Notes from the life of a bioinformatician
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Science, Nature and Wiley journals will not accept Microsoft Word 2007 documents. Presumably for practical reasons (they can’t deal with them), but I’d love to think that this signals something deeper – i.e. a move towards (open?) standards in science publishing.
Staying with both science publishing and Attila’s blog, he’s going to try blog editing of his thesis. Congratulations and good luck to him.
I thought Office 2007 did use an open (XML based) format? Or are you getting at something else?
I’ve no idea what Office 2007 uses, but I’d be surprised if it’s “open” or “standard” in the sense that I understand. I guess by standards I mean something cross-platform and OS-agnostic where my document and your document look the same when we create them.
It’s because they can’t handle the new docx format. I think it is in an xml format that microsoft would like to see standardized, but it would be so much better if it was all in ODF.
I’m not surprised, publishers seem to delight in making life just that little bit more awkward for authors. Recently I submitted a paper which required all the documents to be in pdf format. This was fine. It also required the figures and tables to be pdf’d according to a specific profile. Again this is fine, I can understand why printers would want control over dpi and so on. However, they only provided the profile for Acrobat 4, which I don’t have access to. I emailed them asking for an updated profile six weeks ago, and I have yet to get a reply. In the meantime I have submitted the paper to another journal.
Almost makes me nostalgic for Letraset and developing one’s own film…
There have been quite a few articles in the newspapers, eg the NYT, about the new MSOffice2007. The company has bought out a system that is not back-compatible with previous versions (becuase of the “ribbons” feature. We could handle MS2007 if authors were prepared to use a particular type of back-saving for tables, equations, etc, but we thought it would be too fiddly and too much hassle for them, so we are at present suggesting that they continue to use exisiting formats.
The MS “XML” is nowhere near a publisher DTD standard. One of the processes of typesetting is to put in XML and we, in common with other publishers, use a custom macro called Extyles to do this. MS 2007 is incompatible with Extyles, so we’d have to change our entire production and typesetting system — for what? So we’d have unusable, below standard XML? Then dois would not work, searching/tagging wouldn’t work, etc.
We spent a long time looking into this (with no help from MS, whom we frequently contacted pre-release of MS 2007 but who didn’t answer), and in the end we decided that it would be much better for authors if they carried on using existing versions of Word or mac equivalents for the time being. We have hopes that the MS Office 2007 system will evolve in response to user feedback.
While it would be fantastic if they moved to ODF, I kinda have to wonder why microsoft’s XML is causing so many problems. I thought the whole point of XML was to get around publishing software-specific formatting.
Wouldn’t things be so much easier if nature just provided a template into which authors could copy and paste their manuscripts using a plain old text editor? You know, like Title goes between the [title]tags[/title], abstract goes between abstract tags, and so on? That way authors would have to do no formatting whatsoever, and it would make it easier for Nature to format things how they’d like. I mean, you’re not going to get every life scientist to learn LaTeX, but I don’t know why a simple, publisher-provided template into which authors could just paste stuff wouldn’t work.
publishers seem to delight in making life just that little bit more awkward for authors
I think that authors are increasingly required to do a lot of work in preparing manuscripts. I’m happy to convert colour figures to CMYK for instance, but I have colleagues who have no idea what CMYK is. I guess the publisher should expect a certain standard from the writer – spell check, correct citations, but ultimately, scientists need to concentrate on writing, not typesetting. After all it’s the people employed by the publisher who have the expertise in document preparation.
Maxine, thanks for the background on MS2007 – always interesting to know what goes on behind the scenes.
you’re not going to get every life scientist to learn LaTeX
You’re not – but ultimately it would make their life easier. LaTeX is essentially plain text plus tags. I just finished my first paper prepared using LaTeX; there was a learning curve of a few weeks but I think it was very worthwhile. Like anything once you have the skills, you have them for ever and can apply them many times over. And there are plenty of resources out there for anyone trying to learn.
Just a couple of comments:
CMYK is needed for print colour reproduction. RGB is a web format. All publishers who have print products have to use CMYK to get the colours to appear on the page, the requirement to use it has nothing to do with the publisher making people do it just to be difficult. We ask authors to supply in CMYK so that the author can be sure that the colour in the print is the colour they want. Sure, we can convert the author’s RGB into CMYK, but then we have no reference standard to check against.
Nature does provide templates for all versions of Word (mac and pc) becuase the vast majority of our authors use Word as their main software — this is not political, just a fact of life. Some of the other Nature journals, the purely physical science ones, do process in LaTeX, but Nature itself does not. However, we do convert LaTeX for any author whose manuscript is accepted for publication and who can’t or won’t use an alternative format.
It fascinates me how people like “Mr Gunn” can speak with such authority about Nature’s procedures and why they are there! They are all explained on our freely available author website and in our author instructions, we put a lot of effort into explaining why we do things to our authors and making life as easy for them as possible in this technological age. We also regularly survey them and act on what they tell us they want in terms of author services, as far as possible.
Mmm, OK CMYK conversion was not a great example. What I’m getting from this discussion is that researchers feel that manuscript preparation is a lot of work and perhaps that their workload is increasing. I don’t have any issues with journals on the whole – they all provide templates in a variety of commonly-used formats, what more can they do?
It seems to me that the issue is ease of document preparation in general. That’s solved by better software and more computer-literate users; are there avenues for journals to influence and educate in those areas?
Yes, that is a good point == let us know! We invite authors and potential authors to contact us with any feedback and comments — for example there is a standing invitation at the top of Nautilus, our author blog, and every page of our Author and Referee website has a feedback channel (which goes direct to the editors). So we are listening to ideas — if you know things that you think we should know, tell us — we make it as easy as we can for you to do so. We are doing our best. Our jobs too have got much more technical now that we have to provide curated web publication and permanent archive as well as a print product — in the case of nature, printed in three international venues and with subscribers a couple of days after the last few news pages are passed for press. We adapt and evolve as fast as we can, sure we can do better as we all can, but we do strive to provide the best service that we can with the tools and knowledge that we have.
