Pronto pre-print

Without quite meaning to I realise that I have been generating a series of blogposts about the publication process.

Initially I wrote about my struggles to finesse the figures needed to show off the important aspects of our structure of the complex of the 3C protease with a peptide substrate. After we had submitted the manuscript, I discussed the issues surrounding our use of language that had been raised by one of the reviewers.

Then Richard weighed in and kicked off an interesting discussion on the costs of Open Access publishing. There is a fair amount of enthusiasm for this dissemination innovation among many scientists — it chimes with our amateur ethos — but in these straitened times the costs to authors are starting to bite.

When our paper was accepted by the Journal of Molecular Biology last month I had to decide whether or not to shell out the $3000 charge that the publisher levies to make the final, edited and prettified version of the paper freely available via PubMed Central.

The work reported in our paper was funded by the BBSRC on a grant that started before 2006 and has now finished. That meant that, although the BBSRC encourages OA publishing, we were not required to deposit the paper with PubMed Central. If we opted to go down that route, we would have to stump up the OA fee.

However, it is still possible to make the article freely available. According to Elsevier (the publisher of J. Mol. Biol.), authors retain

the right to to post a revised personal version of the text of the final journal article on the author’s personal or institutional web site or server, incorporating the complete citation and with a link to the Digital Object Identifier (DOI) of the article.

Now, I am well aware that this is a second best solution since anyone searching for the paper within Pubmed will not automatically be presented with a link to the OA version of our paper. But $3000 is $3000.

Moreover, I am not permitted to upload the final, journal-polished version of the paper on my web-site. But it did occur to me that I could, without too much difficultly, convert my double-spaced manuscript into something more akin to the look and feel of a published paper. Our manuscript was written in Microsoft Word, a necessary medium since it is used by all the co-authors and integrates with Endnote, but I turned to Apple’s Pages program to prepare the pre-print because this made it easy to integrate the figures and tables within the body of the text.

Preprint Pages
Publish with polish?


With an hour or so of fiddling and formatting I had what I thought was a passable imitation of a published article, double-columned with inlaid figures and figure legends. On top of that, given the noises I made recently about the frustrating fragmentation of supplementary information, I had the opportunity to show how I would like it to be done.

The final document is a single file integrates the text, figures, tables and Supplementary Information as an openly accessible bolus of information. You can download the PDF from my web-site to guage for yourself how digestible it is. No purchase necessary. If still not completely sated, you may even wish to have a gander at the morph animation (with commentary) that was made to accompany the paper.

I was pleased to discover how relatively quick and easy it was to re-format the manuscript. So open access pre-prints don’t have to be the cumbersome files that we often handle as reviewers. And, if this science gig doesn’t work out, maybe I can forge a new career in desktop publishing.

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26 Responses to Pronto pre-print

  1. Eva Amsen says:

    Very pretty! In a course I helped out with last year, students had to make one “paper that looks like a journal paper” and some were SO NICE they looked like they had already been published.

  2. Stephen Curry says:

    Thanks, though it was surprisingly straight-forward. Of course it is substance that matters, but it is all the more pleasant when served with a little bit of style…! ;-)

  3. Matt Brown says:

    Nice solution. And a business opportunity. Maybe some enterprising freelancer could set up a service where for, say, £30, he would lay out author-original papers into publisher-like formats. Hmmm

  4. Stephen Curry says:

    Pronto Pre-print™ © S Curry (2009)!
    I’ve got witnesses, Matt. I want 10%!

  5. Richard P. Grant says:

    Hoorah for Pages!
    That looks really nice, Stephen. Maybe Apple should take up the OA banner…??

  6. Stephen Curry says:

    Pages is to Word what Keynote is to PowerPoint: slicker & quicker (and more fragrant). And now that it works with the latest version of Endnote, I’m tempted to make the switch but for the sad fact that I have to interact with the rest of the world.
    Can’t see Apple jumping onto an OA bandwagon though. Safari aside, that’s not really been their style…

  7. Samantha Alsbury says:

    Nice (nodding), I love macs and the’re not entirely incompatible with the rest of the world…just mostly!! I have PC for the lab and a mac at home.
    Maybe we should do away with journals and just publish all our own papers on the web, then we can just send them to f1000 for peer review, much cheaper (or is it too heretical to suggest that on NN, hehe).

  8. Stephen Curry says:

    Thanks for the comment Samantha – and welcome to NN!
    Maybe we should do away with journals…
    That’s a view shared by some but in the real world as currently constituted it would probably entail career suicide. This debate has been much rehearsed here and elsewhere but, for what it’s worth, I still prefer to have at least some peer review prior to publication – it helps to ensure that less rubbish is published. Plus I’m not sure that f1000 would want the added burden of checking over everyone’s papers.

  9. Richard P. Grant says:

    Stephen, Pages and Keynote handle their respective MS cousins better than the MS software itself, in many cases.
    Funny you should say that, Samantha. Remember that we have 5k+ people around the world who are already pretty good at doing peer review. Now, if we were to start soliciting for original research papers, (hang on, there’s someone at the door)…

  10. Richard Wintle says:

    Yes, that is rather nice, Stephen. Well done!
    Not thinking of starting your own OA journal are you?

  11. Raf Aerts says:

    Well done. Your PDF even looks better than the Elsevier version. I would have included the DOI (doi:10.1016/j.jmb.2009.10.048) in the header though.

  12. Stephen Curry says:

    @Richard G – have they gone yet?
    @Richard W – Not thinking of starting your own OA journal are you? Not just yet… I think it could soon become wearisome to spend all day formatting papers.
    @Raf – that’s a good point. I even think that I am supposed to add the DOI. But it is very easy to do so I can quickly update the PDF. In fact, ’tis already done! I also intend to include the full citation once the paper appears in the print version of JMB.

  13. Mike Fowler says:

    Excellent enterprise, Stephen!
    At the risk of raising hackles again, this sort of exercise still makes me wonder exactly where all that $3000 goes. I understand where some of it goes, but not quite all of it… Wouldn’t it be nice to get an honest breakdown of the costs.

  14. Darren Saunders says:

    Nice Stephen. Having gone through the nightmare of trying to put my thesis together in MS Word a few years back, I’ll be giving Pages a close look in the near future.
    One of the assessment exercises in a Biochem class I used to teach involved getting the students to write up a report as if they were preparing a submission to JBC. One of the students slightly misinterpreted and spent who knows how long trying to match exactly the printed format of the journal, right down to matching fonts etc etc. Hmmm
    @Richard, so it’s actually F5000+ ?

  15. Richard P. Grant says:

    Darren, I want to change the name to F2^13 but that might be too geeky.

  16. Darren Saunders says:

    Darren, I want to change the name to F2^13 but that might be too geeky.
    maybe just a little.
    BTW, just browsing your site. I have a question… what’s difference between a faculty member and an Associate FM in terms of their role(s) in assessment? It’s not immediately clear from the FAQs.

  17. Graham Steel says:

    Pronto Pre-print™ © S Curry (2009)!
    Hhmm. There must be milage in such a service, IMO. I wonder whether the likes of Mandelay sorry Mendeley might be interested in this. Srsly, you should ask them….

  18. Stephen Curry says:

    @Mike – I’m not sure how the calculation is done. I imagine some of the charge is ‘compensation’ for lost subscription information. I don’t feel inclined to complain too much because one of the attractions of JMB to authors is the lack of page charges or charges for colour figures. So my total outlay for this paper is zero.
    @Darren – Pages is an even more attractive proposition these days since it now works with Endnote (as of version X2 of Endnote) – there’s an instructional video here.
    @Graham – Are you suggesting that Mendeley might host the pre-prints? If so, that would be disallowed by the agreement I’ve signed with Elsevier. I can only serve my pre-print pdf from a personal or College-based web-site. Though perhaps Mendeley (or even Pubmed?) could be persuaded to facilitate inclusion of links to these sites as a way of promoting access to the literature?

  19. Clare Dudman says:

    The pdf looks very impressive to me – and I really enjoyed the video too. It made the binding site really clear and I found it quite remarkable. I know I’m pretty much out of this world, but I do like taking a little peek inside to remind me what it’s like.

  20. Graham Steel says:

    Yags – we is back to the green/gold thang [1]

    @Graham – Are you suggesting that Mendeley might host the pre-prints?
    Nopes. I was just suggesting that they might be interested from the perspective of providing some input into this issue/discussion from a technological level. This thought came about after reading the comment from M@ above.
    I too think that you have produced a most impressive pdf, way way better than my only nimble attempt thus far hosted here at Nature Precedings in 2007. Blood ‘n sweat to produce that one.
    So the concept of paying a small fee for having “an entity” err, “converting” a pre-print is an interesting one.

    Am a Gold person myself.

  21. Graham Steel says:

    Missing link [1] is The green and the gold roads to Open Access from NPG.
    As stated here on FF, New Power Generation (NPG) should not be confuzzled with another NPG !

  22. Stephen Curry says:

    Thanks Clare – if you liked the animation, then I have a 70 min ‘treat’ coming soon. Watch this space! ;-)
    @Graham – thanks for the link, I hadn’t seen it or heard about the Open Archive Initiative (mentioned within) which, at first glance, might provide some kind of centralised access to self-archive pre-prints. Has anyone used it?

  23. Graham Steel says:

    Has anyone used it?
    OAIster statistics via here

  24. Graham Steel says:

    Also worth mentioning Repository 66

  25. Stephen Curry says:

    Thanks for the links Graham though I confess I’m not sure how to navigate through all this. OAIster seems to be a wide-ranging depository. Is there any sense that it might emerge as the depository for open access life science articles? I suspect there won’t be much motivation to deposit there unless people are reasonably convinced that it is emerging as the most likely search point. From your stats it certainly looks like usage is increasing but I guess I’m surprised to have only discovered it in the past few days.

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