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.
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.