the process.

The move from print to electronic journals has been embraced enthusiastically by scientists. They love the speed and convenience of instant desktop (and even mobile) access, and the flexibility of searching and linking. But this week two separate people have commented to me what a shame it is that they can no longer flick through print journals and chance upon unexpectedly interesting papers.

So, here’s a challenge – how could we (we being libraries, publishers or readers) recapture that feature of serendipity? In an earlier post I noted how lecturers are frustrated that their students do not read more widely, and one comment suggested that academics in general have a narrow range of reading. Specialisation and the growth in the volume of literature have combined to make a wide reading habit a challenge for all but the speediest of speed readers. The poor browsability of electronic journals and consequent lack of serendipity accentuate this trend.

There is nothing new about this. The SuperJournal project 15 years ago noted the importance of serendipity when browsing print journals. A 2002 study into the effect of journal format on use stated

current electronic formats do not facilitate all types of uses and thus may be changing learning patterns as well

noting that

these data also have implications for publishers and educators;

An editorial in Nature Genetics about research creativity reported a scientist saying

we should not lose paper journals for browsing; [they have] an effect on serendipity

Printed scientific journals are a thing of the past; I cannot envisage the change from P to E going into reverse. So, what can we do to ameliorate these alleged consequences of reduced serendipity and impoverished reading patterns?

Some ideas have a ring of job-creation-for-librarians, and harking back to print. The blog post,
Seven Ways to Add Serendipity to Your Research in the Digital Age, suggests browsing library stacks, browsing in the library catalogue, or asking a librarian, along with recommendations to use browse functions in databases. I like the title of another blog post: Add a little more random to your product. We want a reading list to be in between boring predictability and total chaos, it suggests, citing the iPod shuffle as a useful model.

I wonder whether services like Faculty of 1000 and Mendeley have a role, but they are both based on peer recommendations, rather than off-the-wall suggestions. I haven’t used StumbleUpon but perhaps a science version of that would be the answer. Maybe it already exists? For myself, I have found that Twitter is quite a good way of stumbling across things of interest, though there is a danger of straying into chaos.

Do you think that technical solutions (improved online browsability or greater search randomness) or social solutions (more incentives to wider reading) will work? Is the semantic web (semantic journal, semantic article) a solution? Is the whole thing a non-problem?

I’d be interested to hear your views.

Posted in Information skills, Journal publishing, Scientific literature, Searching | 21 Comments

News can be very odd sometimes

Posted on May 12, 2011 by Frank Norman

Three news stories this week made my jaw drop, my eyes widen, and my reservoirs of mirth overflow (though not all at once). Maybe they shouldn’t make me laugh but these stories are just rather odd.

Rome earthquake
The BBC website stated earlier in the week that:

Thousands of people are reported to be staying out of Rome for the next few days, over fears the city will be hit by a huge earthquake. The panic was sparked by rumours that seismologist Raffaele Bendandi, who died in 1979, predicted the city would be devastated by a quake on 11 May.

Others say there is no evidence that Bendandi ever made such a prediction, much less that the prediction was correct. The Spoof, a satire site, ran a humorous version of the story. Now that 11 May has passed with no news of any Roman earthquake (though there was one sadly in Spain) those people who fled the city must be feeling a bit stupid. OTOH, if someone says there is going to be an earthquake perhaps it is rational to flee?

Morgellons
Even stranger was the story in the Guardian about an alleged epidemic of itching. Sufferers claim that the itching is a result of morgellons syndrome, though they are not clear what causes it – the article suggested alien matter, fungus and parasites among other things. Others suggest that a more likely explanation is DOP, or Delusion of Parasitosis. The Guardian article is a bit sensationalist, to my mind. It has a very long comments thread, mostly poking fun. Wikipedia has a reasonaby calm piece about Morgellons, noting the role of the internet in spreading belief in the condition. I note that there is even a Morgellons Research Foundation.

Bees
The Nature News blog had the story of the stolen bees:

Several thousand lab honeybees were stolen from a facility outside a Scottish hospital on Sunday…Two middle-aged men in a white van were seen pulling up beside the hives … clearly whoever did this knows what they were doing and how to handle bees. One of the suspects also sported a bonnet.

A bonnet??? That just sounds a bit odd to me. And then NatureNews did a naughty thing, finishing their story with:

No word on whether the police plan to organise a sting.

Well, that sent the comments into a frenzy of pun-making:

  • I just can’t bee-lieve it.
  • This story is sure to create a huge buzz
  • I already read this story on the Bee Bee C.
  • The police should trap the miscreants responsible for this crime using a honey trap.

It’s nice to know that the world can be such a surprising place.

Posted in Froth | 7 Comments

Managing and sharing data

Posted on May 5, 2011 by Frank Norman

The UK Data Archive (UKDA) has published the third edition of its guide Managing and sharing data. The 36-page guide is available as a free pdf download, or you can request the UKDA to send a print copy. Although written and published by the UKDA – an archive for social sciences – it is mostly generic and has been endorsed by BBSRC, NERC, JISC, the British Library and the Research Information Network. Strangely neither the MRC or Wellcome are on the list of endorsers.

The guide starts by looking at the need for data sharing, driven by research funders policies (here MRC and Wellcome get a mention), journal publishers’ requirements and a belief that it is good for science. It then talks about data management plans, a way for researchers to assess what they can do to share their research data and what the barriers to sharing might be. The guide cautions:

A data management plan should not be thought of as a simple administrative task for which standardised text can be pasted in from model templates, with little intention to implement the planned data management measures early on, or without considering what is really needed to enable data sharing.

It goes on to stress the importance of documenting the data, that is creating metadata to provide “sufficient contextual information is required to make sense of the data”. The guide examines the pros and cons of various data formats and the need for format conversions, and has good advice on data storage, security and disposal. A section on ethics and consent and one on copyright round off the general advice. Finally it has some advice for data centres.

The guide includes case studies throughout, to make the issues discussed feel more real, and also gives references to further reading. It also has a useful data management checklist – a series of questions that researchers should ask themselves about their data handling procedures and approaches.

Late addition
Just spotted on Twitter: RCUK have published their Common Principles on Data Policy.

Posted in Research data | 1 Comment

Open season in biology

Posted on May 3, 2011 by Frank Norman

On Thursday my colleague alerted me to a new open access journal from the Company of Biologists called Biology Open. Today, after a four-day long weekend (thanks to the Royal Wedding and Mayday celebrations) one of the first emails I opened was an announcement about a new open access journal from the Royal Society called Open Biology. I thought I’d got confused or mis-remembered but after checking I can confirm that there are in fact two new journals launching with almost identical titles. There is a slight difference in addition to the word order: Biology Open is calling itself Biology Open (BiO).

You might think you have seen the title already, and you would be almost right. There is also The Open Biology Journal from the publishers Bentham Science (a rather less prestigious publishing house than the CoB or the RoySoc).

I naively wondered at first why we needed so many journals in the field of open biology but then I read the announcements a little more closely and realised that neither of the new journals (nor, indeed, the older Bentham Science journal) is devoted to “open biology”. Rather they are broad journals of biology that happen to be open access. It is the journal that is open rather than the biology. It´s a bit like the old days when people set up “The Internet Journal of XYZ”.

Open Biology will offer

rapid publication of research in cell biology, developmental and structural biology, molecular biology, biochemistry, neuroscience, immunology, microbiology and genetics.

Biology Open (BiO) will be publishing

original research across all aspects of the biological sciences including cell science, developmental biology and experimental biology.

So far, so similar. But whereas Biology Open (BiO) says it will focus on “the timely publication of sound research rather than that with perceived impact or importance”, Open Biology says that acceptance criteria will be “high quality, importance and originality”.

Librarian Charles Greenberg, author of the OpenBiomed blog, suggests that Biology Open (BiO) is in effect a PLoS ONE lookalike journal. Or perhaps a Biology Direct lookalike, though that BioMedCentral journal has not had such great success as the PLoS title so I don´t suppose anyone wants to look like it.

While I´m on the subject of new OA journals, here is another one. The Genetics Society of America have launched G3: Genes|Genomes|Genetics, which aims

to meet the need for rapid review and publication of high-quality foundational research, particularly research that generates large-scale datasets such as genome maps, genome-wide association and QTL studies, mutant screens, advances in methods and technology, and more.

The biggest question in my mind is whether those pipe symbols (|) are a necessary part of the name. How will Endnote etc cope with this journal name? I can´t help wondering what is wrong with good, old-fashioned commas. It also reminds me a bit of Proteins: Structure, Function, and Bioinformatics, which is often known as just plain Proteins, leading to some confusion about its proper title.

That´s enough wittering about journal names from me. I´m sure an enormous amount of thought and effort goes into coming up with names for new journals, but sometimes we librarians despair of the end results.

Posted in Journal publishing, Open Access | 13 Comments

Now that’s what I call inflation!

Posted on April 27, 2011 by Frank Norman

A great snippet from Science Insider on an out-of-print book that was advertised on Amazon for $23,698,655! The book was The Making of a Fly by Peter Lawrence (from MRC’s Lab Molecular Biology at Cambridge, not University of Cambridge as Science Insider had it). The book was published in 1992 but is now out-of-print, however there were a number of second-hand copies available on Amazon ranging in price from $35 … up to that incredible $23m figure.

It appears that many sellers on Amazon use algorithms to set book prices, automatically adjusting their prices when the price of another copy of the book is adjusted. I don’t quite understand how it got up to such a crazy figure but it shows how things can go wrong if the algorithm is faulty and there are no human checks.

It reminds me of one chemistry assignment that I got badly wrong, by quite a few orders of magnitude. My tutor wrote on my paper (probably in red ink) “Your answer is more than the total amount of energy that the sun has emitted since the universe began!” and enjoined me to switch on my brain before submitting my next answer.

Peter Lawrence notes that the fact people still want to order a copy of the 1992 handbook suggests that, despite 2 decades of breathtaking advances in developmental biology, he succeeded at his intention to “write a book that lasts.”

Posted in Books | Tagged , , , | 4 Comments

SameAs – Science, Technology and Art

Posted on April 21, 2011 by Frank Norman

This week I attended a meeting about art and science, organised by SameAs. This is a newish group that aims to bring together “interesting people from diverse backgrounds to discuss science, technology and everything in-between”. Basically it is a free meeting held in a pub with some interesting speakers and a good crowd of people.

The evening event was all about science and art, or art and science (or even Art and Science), a plum pudding of art and science mixed up together in different ways.

Chris Thorpe was the highlight of the evening, for me. He spoke about art and technology rather than art and science, giving a riveting account of the Artfinder project.

In a slightly rambling but very effective way, he teased apart some aspects of our interaction with technology, notably mobile phones and tablets, and possibilities for using them in the world of art. He pointed out that they can locate us in time and space, telling us where we are and when, and what else is around us. How about an application that knows which artworks are nearby? That is quite a job – for starters you need a system for uniquely identfying all works of art. We also use our mobile devices as distractions – playing all kinds of daft games on them, or reading books and news (or even blogs). How about an application that makes it possible to view artworks, or to play games with them? Chris wants to unleash waves of creativity based on interacting with artworks in new ways.

He also mentioned work that the project has been doing on size factors – the size and shape of mobile devices is important – and on context. Using a device on the move is a different experience from using it on the sofa, in bed or at a table. He has been observing people using phones in galleries and he notes that mostly people take photos there in order to remember what it is that they have seen. He complains that current audioguides can create problems as gallery visitors crowd round an exhibit trying to see what number they have to press next. Technology should get out of the way of the art. He suggested that we need a Shazzam for art – you take a photo on your phone and it tells you what the work is and offers links to further information.

He thinks we need recommendation engines for art – both for artwrks and for museums. How often do we overlook small or specialised collections in favour of visiting the blockbuster galleries? He recognises that there is a danger of ever-decreasing circles of recommendations of artworks, where you become trapped in a monoculture of similar works. He aims to build in a degree of serendipity, citing John Peel as the ideal serendipity engine for music.

Artfinder should be hitting the marketplace soon and I recommend you to try it out.

Other speakers I enjoyed were Wynn Abbott, Julie Freeman and Tony Langford.

Wynn Abbott (director of the London Science Festival) talked us through a few art-medicine exemplars, some of them rather gruesome.

  • Orlan, a French artist, uses her own body as her canvas. She has planned a series of seven plastic surgery operations, each inspired by a different work of art. When complete, she will have the forehead of the Mona Lisa, the chin of Botticelli´s Venus, etc. Each operation is filmed, and the income from the sales of the film helps to finance the next operation. Orlan remains conscious throughout each operation, with only local anaesthetic used.
  • Marilene Oliver is a London-based artist. Her project I Know You Inside Out took the Visible Human dataset as a starting point. She printed the images onto sheets of acrylic as a way of recreating the original human body. Later she moved on to using images of MRI scans to achieve a similar effect.
  • Annie Cattrell works with glass, and has produced beautiful recreations of lungs; nervous system; and parts of the brain. An exhibition of her work was reviewed in The Lancet.

Julie Freeman started out as a technologist but moved through creative technology into art and ended up as a digital artist, working mostly with scientists. She admitted that she secretly wanted to be a biologist! She spoke mainly about her project called The Lake. This involved tagging fish in a freshwater lake and then tracking their movements using sonar. The tracks were then digitally transformed into sound and animation. She built a viewing tower by the lake so that visitors (mostly anglers) could see the work, gaining a new insight into the life of fish. You can read more about her work on her website translatingnature.org.

Tony Langford is the co-founder of the Kinetica Museum (a museum of electronic and experimental art / technology) and the Kinetica art fair. He said that Kinetica aims to bring together scientists, artists, philosophers, and others. He described its exhibits as living art, and he cited Marcel Duchamp and Alexander Calder as early exemplars of the genre. The museum currently has no permanent home but there are plans for a series of exhibitions.

Posted in Art, Social networking | Comments Off on SameAs – Science, Technology and Art

Pssst! Want something to read?

Posted on April 21, 2011 by Frank Norman

Lecturer Nicholas Morton recalls his shock on being told that “Students don’t like reading”. He found this to be true – most of his students prefer computer games to books. In the Times Higher he describes his practical response to this situation

Recently, I decided to act on this expectation and launched a “Reading Challenge” to my history undergraduates. This voluntary event encourages them to read 20 books for pleasure during their degree. It is not an attempt to force on them a “canon” of worthy literature; it presents them with a wide range of books from which they select titles that interest them.

Those who wish to take part receive a long bibliography broken into sections, including 20th-century fiction, philosophy, short stories and so on. The idea is that they choose and read at least two works from each area until they have reached the required number. Successful participants will receive a certificate and a small prize, but this will not be large enough to be an incentive in its own right.

He says it is too early to judge whether it is a success, but the initial response from students has been positive. He hopes that the reading challenge will help to form informed, rounded human beings.

I wonder if this is something that would work in the sciences? What should science students be encouraged to read – popular science and science history, literary fiction, philosophy, lablit?

Posted in Reading recommendations | 17 Comments