Writing a scientific manuscript ─ getting started

Last Updated on May 13th, 2024 by Sharon Johnatty

As scientists we are not all gifted writers, nor is writing a manuscript a particularly enjoyable task compared to other aspects of research. Very few researchers actually ‘enjoy’ writing a scientific manuscript. Considerable time is involved, and there is the possibility of rejection by a reviewer who does not consider the months or years of hard work summarized in ~5000 words or less. Sometimes the ‘getting started’ stage can be the most difficult. This article is an overview of the process of writing a manuscript.

In general, you are ready to write your manuscript when you have reached that point in your research that suggests your results are publishable. That point may be fairly self-evident if you have closely followed an a priori hypothesis with a well-defined end-point. Some types of research can go on indefinitely (or as long as you have funding) if the answers to the research question generates more questions.

I have often heard senior researchers comment on the very clever researcher or collaborator who cannot write to save her/his life (or career). Getting into the necessary headspace to write can be the hardest part of research.

Here are some tips, gleaned from over three decades in research, on getting started with that manuscript that you’ve put on hold.

  1. Choose your journal. Create a list of journals that are suitable for your subject area and review their aims and scope. Try not to dwell too much on impact factor in the first instance, but think of where the articles that your research builds upon were published. For more on journal selection, see my earlier blog titled ‘Choosing the right journal – think before you submit’.
  2. Review your results. Thinking about the ‘design’ of your manuscript as you review your results will help you decide what other experiments you need, and what questions potential reviewers may ask. Plan your tables and figures before the write-up stage. These can be anything from flow-charts to graphs or illustrations that can be updated as more data comes in. You will know when the write-up stage is ready when the tables and figures tell a story. ‘A picture tells a thousand words’, so use them to your best advantage.
  3. Start with an outline. Create a blueprint that will guide your manuscript. This can be as detailed or as basic as you wish, and helps to ensure flow and logic. Lay out the different sections in your document according to the journal requirement and include any relevant formatting or word count so you don’t have to repeatedly refer to the online author instructions. Think of any subheadings in the Results section and include them in the blueprint. It is not necessary to list these chronologically, but I have found that it does help with outlining the logical thought processes that guided the work. The ultimate goal should be to tell the story as simply as possible without the day-by-day diary of events that led to the final result. Consider whether to include experiments that did not substantively contribute to the result. It is a judgment call whether a failed experiment (I don’t mean negative results) adds to the current manuscript, or is a distraction from the main finding.
  4. Create or update your referencing software. Whether you are using Endnote or another referencing software, check that you have imported all relevant references and you have the correct output style in your referencing software. Linking your manuscript to referencing software will make life a lot easier if you do this before your start writing. 
  5. Order of writing. Choose the order according to what inspires you most. Like a jig-saw puzzle, you can start at the top or bottom, left or right. I personally find it helps to write the Methods first, as this should be the least difficult section. Keeping a good lab book (a requirement of most research institutes) will help avoid frustration and ‘memory loss’ about complicated experiments you did months (or years!) ago. It may be helpful to write up results as you do your experiments or analyses, rather than waiting for the penultimate experiment.
  6. Write now, edit later. Very often my first draft will be full of ‘notes to self’ and ‘stream of consciousness’ text. There will necessarily be several rounds of editing before you are ready to share it with collaborators and co-authors. At the editing stage, aim for clarity and conciseness. Avoid overuse of transition phrases like ‘Next’ or ‘We then showed that’ etc. Any sentence that you need to do a double-take on needs to go! Fragment long sentences. Don’t get caught up with formatting requirements at this stage. That should be the last thing you do prior to submission, along with ensuring you have met the required word count. Remind your co-authors that you need substantive comments back when you send them the first draft — not formatting suggestions! 
  7. Keep a close eye on potential plagiarism. Most journals use plagiarism software, as do most reputable research institutions. Invest in plagiarism checks with your institute. Automated software will almost always detect a level of plagiarism. I recently got a report back from a fairly reputable journal, and was somewhat amused that standard phrases in my manuscript, like “associated with an increased risk” and “as a risk factor for” were flagged as plagiarism! Reasonable journals will not ask for changes to every phrase that the software picks up on, but will highlight the ones that require your attention. At all cost, avoid lifting entire paragraphs or sentences from published manuscripts or online resources. Also, ‘self-plagiarism’ needs to be avoided. If your manuscript is a follow-up to one you have published before, it can be tempting to save time and recycle sections that you legitimately wrote in a previous publication. This should be avoided because regardless of who originally crafted the words, the software will pick this up as legitimate plagiarism. 
  8. The nitty-gritty.
    • The title can be written at any stage of the process, and crafting one is not a minor element of the paper. Avoid long drawn out titles. Some journals put character limits on this. As a general guide, titles that run into 2-3 lines are too long. Try to find the phrase that ‘sells’ your work and encourages the reader to want to know more. Also, shorter titles that are easy to understand and informative are more likely to reach a wider audience and shared on social media than those with scientific jargon (reported in Journal of Clinical Epidemiology 2017). More on crafting a title can be found in my blog titled “It matters how your write”.
    • The Abstract may be one of the last sections you write. Word count limits will force you to again focus on the main message. Where there is a lot of information in the Results, prioritizing what to include in the Abstract can be daunting. Work your way back to the a priori hypothesis and the main result. Remember to include key words and search terms in your Abstract that may be used by other researchers for PubMed or Google Scholar searches.
    • The Results section is what reviewers tend to focus on. Take the time to properly format your tables and figures, and avoid sloppiness. As a reviewer, I have seen manuscripts with tables that look like they were just pasted into a Word document from Excel without any attempt to reformat them. The same applies to images. Be pedantic about data presentation. You run the risk of a reviewer expecting the rest of the paper to be sloppy if they cannot make sense of your data.

              Planning for a manuscript takes time and commitment. My best advice to doctoral students and early career researchers is try to start writing early on in your career, as there is no avoiding it. Pay attention to the writing styles of your mentors, and be open to their advice, edits and comments on your draft. Good mentors will also provide guidance in developing writing skills. Some universities and research institutions will offer writing workshops. Take advantage of these opportunities whenever possible. Allocate time at the end of each day to actually write up your results as your research progresses. Writing skills take practice, so start early. 

              Finally, celebrate your achievements!! Publishing your research is a major career milestone worth celebrating with your colleagues. Make it memorable!

              At SugarApple Communications we are experienced in all stages of the publication process, and can advise on data presentation and analysis. If you are time-poor and need to get that manuscript out, get in touch today and let us talk.

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