How to Write the First Draft of an Academic Research Paper

Actually making a start and putting together a first draft can certainly be the biggest stumbling block to getting a paper submitted. Unless you make a start, it’ll never progress! Drafting your first paper is even more difficult when you don’t yet have experience writing papers and submitting them to journals.

I know from experience how daunting the prospect can be and just how easy it is to unnecessarily procrastinate for months. But it doesn’t have to be difficult and the main thing is making a start. I’m here to try and help making the process less daunting for you!

This guide to drafting your first academic paper forms part of the publishing series. I suggest reading these associated posts in particular:

• What to publish
• When to publish
• Where to publish

What to include in your first draft of an academic research paper

Let me start by saying that no one should be expecting for your first draft to be perfect! I wasted months of time on my first paper because I wanted to perfect everything, down to the wording, before sharing it with my supervisor. This is completely the wrong approach!

Instead of perfecting your first draft, just work to form the rough structure of your paper around whatever you want your key message to be. We discussed this further in the separate post: Deciding what to publish from your PhD work. Simply try to ensure your first draft roughly tells the story of what you want your main message to be.

It is absolutely fine for your first draft to be a rough cut, it should simply serve as a starting point. Therefore for example you can include extra figures you’re not sure about to be able to discuss with your co-authors whether or not they should be included. Throughout the drafting process you want to aiming to make your key message as clear and robust as possible but for now it’s fine to not be sure on the finer details. It may help to look at your favourite papers from the literature to get an idea what papers in your field typically include.

For now, don’t worry the quality of the written text, or finalising your figures. You want to use the first draft to form the rough structure and be a starting point for discussion with co-authors.

Let’s now discuss how to structure your first draft.

Structuring your first draft

If you already have a certain journal in mind to submit your paper to, how you structure your draft may slightly depend upon the format that the journal asks for. It’s a good idea to check their Author Instructions page which should include a “Guide for Authors”: a walkthrough of each section of the paper. Oftentimes there may even be a template you can download including section titles and advice for structuring your text.

If you don’t yet have a journal in mind, don’t worry. For the most part all journals follow the same format. For an original research paper, usually you’ll include sections as follows:

1. Abstract – typically around 200-250 words or less.
2. Introduction
3. Methods
4. Results
5. Discussion
6. Conclusions – sometimes appears as the final paragraph of the discussion section.

Then followed by Author Contributions, Funding sources, Acknowledgments, Conflicts of Interest, any Supplementary files or Appendix and finally the list of References. None of these sections you really have to worry about at this stage.

Let’s go through roughly what to include in each section:

Introduction:

• A brief review of previous literature to set the scene;
• The motivation for the study;
• The aims of your study;
• Sometimes you may include a very brief overview of your main findings. See what other papers in the journal do.

Methods:

Always include enough detail for someone else to be able to repeat your experiments, including:

• How many samples did you test? How did you process them? Were there inclusion/exclusion criteria?
• If you synthesised or processed physical samples, what materials have you used? Include processing temperatures, durations of each step etc.
• What equipment and consumables did you use? Include the item code, model number and manufacturer.
• How did you process the data? Name the software package, version and operations you performed.
• Details of any statistical analysis: software packages, models, methods, inclusion/exclusion criteria and so forth.

In all instances where you followed a method developed in another paper, include a reference to that paper. Not only is it good practice to give credit where it is due but you’ll have an easier time with peer review demonstrating you’re following the convention.

Results:

Remember, you shouldn’t be discussing findings in your results section, simply presenting them. Therefore there shouldn’t really be any suggesting why the results are a certain way. The exception is where the journal specifically allows results and discussion sections to be combined. Further on in this post is a section about choosing figures and results to include in your paper, and most of these will appear in your results section.

• Your results should aim to convince the reader of your key message.
• Be conscious that when first looking at your paper, most readers will go straight to looking at your figures.
• Cite every figure you include, in the order you include them. Clearly explain what is being presented.

Discussion:

The way I was taught to write a discussion was to simply use four paragraphs/sections covering:

1. Your key finding. You can even start it with the sentence “The most important finding of this work was”
   
2. Comparison to previous literature. How do your findings compare to other papers? What was the same? What was different? How do your findings progress the field? What would you recommend next?
   
3. Limitations. Every study has limitations, don’t try and hide them. Be honest with what wasn’t ideal during your study. Examples may be: small sample size, imperfect analysis, impractical sample processing. If you can, cite other papers which relate to these limitations: either in regards to why it’s not such a big problem, how it is common problem, or potential solutions or improvements for future studies. In any case, be honest. You can recommend future work to overcome these limitations if appropriate.
   
4. Conclusions. Give a brief set of conclusions with reference to the potential impact of your work for future studies.

You can see how I used exactly this format for a recent paper available here.

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Eager to learn more about the steps involved in publishing your first paper? My academic publishing series is now available as a free eBook which you can read offline. Click the button below for access.

In which order should you write the sections of the first draft?

Everyone writes papers differently, so what works for me may not work well for you. Personally once I start a document for a new paper, I typically write notes for each section as I think of them but go with the following strategy to get the text written.

Generally it is acknowledged that the methods section is an easy section to write, so I would suggest starting there. Even if you’ve got writer’s block, writing your methods is pretty robotic and shouldn’t require much thought. It simply involves writing down the process you went through to collect all your data. Writing the methods is an easy starting point which should give you confidence to dive into the other sections. In the above graphic I’ve separated the conclusions from the discussion but often the conclusions will simply be the final paragraph of the discussion section.

After the methods you can start drafting your key results and your discussion will naturally follow from there. If you follow the structure for the discussion as outlined in the section above, it should also be formulaic and pretty easy to write if you’ve got a clear message.

By all means crack on with the introduction whenever you fancy. If you’re in the mood to write it, don’t stop yourself! I personally like to write notes for it and include key references as I’m going along, but write the bulk of it after the methods, results and the bulk of the discussion.

Usually it is recommended to write the abstract last once everything else is finalised.

Choosing which figures to present

Remember you’re creating a story around your key message. As such all your figures should be helping to convince your reader of your key message.

• Be aware that there are sometimes limits on the maximum number of figures you’re allowed to include (around 8) in the main text of your paper. Usually you can move figures to a supplementary section if necessary. Prioritise the most impactful figures to illustrate your main point.

• Each figure should aim to address a certain point around your key message to convince readers. You can combine figures as panels within a larger figure but only do so if they address the same overall point. Don’t confuse readers by combining loads of unrelated things just because you’re running out of space!

• Always make sure the caption fully describes what the figure is showing. The figure and caption should explain what is going on without the reader having to read any of the main text. What type of equipment generated the data? How many samples were tested? What do the error bars show? What is the scale? For stats: what is the p-value?

You may need a figure to describe your methods but after that usually you’ll try to include figures in an order which tells a story. Importantly: this order may not be the one in which experiments actually took place. You’re trying to tell a story to get a message across, not write a diary! It’s no problem to move sections of results around if it makes for a more convincing message, especially for readers who may only have a quick glance through your paper.

For example you may wish to start with your key finding, then follow with any validation work, then finally include more details to convince the reader. It will really depend on what suits the work you’re doing, but remember that you have full control and your aim should be to make a clear story.

My top tips for putting together your first draft of the paper

Iterate Quickly

My main bit of advice is to get a first draft put together pretty quickly otherwise you risking wasting lots of time like I did! I wish I had sent the initial drafts of my first paper to my supervisor sooner. I spent far too long trying to perfect it down to the exact phrasing of sentences. There is no point getting to this level of detail if there is potentially an improved completely different direction to take the paper in!

What I’ve found to work really well is to set deadlines with your supervisor to ensure you are making progress to submission. You don’t have to have the full paper available all at once. I have had calendar invites set up saying by a certain date I’d have sections of the paper sent across, and to limit procrastination no date was more than four weeks away.

After your supervisor(s) has had a look, send it across to any co-authors. It may take a few iterations until everyone is happy. Once you have the backing of your coauthors, don’t be scared to submit your manuscript slightly sooner than you feel comfortable.

A reviewer is pretty unlikely to outright reject your paper if they want more experiments to be carried out: they’ll ask for what they want in the review process.

Always think about the next publication

Once you start writing, you may struggle deciding what to include and what not to. Remember though that this doesn’t mean you need to delay publishing if you already have a clear story. Unless all your work sits together very neatly, please resist the urge to include everything in a single paper.

If you’ve got results you’d like to publish but they don’t sit nicely with the main message of this paper, you can always consider publishing them separately later. It is much more important to create a clear message with a coherent story than to include extra work just because you did it!

Although some academics shun the “salami slice” connotations of having many smaller papers, it doesn’t always make sense to force different experiments together in to one paper. I recently published two different papers in the same special issue of a journal, both were related but had very different messages:

• Quantifying 3D Strain in Scaffold Implants for Regenerative Medicine
• Exploratory Full-Field Mechanical Analysis across the Osteochondral Tissue—Biomaterial Interface in an Ovine Model

It wouldn’t have made for a stronger paper to combine them because in essence they were telling separate stories.

It’s fine for your first draft if you’re not exactly sure what to include. Once you’ve got the rough form of the paper sorted, you can add or reduce bits as necessary. The key thing is to get a first draft done to get the framework for the paper. No one is expecting it to be perfect!

Word vs LaTex

I know some people enjoy using LaTex for their documents, but I’ve never used it. Everyone I’ve always worked with uses Word, so even if I was keen to use LaTex I’m not sure that it would be that easy to collaborate on documents to track changes etc. Journals will often request the paper to be submitted as a Word document so probably save using LaTex for your own internal reports or theses.

Keep your data, files and figures organised

This point extends far beyond your first draft of a paper! Once you start iterating on papers, it becomes more important than ever to know where all your key files are. Ensure you keep different version of documents clearly labelled.

Be prepared for reviewers to ask for modifications to figures or data to be reanalysed.

What I do is keep a folder for the paper and include the main working draft plus other relevant documents like notes or draft of the cover letter. I then have subfolders for data, figures and old drafts.

Aim to present figures with a clear message which are easy to “get”

Making figures is the focus of a whole other post which will follow this one. In short:

A lot of readers will initially flick through your paper and skip straight to your figures. It’s really important that the figures tell the story clearly and can be understood by just looking at the figure and caption. Also, if the readers don’t like the look of your figures, or can’t understand them, they’re less likely to bother reading the rest of the paper. Again, have a look at how published papers present their work to get some ideas.

You’ll want to make your figures in such a way that they can be amended easily to account for any adjustments suggested by co-authors or reviewers. I use a combination of Excel and Photoshop for most of my figures. There are lots of alternatives depending on what you’re presenting, GIMP is a free alternative to Photoshop.

If you make them in Paint and someone suggests making some alterations, it could take you ages. Instead if you make them in a non-binding software like Photoshop you can easily make non-destructive changes element by element.

It is worth spending time creating nice figures. Having polished figures makes your submission look more professional, ensuring the underlying science is easy to understand is critical too. Plus you can use them elsewhere, such as in presentations or other documents.

Got a draft? What happens next

The hard work is far from over once you have your first draft but you’ve overcome a really big hurdle in the journey to getting your work published. Now it’s time to discuss your draft with co-authors, incorporating feedback and changes into subsequent drafts.

There is no certain number of drafts you should expect to go through before submission, just know that you could endlessly spend time finding things to add (discussed here) and you should be very conscious to avoid doing! For my papers I think it took around four drafts until we felt happy enough to submit. Not all of your co-authors have to give feedback for every draft, I’d suggest the main people you’ll be liaising with will be your supervisor(s) though it’s certainly important that everyone has an opportunity to help.

Once all of the authors, including yourself, are happy with the paper, speak to your supervisor for how to proceed with submission. Some supervisors like to lead the submission whereas others prefer for the student to do so, and then to transfer “corresponding authorship” at the final stages before publication.

In any case, be prepared to feel vulnerable when you do eventually submit the research paper to a journal. This can be completely normal, your work is going to get critiqued! But remember that you’ve done great and rather than leave the data on a computer you’re motivated to pursue publication in turn helping progress your field. Well done!

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I hope this post has helped with your first draft of a paper! Remember that you can find the other posts in the series here: Writing an academic journal paper series. Next we’ll be covering creating figures and dealing with reviewers.

Please let me know what you thought of it or if there are any other details of publishing which you’d like help with.