How to Start Writing a Scientific Manuscript

Today’s blog is adapted from a presentation by Danette Daniels, PhD, in our webinar “Writing About Science: Tips and Tricks for Communicating Your Research.”


As scientists, we can do science forever. The beauty about science is that the questions never end – we can keep asking, and every time we find an answer, we have a new direction to pursue. But it’s very important to know when it’s time to write up your results.

Publishing may be connected to leaving or transitioning your position, but at all times you should be thinking, “What is my end goal? What is the big question I want to answer? What are the questions the field has about my research?” As you reach milestones and make discoveries, whether big or small, consider whether you will have a complete and compelling story to tell in the end.

Any time you have a new discovery, especially one that will be controversial, you can’t publish a paper with just one example. You’ll need to have orthogonal data or different approaches that support this new discovery. Along with this, you’ll need sufficient data to make a confident conclusion. Otherwise, the paper may not go out for review, your reviewers may ask for a lot more experiments, or you could be rejected.

What are the new results? How do they contribute to your field? How do they advance your field? Why would people be interested? Are there other areas of research that may be interested in hearing about your work? All of these questions can help you determine whether you have a compelling story for your article.

After you’ve determined whether you’re ready to write a manuscript, there are three main things you must do to assemble your article and prepare for publication.

1. Assemble your figures.

Figures are the heart of the paper. They help both you and your reader understand the work being presented. You may have ben working on your project for several years, or maybe multiple people have worked on the project. If you’re the primary author, assembling the figures allows you to start answering the question, “What have I accomplished?”

  • Lay out all the figures and choose the ones that are most supportive of your key conclusions. Gather all the figures – big and small – that you might want to put in the paper. Choose the ones that are the clearest and most important for representing your work.
    I like to think of this like a children’s story. There are tons of pictures in children’s stories. They’re trying to get you to visualize the story and see where it’s going without reading the words. Your figures should almost be able to do this. With so many publications out in every field, people will often take a paper and look at the first few figures and abstract to decide whether they want to read the rest of the paper. Could someone get the main points of your paper by only looking at the figures?
  • Put the figures in order of how you want to tell the story. Your experiments were done in a chronological order as you tried to answer questions, but the order in the paper is almost never the order that the experiments were done in. You want to put your most compelling figures first, to get the attention of the reader and set them up for your big breakthrough. Then, add the support of that breakthrough through the next figures. Finally, you want to save your most relevant data for the last figure. If I’m studying a new drug compound, for example, I’ll introduce it at the beginning, add the supporting data on the mechanisms and how it works, and end with data showing its effectiveness in different cell lines. This kind of story, from the beginning to the end with an impactful finish, helps you put together an outline that you can use to write.
  • Find a balance of main body data and supplemental information. Some journals may have limitations on the main body figures, but typically you should be able to have four or five main body figures without crowding the text.
  • Build your final model and make it clear. I like to put a schematic at the beginning demonstrating the overall concept and what’s unique about the approach. The last figure is also often a schematic or model, which is referred to in the discussion. If you can’t come up with a model in your head about how your discoveries have changed your thinking about a process, pathway or technical approach, then it will be very difficult to write a full paper. Think about the conclusion you’re driving your audience toward, or what you’re trying to convince them.
  • Don’t get sidetracked on making perfect figures. We could talk forever about the style of figures, but don’t get caught up trying to make them perfect at the beginning. The colors and formats can be fine-tuned later. Just lay them out and get the outline done, and you can go back for cosmetic work later.

2. Select journals for submission.

It’s easy to get caught up in journal prestige and the index for citation, but then you aren’t getting your work out there. There is a good home for all good papers.

  • Know the community or audience that is most interested in your findings. This can sometimes be more complicated than simply knowing the journals most closely related to your field. Sometimes the story may actually be two stories. You may have a fantastic biological story, but you have to do a lot of unique chemistry to get to the biology story. What is the scope of your paper? Is it a broad topic with two different audiences? You may have to think about a journal where both topics would fit, or consider breaking the specialty areas into a different paper.
  • Understand and appreciate the competitive landscape. You may be working on a competitive project where you need to get the paper out as soon as possible to avoid being scooped. You need the urgency of publication or you’ll lose your story, in some cases. Think about the typical review times – you talk to other people who have submitted articles to a specific journal to get an estimate of how long their process takes. Sometimes, you could choose a journal that can move a little bit faster just to be the first person to get the story out.
  • Try the best journal first, but be reasonable and realistic. We can’t all get our papers in Science or Cell, unfortunately. It’s easy to either underestimate or overestimate the importance of your work, especially if you’re a scientist who gets excited about even the smallest discoveries. Understanding where your discoveries fit in can be very difficult, and you need to ask, “Which journal is the best fit for this story?” I like to make a list of three journals and read the latest articles in each one. This helps me see which journals are publishing a lot of work in my area. You can lean on that information to say you believe your article fits a journal because it aligns with other articles the journal has published. I do generally try for the highest tiered journal first, but remember that if that doesn’t work, you’ll have to reformat and resubmit, which can cost valuable time if you’re in a competitive landscape.
  • Send your abstract for advance consideration. I like to write my abstract early and send it to the editor of a journal I’m considering. Sometimes they will ask for the abstract and initial figures. Editors can give you great feedback, or say they aren’t interested.
  • If an editor is not interested, it doesn’t mean your work is not valuable. Don’t take rejection personally. There are a variety of reasons why an editor isn’t interested in your article, and it likely just means your article is not suited for the goals of that specific journal. Take all information, even rejections, as an opportunity to learn. Maybe you need to rewrite your abstract because it isn’t clear. Think about your feedback, and then continue looking for the journal that will be a good fit.

3. Start writing!

No matter where you start, starting to write is the most difficult part of the entire process. Be happy to get words on the page, and start anywhere. We all get stuck – sometimes I take a break to walk or run around. Save the editing for later and just get words on the page. Get other people to read and help you edit. You are never alone, and you shouldn’t have to write a paper alone. Different perspectives on the arguments you are trying to make can help you strengthen the paper.

  • Start with an outline. The journal that you submit to might have its own guidelines for sections, so it’s important to tailor your message for a specific journal. Once I have the structure, I write out the big concepts. What do I want to cover in the abstract? Or the introduction? How do the figures define the results, and what are the big picture ideas I want to cover in the discussion? You don’t have to write it nicely, this is just an exercise to get thoughts on the page.
  • Gather all the papers you want to reference. This process can be long, but reviewing the papers in my field and seeing how their work is relevant to me gets my mind in the mood to write. I make little notes on them where I want to cite important facts, or where their results differ from mine. This helps you crystallize how your work is different. I also find it gets me enthused to see where my work fits into the field.
  • Results. If this is your first paper or you’re new to being lead author, the results section is the easiest place to start. It’s just logic. “I wanted to answer this question, so I did this experiment, and this is what I saw.” Sometimes, as you write the results, you’ll realize you want to change the order of the figures. That’s okay! It’s good to be flexible during this time.
  • Abstract. This is often the most challenging part, but it’s where I like to start. An abstract is short – typically around 250 words. In the abstract, you’ll make a short argument about the state of the field, what your big question was, what you did, what your conclusion is, and why your results are important. You have to do all of that in the abstract. Doing this early can give you the opportunity to get feedback from an editor.
  • Introduction. If you’ve already gathered the papers to reference, that can guide your introduction. You can just put placeholders in for the citations, and then add the details later. Remember, it would be better to reference a paper with different results or conclusions than to have a reviewer bring it up later.
  • Discussion. The discussion is usually written last. This section gives you a chance to restate your results and frame them in the context of the field. You also have some liberty to show your forward thinking. You can mention experiments you were unable to do, or propose next steps. Maybe you want to set your audience up for your next paper on the subject. This is the space for you to show your creative thinking as a scientist and demonstrate not only that you saw a problem in the field and solved it, but that you’re thinking about the next problem as well.

Looking for more information on science writing? Check out our recent webinar: Writing About Science: Tips and Tricks for Communicating Your Research.


Check out our Student Resource Center for helpful articles about basic molecular and cellular biology techniques, as well as resources for professional skill development.

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Promega products are used by life scientists who are asking fundamental questions about biological processes and by scientists who are applying scientific knowledge to diagnose and treat diseases, discover new therapeutics, and use genetics and DNA testing for human identification. Originally, founded in 1978 in Madison, Wisconsin, USA, Promega has branches in 16 countries and more than 50 global distributors serving 100 countries.

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