Nature Methods | Methagora

Methods section remake

Many of our readers have no doubt noticed a pronounced change in the Methods section of Nature Methods papers published online over the past several weeks. Brief Communications now have a Methods section for the first time ever and in manuscript types that already had a Methods section, the section has been expanded and moved to the end of the paper.

These changes are described in detail in an Editorial accompanying the May issue of the journal. The new design is similar to what Nature implemented in 2007 and we hope our authors and readers appreciate the greatly expanded space this provides for methodological details. We are relieved that we will no longer have to relegate important methodological details to Supplementary Information and we expect our authors will appreciate being able to include more citations in their papers.

A potential downside of this change is that the print and online versions of papers have quite different levels of methodological detail. What do you think? Those of you who are online readers may not have very strong opinions on this, but what about our print readers? If anyone who regularly receives a print copy of the journal is reading this, we would like your feedback as well.


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    Alex Borovkov said:

    I’m confused. 1. Should we submit two versions of the methods section or the editors will do it themselves. 2. How authors suppose to estimate the size of the submission without knowing the paper version of the methods? Page 3 on the guide said under 3500 words with the methods and page 6 20000 for the methods alone. ???

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    Daniel Evanko said:

    We apologize for any initial confusion but are confident that authors will be able to adjust to the changes once they see examples in print. In answer to your questions.

    1) Authors should only submit a single Methods section. This will appear as the Methods online at the end of the paper. You can see examples in the current issue.

    2) I’m afraid I don’t follow the question. However, we did neglect to change the description of the Article format which may be the cause of the confusion. The text which says “The main text (excluding abstract, references and figure legends but including Methods) is 2,500 – 3500 words.” should be changed to indicate that Methods is excluded from this calculation. This error will be fixed.

    3) Same as explanation above. In addition, it is 20,0000 characters including spaces, not words. This is approximately 3,000 words. We chose to use characters to determine length instead of words because equations and other types of content can skew the apparent length when measured by word count.

    I hope this clarifies things.

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    Patrick Mears said:

    1) Can the new Online Methods contain additional figures, or should they be in a seperate Supplementary Figures file?

    2) We had prepared a manuscript with a large Supplemental Methods section. Should this now be changed to “Online Methods”.

    3) When submitting the manuscript, can/should the Online Methods section be including in the main text, or should it be seperately uploaded?

    4) How should details in the Online Methods be referenced in the main text? For example (see Methods Online), or (Online Methods Fig. 1)?

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    Daniel Evanko said:

    To be completely honest with you, it is unnecessary to format the paper precisely for Nature Methods in an initial submission. There is too large a chance that a submission will not be published and it isn’t worth your effort doing detailed formatting that might never be needed. We don’t require this level of formatting until we conditionally accept a paper.

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    David Micklem said:

    I’m a regular reader of the print edition (which I get as a free subscription). The problem with the new system for me is that essentially NO information about the method is included in the print version. The Online Method is only available through a paid for subscription, which I do not have access to.

    This makes the free print version effectively worthless to me, which is a shame.

    Is there any possibility that the Online Methods section could be made available via the “Supplementary Data” pages, which are freely available to all?

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    Daniel Evanko said:

    When this was being planned for all the Nature research journals by the publishers we did realize that Nature Methods would be in a unique position compared to the other journals in that we would be supplying free print copies to some people who didn’t have online access through their institution. While the vast majority of our readers do have access through either their institution or a paid print subscription, there are some people like yourself who don’t have such access.

    In answer to your question; since the online methods is now appended directly to the end of the online paper PDF we can’t put the methods in supplementary information.

    Thank you for providing this feedback though. We will keep track of all the feedback we receive and maybe something could be done if the problem is serious. This would be up to our publisher though.

    If you can wait 6 months you will be able to access the methods of many papers through PubMed Central when the full paper gets deposited there. While all papers probably won’t be deposited, we hope that most will be.

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    David Micklem said:

    Thanks for your response.

    I think there is (at least) one other significant way that Nature Methods differs from the other Nature journals with respect to this policy: For most Nature journals the scientific result is of primary importance and the details of the method are interesting to only relatively few readers. In contrast, for Nature Methods the method is the “raison d’etre” for the paper and the details of the method are essential for a good understanding of the paper.

    “…since the online methods is now appended directly to the end of the online paper PDF we can’t put the methods in supplementary information.”

    This is a non-sequitur. It should be technically possible to duplicate the methods portion of the pdf in the supplementary information section.

    I’ve always been slightly puzzled that you do not allow online access to Nature Methods for people with free subscriptions. Is there any possibility that you might reconsider this policy?