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After having written a manuscript and formatted it to the publishers specifications, are there any additional things you do before submitting it (or right after submitting it) that make the review process easier. For example, for journals that I know the approximate time it takes to review, I make a note in my diary to check on the manuscript around that time. I also print out a hard copy and move the digital files into my lab notebook. Are there other things that I should be doing?

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Thank your co-authors ;) –  A.Schulz Dec 13 '12 at 15:01
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Do this: youtube.com/watch?v=0SYgCsevCLk –  JeffE Dec 13 '12 at 15:55
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"formatted it to the publishers specifications" Seriously, why do some publisher ask that? Why do some author agree to that? This seems like a complete waste of time in case of rejection, and completely indifferent to timing in case of acceptance. –  Benoît Kloeckner Jul 28 '13 at 21:02
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7 Answers 7

up vote 20 down vote accepted

Putting together also some advice from the previous answers, here is my suggested checklist:

  1. Run a spellchecker :)
  2. Prepare a cover letter. If the manuscript has a previous history (e.g., it is a modification of a rejected papers; overlaps partially with a conference proceeding), you should state it. Some may want to suggest possible referees in the cover letter; I find it ethically dubious, so I never do it. In case, you may want to suggest referees to avoid. (maybe we should have a separate question on this point).
  3. submit a preprint, either at your institute or on arXiv, or at least think about it. Check the terms of the journal you are submitting to (this is a great resource) to make sure you can; often the submission is the best moment to do it, since the journal can have no reasonable copyright claim on what happened before it.
  4. Even if you don't submit a preprint, make a backup copy of the .tex and .pdf files. If you use source control, tag the latest version as "submitted". This way it will be easier to recover that exact version when the referee report mentions "line 4 on page 2".
  5. Send a copy to your co-authors, for backup and self-archiving.
  6. Relax and celebrate.

You speak about applying the journal style in the manuscript; I suggest not to do it at this point. Referees won't care; it is really needed only after the manuscript is accepted, or if an over-zealous editor asks you to do it. You might spend lots of time without reason, resizing figures and line-breaking formulas that will be dropped after the referee comments.

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It is of utmost importance that, immediately after the submission of the manuscript, you bake a cake and offer it to your co-workers. You might also want to invite close family and others who have indirectly suffered from your hard work. Invite all co-authors that are close enough to reasonably travel to your place and celebrate!

Cake! Picture from Wikimedia commons, user Scheinwerfermann.

Otherwise, you don't need to do anything. That's the nice thing about submission: from there on, everything will happen automatically. Reviews, proofs, etc.: everything that comes back comes with a deadline, which means you will do it. Until submission, you can postpone things indefinitely. After submission, you can't.

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+1 for CAKE! Relaxing and celebrating are important. Celebrate again when the manuscript is accepted. –  Ben Norris Dec 13 '12 at 16:00
    
At our department we save the cake until after acceptance, although eating cake at submission might be a good idea, especially when a paper is rejected and needs to be re-submitted (more cake!). –  Paul Hiemstra Dec 15 '12 at 8:55
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Pat yourself on the back, put the manuscript in a drawer, put it out of your mind, and move on to the next thing.

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While excellent advice, make sure you do this part after submission. –  Fomite Dec 15 '12 at 1:58
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Send it for approval to all co-authors.

Maybe this sounds obvious, but there are so many examples of people breaking this rule in either small (“they read the penultimate version two days ago”) or very big way (there are many examples of people actually learning when the paper is published that they are a co-author), that I think it is good to state.

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If you need to do this, you may be practicing gift authorship, in which case there is a bigger problem. –  David Ketcheson Dec 14 '12 at 20:38
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@DavidKetcheson: No matter what kind of collaboration you have, there is always someone who makes the last edits before the submission. It is absolutely necessary to make sure that all coauthors have noticed the edits, they have enough time to react before the submission, and all coauthors explicitly agree with the submission. Do not assume that things are fine simply because all coauthors have been active with the preparation of the paper. –  Jukka Suomela Dec 15 '12 at 0:32
    
@JukkaSuomela You're completely correct. My point is that if you would consider the paper ready for submission without having ALREADY done this, you're probably practicing gift authorship. –  David Ketcheson Dec 17 '12 at 12:37
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In addition to all the other excellent suggestions I would like to add something. When you submitted your paper you could invest some time in ordering your files/notes/scripts. Make sure they have a logical structure, enabling you to easily start working on the paper again when the reviews come back. Especially scripts that you use to process data and generate figures can be hard to understand if they are messy, e.g how did I generate figure 3. Ofcourse, it is much better to organize your files/notes/scripts during writing the paper. But if you have not been disciplined (busy, busy), this is a very good time to correct that mistake as everything is still fresh in your memory.

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Relax for a bit.

Also, pretend you're a reviewer and ask yourself if there's a really obvious question to ask (control experiment, comparison with another method, etc.). If so, maybe you want to get started on it before the reviews come back, so the turnaround is faster then. But send it out first, then relax, and then get to work on the obvious experiment.

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Upload your manuscript to the arXiv.

Note: you should check The Romeo website to make sure that the journal you're submitting to won't object to this.

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Stated as a universal advice, as it currently is, that answer is very wrong. At the very least, check the terms of the publication agreement you just signed with the publisher to see if they allow arXiv deposition. –  F'x Dec 14 '12 at 12:04
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Who signs an agreement with the publisher on submission? –  David Ketcheson Dec 14 '12 at 12:33
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I've submitted papers to Elsevier journals and never signed anything when I made the submission. Are you thinking of copyright transfer agreements, which are signed after a paper is accepted? –  David Ketcheson Dec 14 '12 at 16:22
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I have never heard of submission-time agreements. Publication-time, yes... –  Suresh Dec 14 '12 at 16:28
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Re “copyright transfer” vs “publication agreement”: terms depend on the journal/publisher. Many of the articles of the above-listed societies (in chemistry and physics) require the author's agreement to be signed (in print) or accepted (online form) as part of the submission process, before the manuscript is even sent to an editor. In Phys. Rev. Lett., you sign a “right to publish” form upon submission, in ACS journals (e.g., J. Am. Chem. Soc.) you sign a “Journal Publishing Agreement”. Wiley chemistry journals require you to sign a “License Agreement & Copyright Transfer”. –  F'x Dec 14 '12 at 19:52
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