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Post-publication peer review

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Everybody’s Talkin’

Posted by rpg on 15 April, 2010

It’s been a while since I’ve said anything about the F1000 website. You might remember that’s what I was working on when I first arrived at SNG (much to my surprise, it has to be said); since about February I’ve been increasingly full time on The Scientist. I still maintain a professional interest in what’s going on across the office, though, especially when it comes to a couple of my pet projects.

One of those projects is user comments.

We’ve been having a bit of a discussion about comments on evaluation pages. My original plan was to have a separate forum so that people could talk about articles evaluated by Faculty Members. But for various reasons that morphed into comments directly on the evaluation itself, which I think is probably a better way of doing things. This does cause a few headaches, though: we don’t want to ‘dilute’ the impact of what our FMs say, we’re a serious site—by professionals, for professionals—and need to honour the trust our users place in us (so can we allow comments from just anybody, and how are you, as a reader, to judge the worth of those comments?), we want to avoid trivial and inappropriate content but at the same time commenting for the bona fides should be as easy and straightforward as possible.

I’m encouraged that Nature are now allowing commenting across the site, and will be watching what happens with interest. In the meantime, Neil Saunders has some useful advice for publishers who want to encourage comments.

My question to you is, what else would you like?

I should point out that we’ve already decided that only registered users who are in a ‘subscription zone’ can comment (only subscribers can read the content anyway; except for the articles we make free), and that all comments will go live immediately, and there’ll be the ability to flag comments as inappropriate. That’s on the advice of our lawyer, so is unlikely to change! But have at it: what really annoys you/stops you from commenting on other sites?

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On the run-04Feb10

Posted by rpg on 5 February, 2010

What was that? I think it was the sound of a week flashing past.

I keep saying things like “We’ve got a brand new website… but you can’t see it yet.” This must be quite frustrating. Truth is, the dev team are working very hard (and specs have changed and changed again—but let’s not go there now) and a lot of stuff has to come together all at once. There’s actually no point showing you what we have at the moment because it’d all “ignore that, we’re changing it” and “the design is going to be different than this” and “oh, yeah, we know about that bug”.

But I can tell you that the new search is very funky and we all like it, and that the new design is very spiffy (hang on, I did that already). On Monday we’re going to work out once and for all what we can deliver and work to that. So far, the ‘definite’ list contains the new design (both what it looks like and functionally), the improved search, comments on evaluated articles and RSS. There are a heap of other behind-the-scenes changes too. Then after we go live we can add on all the other things that are on the backlog, so you will see new things appear as we keep building and tweaking and rolling out new features.

I spent some more time on our journal rankings this week. The critical thing appears to be the timing: as I’ve said before, most of our evaluations are published quite quickly after the original article appears. We get around 90% of all evaluations within about three months of the publication date. So what we want to do, for yearly journal league tables, is capture as many as possible while making our stats as up-to-date and relevant as possible. The issue is that if we took April, say, as the cut-off for the previous year we’d end up giving the journals that publish more stuff towards the beginning of the year an unfair advantage. So we’re going to implement a rolling cut-off, with a provisional ‘current’ ranking and publish the official f1000 stats somewhere around May each year, which gives us four months to collect evaluations for each original article.

However, the big news this week is that we welcomed Sarah Greene into the office. This is part of the move to bring f1000 and The Scientist closer together: f1000 is going to start seeding The Scientist‘s scientific content, and use it to help build a community around the service.

As part of this, my own role is changing. I’m going to move away from web development (although I’ll still have input into the design and user experience), which will free me up to be more editorial/journalistic. I’ll still be running the Twitter feed and Facebook page and wittering about things that catch my eye in f1000 (perhaps even more so). There’ll also be the ‘special projects’, such as the rankings, federated comments and various research collaborations. I guess Eva will still be wanting me to make logos for her too.

And finally

The late pick-up of the disenchantment of a small number of researchers with the peer review process is still making waves this week. Cameron Neylon gives his own take on the matter at his blog. I’m not at all sure that I agree with his analysis, having had my own manuscripts subject to both what I might call ‘good’ and ‘bad’ review. I think that too many people view peer review as a stamp on the ‘rightness’ of the paper, rather than a technical check that the experiments and controls are done correctly and that the literature has been read.

Cameron has also been having a go at Nature Communications. The argument hinges on the Creative Commons licences they ask authors to choose. You can sign up and join the conversation at Nature Network.

With that, have a great weekend. And sorry, no cytoskeletal porn this week. Maybe next time.


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On the run-22Jan10

Posted by rpg on 22 January, 2010

Last week I met up with a Certain Editor from a Certain Journal. We had a nice chat about, among other things, the policy of Certain Journals as regards the wind direction in the publishing industry. From the research side of the fence it’s easy to assume that publishing houses are monolithic edifices intent on maintaining a monopoly; unchanging and unfeeling; not to mention dirty money-grabbing bastards. Certain Advocates (not all!) of Open Access/Open Science hold to this view.

Naturally, the truth is a bit more subtle. Publishing is a business, which means that publishers are actually going to drive change, because if they don’t they will wither and die. Cell’s Article of the Future is a case in point (you might not like it, but you can’t deny that Elsevier are innovating). Publishers that see their competitors doing stuff are going to adapt and respond as necessary. Because if there’s a new paradigm brewing and they’re not on board, things will turn out bad for them. (The trick, of course, is to figure out what is actually a new paradigm and what is simply a tale/ Told by an idiot, full of sound and fury.)

Not unrelated to this preamble, you may have noticed a slight addition to the type of things we evaluate. For example, we have something titled Endogenous Forces Exerted at E-cadherin Based Cell-Cell Contacts:

The authors first determine that the traction forces that a single cell exerts on the underlying substrate are balanced across the cell. However, for cell pairs, it was determined that the traction forces exerted on the substrate for an individual cell did not balance, with the force imbalance reflecting the force exerted on the cell-cell contact.

but it’s not a paper being evaluated, it’s a poster.

Poster preview

I have more—much more—to say about this initiative, so stay tuned for updates.

While we’re on f1000, an evaluation you might have missed. (I’ve been meaning to blog about it all week, but as you’ll see it’s not really my fault. Or perhaps it is?) The piece, by Lutz Jäncke at the University of Zurich, starts provocatively:

One of the most virulent disputes between neuroscience and philosophy is whether human beings are equipped with a free will.

The brain is thought to generate decisions before the conscious mind gets involved, based on electroencephalography measurements. The ‘Bereitschaftspotential’ starts up to 1.5 seconds before movement is executed. However, in an elegant but mind-bending experiment published in Neuropsychologia, a diverse group of researchers find that there is a final check that seems to be under the control of the individual, an ultimate ‘yes or no’ that appears to be freely willed:

Planned actions can be subjected to a final predictive check which either commits actions for execution or suspends and withholds them. The neural mechanism of intentional inhibition may play an important role in self-control.

There goes my excuse that the voices in my head made me do it. You can read the evaluation, free for three months, here.

In other news, the dev team have been working on the search mechanism for the new f1000.com website. One of the major criticisms of the current Biology and Medicine sites is that it’s actually quite difficult to find the search bar, probably because it’s never in the same place. The new site is based around search (very Web 3.0, yeah?) and so it’s something that’s essential to get right. I think you’ll like what we’ve done, and once we get the design right I’ll post some screen shots. What I can tell you now is that you’ll have no problems finding it!

Finally, don’t forget to check out our Facebook page. Steve has been busy updating it with press release and video links, and we’ve noticed that several of you are reading the blog through it. Please feel free to ping us either here or on Facebook if there’s anything you’d like to see.

Have a great weekend!

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More to Online than just Information

Posted by stevepog on 2 December, 2009

I visited the cavernous confines of Olympia Grand Hall in west London yesterday, totally unprepared for the mammoth event that is the  Online Information Conference (#online09 on Twitter).

Not sure what I was expecting: maybe a few stands with bored sales reps handing out flyers on data management and XML development (they had some of those) but the last thing I thought I’d see was an actual Formula One car and an F1 driving simulator, thanks to the big-spending crew at Thomson Reuters. The simulator was a tricky beast with very light handling but of course I didn’t try it as I was there to work hard (but somehow scored a top six placing anyway).

Simulator similar to the one at Online Information conference

Apparently the heavily-branded car relates to their sponsorship of the AT&T Williams team, though beyond that it was anyone’s guess what it had to do with the conference itself. Apparently even Williams F1 driver Kazuki Nakajima was dropping in today for a visit. No, that’s not him in the car.

Apart from the overly large TR presence, it was great to meet up with my American counterparts from science conferences and library journals to discuss whatever people like us talk about (i.e. telling everyone how amazing f1000 is and encouraging them to write and talk about us to their colleagues and audience).

Many of the free seminars at the rear of the building filled up quickly but one I did catch from start to finish was an admirable effort on social media by iCrossing‘s Mark Higginson.

Mark had stepped in at the last minute due to a sick colleague, which had some of us expecting a dull diatribe on how Twitter and Youtube work. And given that everyone who’s ever used Facebook thinks they can give a talk or write a book on the magical world of social media, I wasn’t feeling too enthusiastic.

But thankfully Mark actually provided some useful statistics and went into detail on what kind of web traffic is important. As he said, it’s all very well for  Facebook to say they account for 1 in 7 web page views in the UK but it’s what visitors do after they hit the homepage that’s important. So it goes that constantly updating and improving content on your landing page is a big key to a website’s (and hopefully company’s) success.

For those who are starting out in science blogging, his points were adaptable to our area: look to see who the most influential and interesting bloggers are, where they are (the obvious scienceblogging.com, researchblogging.com or more specific sites) and what media they are using (straight-up long form blogs, micro-blogs, video sharing etc). Get involved in the conversations they are having and create your own unique content. For those who are experts on a subject such as nanotechnology, commenting on a piece on the Wired website and referring back to your own blog is one way to drive more traffic to your site.

Overall very interesting afternoon out and for anyone who scored better than a 1.57 on the simulator (and I’m sure by now there will be quite a few), I hope you take away more from the conference than a mousemat or free pen.

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Take the long and winding road to succeed in science

Posted by stevepog on 20 November, 2009

One of our freelancers wrote a great article about a recent review on the f1000 site, so I wanted to reproduce it here:

How do scientists decide what to investigate?  Often, they choose an area that is in high demand,  hoping to get their work into the best journals as soon as possible.

But according to Uri Alon, of the Weizmann Institute of Science in Israel, this strategy can be demotivating if the goals are not met, especially to younger scientists. Instead, he advises researchers to follow a less direct approach, where setbacks are considered part of the  process of discovery.

Ronen Zaidel-Bar recommends Alon’s article How to choose a good scientific problem in a recent evaluation on the F1000 Biology website.

“In the face of the cruel reality of ‘publish or perish’, Uri Alon offers some clear guidelines to help students and mentors nurture self-motivated research”, Zaidel-Bar says.

Alon’s commentary, published in the journal Molecular Cell, gives practical advice for researchers at all stages of their career. He encourages scientists to take time before they commit to a problem and ultimately choose what they find most interesting, rather than what is in demand. (ed. a good argument for ong-term job satisfaction)

Zaidel-Bar, who is a postdoctoral researcher at the University of Wisconsin-Madison, agrees that “research motivated by our true interest is much more rewarding and resilient to the setbacks of scientific inquiry.”

Contributed by Eva Amsen

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Helping the poorest countries get access to science knowledge

Posted by stevepog on 17 November, 2009

Scientists can sometimes be unfairly labeled as not caring about anything apart from their lab, grant applications and drug patents.

So it’s heartening that one of our important causes – offering free subscriptions to institutions in developing countries – gains such a positive response from Faculty Members and the recipients of free subscriptions.

Faculty Members (FMs) who submit regularly are given the opportunity to nominate an institute of their choice in a developing country for free access to f1000.

One of our Plant Biology FMs, Dr John Patrick from the University of Newcastle, Australia, sponsors the Universidad Central “Marta Abreu” de las Villas in Santa Clara, Cuba. He praised the program:

“Ready access to contemporary  scientific knowledge is a recognised major impediment for the developing world to reach sustainable self-sufficiency.  The F1000 sponsorship initiative offers a powerful instrument to bridge this unacceptable divide.”

Our recipients have been just as impressed – Gabriela Echaniz from the National Institute of Public Health, in Mexico said:

“I just want you to know how useful your service has been for all researchers that work here. Not being able to get subscriptions for many regular publications that we use for our research, your help has been invaluable. We appreciate very much your work and hope to be able to keep the subscription for many years.”

Some of our sponsored universities and institutes include:

  • University of the South Pacific, Suva, Fiji (Linda Amos)
  • Centre de Biotechnologie de Sfax, Sfax, Tunisia (Charles Auffray)
  • International Center for Tropical Agriculture (CIAT), Cali, Colombia (Seth J Davis)
  • al-Farabi Kazakh National University, Almaty, Kazakhstan (Sheila McCormick)

Our  sponsorship initiative, which extends upon the free access we already provide to institutions in the poorest countries (via HINARI),  and the global Research4Life program looks to be having an impact.

Statistics released at the World Conference of Science Journalists in July showed a six-fold increase  in research output by scientists in the developing world since 2002. A great result from a program that will continue to reduce the research divide between rich and poor countries.

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Give us an S, give us a C, give us an I

Posted by stevepog on 3 November, 2009

In a previous post I mentioned the lovely Darlene Cavalier, the former cheerleader turned science boffin who, among many other projects, is bringing science concepts to the people in a way they can always understand, ie by having Philadelphia 76ers cheerleaders give sciency facts while looking pretty and shaking their pom poms.

Darlene (also known as the Science Cheerleader) has kindly given F1000 a mention on her blog so it’s only right that we help her with a project her team is using to get more regular people into science.

Called Science4Citizens, the project links up researchers with volunteers to work on efforts such as counting fireflies, sorting through galaxies, monitoring water quality or tracking air pollutants using cell phones. More details are at this link. While many of the projects are US-based, Darlene tells us she’s looking to branch out internationally.

Science4Citizens was recently publicised in the NY Academy of Sciences magazine and planned extensions include a dedicated website.  Great concept and one we’re happy to support.

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I see red

Posted by rpg on 8 October, 2009

There was some serious geeking-out going on in the office just now—at least, in the part where the dev team and myself interact. IT have been wandering around the joint with little white boxes that have aerials sticking out of them, and then Phil came over and asked for my MAC.

A little while later I turned on my iPhone’s wireless connection and entered the URL of our development server, and this is what I saw:

new f1000.com site

new f1000.com site

And that, ladles and gentlespoons, is why I’m at f1000. For the past six months I’ve been managing and organizing a rebuild of the user site. This is a preview of the revamped website, which we aim to launch to you lucky boys and girls in early December. Just in time for Christmas.

Rather happily, even though it’s not specifically designed for mobile browsers (the screen capture above is our development server on my iPhone: it’s not using mobile stylesheets) the new site looks (and works!) pretty nicely. Richard P has been showing it off on his ITC HTC Hero, too (none of the dev team would be seen dead with a Blackberry, natch).

Of course, I could have just showed you a preview in Safari or Firefox from my desktop, but that wouldn’t have been half so cool.

Huzzahs all round.

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