1. Learn how to write by reading how to structure a paper and Writing Science (sorry that I am recommending purchasing a book, though it should be available for free from any academic library, and I recommend all PIs own a copy for themselves and their students, so it does not cost students to read it at a minimum).
  2. Main result write draft paper title and draft killer fig that visually makes the main point of your story
  3. Abstract write title and abstract based on OCAR story structure (described in Writing Science)
  4. Figures draft the remaining figures
  5. Outline generate a 1 sentence per paragraph outline
  6. Venue choose the publication venue
  7. Draft flesh out details of paper
  8. Revision revise
  9. Submission post to arxiv, submit to journal, tweet to world
  10. Rebuttal respond to reviewers

Upon believing that you have completed work sufficient to write a peer reviewed manuscript, follow the below steps in order. If you are simply writing an abstract (for a conference, for example), just do the section entitled “Outline and Abstract”

  1. Learn how to write Before you write any paper, I recommend reading How to structure a paper. I also recommend reading Writing Science, if care about writing clear compelling stories. You only need to do this once ever, not once per paper. Once you’ve read these things, follow these steps:

  2. Main Result

    1. Write a one sentence summary of your work (will become your title; ~5 min). This sentences describes the main take home message / main result. Avoide jargon to the extent possible, and grab the attention of your readership with strong substantiated claims. It is often required to have less than 88 characters.
    2. Draw (or make) the “killer fig” that makes the point as clearly and concisely as possible. Guidance for making paper quality figures is here. (~5 min)
    3. Get feedback from your PI and other principle authors. If the author list is unclear, send this summary and figure to everyone you think might believe they deserve to be authors on the manuscript, and invite them to be co-authors. Tell them that if they agree (by responding to you and the corresponding author), they can expect to get emails from you with updates, each of which will request feedback. And if they provide feedback, it will be carefully considered. Explain to them that the goal of feedback at this particular stage is that you’d like to know what they gathered was the main point of your paper, based on reading the title and looking at the killer fig (without sending them the caption). If they don’t get it exactly right, iterate until they do (don’t tell them the answer, just update the title/figure).

  3. Abstract

    1. Choose a writing medium. I recommend google docs unless there are a large number of equations, in which case I recommend overleaf. In either case, you want people to be able to comment easily directly on the draft, in real time, as to avoid the possibility of collisions. Prior to sending it to anybody, make a local copy, so they can’t screw it up (and update your local copy prior to each round of feedback).
    2. Describe the other results, typically 3-5 additional figures or theorems. The goal of each of these is to support the main claim, for example, by further refining, adding controls, etc. Ideally, they are sequenced together in a logical chain, like a proof, each building on the next, to tell the story. (~1 hr)
    3. Write a one paragraph summary (will become your abstract; ~30 min). This will be about 250 - 300 words, more than 500 words is a page, not an abstract. To include:
      1. Big opportunity sentence: what is the grandest opportunity that this work is addressing? In other words, what is wrong in the world, impacting people (not just scientists), that you are working on righting? Potentialy answers include disease, world hunger, data deluge, etc.
      2. Specific opportunity: what opportuntity specifically will this manuscript address? This is filtering down from the above, we are not going to try to solve all of world hunger, maybe just identify the primary causal factors contributing to hunger in India, for example.
      3. Challenge sentence: what is hard about addressing this opportunity? Think about the limitations of approaches that others have taken, they are great in some ways, but incomplete because something was a challenge that they did not overcome. Make sure to comment how great the previous approaches are, the people who developed them are our readers, reviewers, etc., and we all have egos.
      4. Gap sentence: what is currently missing? What is the key insight/innovation that enables us to overcome the challenge that others did not yet overcome.
      5. Action sentence: what did you do to address the gap, overcome the challenge, and therefore meet the opportunity? it should provide the key intuition/insight, the magic that makes this work, where others failed. This is the place where one can write something like “In this paper, we….”, although I would instead simply write “We….” (in this paper should be obvious from context).
      6. Resolution sentence: what changes for the reader now that you have met this challenge?

Note that the above structure is called “OCAR” in Writing Science, for Opportunity, Challenge, Action, and Resolution (tehcnically they use “Opening” instead of “Opportunity”, but I like “Opportunity” more). Steps 1 and 2 form the opportunity, steps 3 and 4 form the challenge, 5 is action and 6 is resolution.

When considering which results to mention in the abstract, consider the following: the killer fig gets two sentences. Any other figure could get up to one sentence, and result that is not a figure does not get mentioned.

  1. Generate a “take home message” for each of the figures you plan to create. These become the first sentence of the figure caption.

  2. Ask for feedback from senior and other co-first authors. Explain that the role of feedback at this stage is for them to tell you whether they think there are any glaring flaws with the basic setup, eg, do they have a different idea about what is the biggest challenge. There is no need to knit-pick about grammar at this stage.

  3. Figures
    1. Make a first draft of all the figures and tables with detailed captions (~ 1 week). Captions should each be about a paragraph long. At this point, the figures need not be “camera ready”, but should have all the main points made.
    2. Get feedback on figures from co-authors and close colleagues (~1 week). Show them the figures, do not show them the captions, and ask them to tell you what the main point of each figure is. If they don’t get it right, don’t worry about it, take notes on what they thought, and ask them to go to the next figure. Then, spend another week updating the figures, and repeat.

  4. Outline

    1. Write a “long-form” outline of the intro (~1 hr). This is essentially an expansion of the abstrast, and is therefore structured as follows:
      1. a bulleted list of ~3-5 main factors that create an opportunity for your work, filtering from most general to most specific, and not including anything ancillary (~20 min)
      2. bulleted list of the ~3-5 main challenges that must be overcome (~20 min)
      3. 1 sentence summary of the gap, that is, the key ingredient that is missing (~5 min)
      4. 2-3 sentence summary of what you did (~5 min)
      5. 2-3 sentence summary on how your work changes the world (~5 min)

    2. Outline the methods. (~20 min)

    3. Outline the results results (~20 min). Allow for at least one paragraph per figure, table, and/or theorem. These paragraphs follow the following form (no need for them to be proper “paragraphs” at this point):
      1. a sentence describing the setting,
      2. a few sentences providing additional details, and
      3. a concluding sentence providing the take home summary.
    4. Outline the discussion (~1 hr), to include (not a summary)
      1. bulleted list of previous related work (~20 min)
      2. bulleted list of potential extensions (~20 min)
    5. Get feedback from your co-authors. At this stage, the question is whether the logic is sound, meaing, based on the challenge you proposed, the sequence of results provides compelling evidence that you’ve satisfactorily addressed it. If they disagree, iterate until there is agreement.

  5. Venue

    1. Read the top 3-5 most cited/downloaded articles from each potential venue to submit to, to see what the readership of that community likes. This will help you both choose the appropriate venue, and write effectively for that venue.
    2. Choose the actual journal/conference you will be submitting to. Until this point, it is irrelevant, since you’ve only been focusing on the logical structure of your story. However, before you start writing, you want to make sure you are writing for a particular target audience, and write for them. This is because different venues have different expectations, which you’d like to meet.
    3. Note the structure and approximate length of the venue of choice for the top articles published there. Do not worry about length at this time, just note down how many pages and figures they have, if they have an explicit methods section, if they have a preferred outline structure.

  6. Draft

    1. Expand the outline into a full draft. Do not concern yourself at this point with the details of what the publisher wants, we will deal with that later. The point of this is to simply have a draft at all.
    2. Check that paper follows all relevant checklists, including:
      1. figure guidelines
      2. paragraph guidelines.
      3. words guidelines.
    3. Read the paper carefully outloud, and remove any words that are unnecessary.
    4. Make sure each display item (e.g., figure, table, or theorem) is enumerated and explicitly refered to in the main text. If you are using LaTeX, use \ref{fig:<informative_name>} to refer to each display item. Recall that when referring to sections or figures, etc., the name of the section/figure is a proper noun, and is therefore capitalized.
    5. Make sure you have sufficiently cited the literature to place your work in context. For conferences, it is typical to have about 1 page of citations (10-20). For journal articles, 30-50 is more typical. Recall, the authors of these papers are likely to be the reviewers and readers for this paper. So, it is important that you highlight all the important work, and say how great it is. In particular, you want your readers to feel good about themselves while they are reading your work, which you can facilitate by citing their work, and explaining why it is so great and important. This is, of course, actually true, since you are building on this work, and your work would likely not even be possible without the work you are citing. If you are using Google docs, I recommend using the Paperpile “Add-On”.
    6. Get feedback again, ideally from a professional editor. At this stage, feedback on logic/etc. is no longer appropriate, so be clear when asking for feedback that you are asking for feedback whether the individual sentences/paragraphs are clear, and random grammar/spelling mistakes. The opportunity to provide feedback on logic has passed.

  7. Revision

    1. Update abstract and introduction to finalize draft on text (~1 day).
    2. Revise manuscript addressing each and every concern you were made aware of by any of your readers at this point (~1 week). This does not necessarily mean making new figures, rather, it might mean clarifying various points of confusion.
    3. Do another round of feedback, give them another week.

  8. Submission

    1. Finalize manuscript (~1 wk). I recommend that you fully ignore all guidelines provided by the journal, and you submit that which you believe will be easiest for the editors/reviewers to read and understand. I have almost always done it this way, and the submission is almost always reviewed anyway. If it gets good reviews, we can modify it so it fits their rules. An exception is conferences, where they actually care.
    2. If your code is not yet open source, make it so, following the FIRM principles
    3. If your data are not yet anonymized and open access, make it so, following the FAIR principles.
    4. Draft a cover letter (in google docs if you are writing in google docs, or in the same overleaf repo as the manuscript if you are using overleaf). The cover letter has the following form:
      1. It is on institutional letterhead
      2. Dear [name of editor that will be reading the letter],
      3. Paragraph 1
        1. We are delighted to submit to you our manuscript submission titled, “[title],” for publication as a [type of article, assuming there are multiple types in the journal].
        2. Establish the gap that this paper is filling is clear non-technical terms
        3. State how one could address this gap.
      4. Pargraph 2:
        1. Summary of main contributions of the manuscript, in non-technical terms. One sentence per contribution.
        2. Conclude by stating what we expect the implications will be for their readership, and more broadly
      5. Signed by the corresponding author, “on behalf of my co-authors”
      6. Add a ps - that all the code is open source and all the data is open access, in accordance with the above mentioned principles.
      7. The language can be more flowery/confident about the expected importance of the contribution than you would write in the article itself.
    5. Submit to journal.
    6. Post to pre-print server.
  9. Rebuttal

Great, you’ve now submitted the work, waiting some number of weeks/months, and received detailed feedback from the editor and reviewers. How to respond? Note, no matter what they say with regard to accept, minor revision, major revision, or reject, we essentially respond in the same way.

  1. Respond immediately, unless you have a grant deadline, revising this paper is now your #1 top priority bar none. All upcoming conference deadlines, and anything else you are working on now take a back seat. The sooner you get the responses, the sooner they read them, and the less they forget what they read/wrote, and the less likely they are to re-read your whole paper, and give us a whole new set of complaints.
  2. Make a google doc, copy the entirety of the comments you received into it. Change the font color for all of their comments to red.
  3. After each “complaint”, make a line break, and respond directly to it. (Basically) Never disagree with them. The game now is simply to address the comments (ego) of the reviewers. Any comment they made is useful, at a minimum, to inform us as to places where readers might be confused about why what we did is so awesome. Sometimes this will mean making your paper slightly worse to appease them. I find it is typically worthwhile. In the response,
    1. Tell them how great they are for identifying this problem with the manuscript, and express gratitude for them finding it, really try to feel grateful, your response will be more productive;
    2. Tell them how you have altered the manuscript to address the issue. Yes, this means modifying the manuscript to address each and every one of their complaints, no matter how big/small they are. This includes certainly citing everything they recommend you cite, and also praising that work in the actual text.
    3. For any big changes, such as a modification/addition of a figure, or a new paragraph, directly append the new/revised content into this document. The goal is to make sure the reviewer does not look back at the original manuscript, lest they might find additional limitations that they want addressed. Quotes from the paper should be in blue, to highlight that they are quotes. Note: send the google doc proposing changes (but without implementing any yet) to your PI to get the green light on how to response, once you have the green light, proceed apace).
  4. Send google doc to your co-authors with track changes on. Often a good idea to also make a back-up copy of the rebuttal prior to sharing with them just in case. Specifically ask for feedback of the following form: “if you were the referee, and you saw that I responded thusly, would you be satisfied or not?”

If you follow the above plan, you will have a manuscript ready to submit two to three months after you start writing. Note that it includes many stages of feedback, and at each stage, a specific kind of feedback is explicitly requested. This procedure helps streamline the amount of work you do between iterations, and streamlines the entire process. Good luck!