We’re going to use the IDEAS framework which stands for:

and this post covers the IMAGINE part where we think about important factors related to our paper before we start writing, thereby eliminating writer’s block.

I've been using this framework for the last 17 years to write and publish my own papers and I've taught many grad students, undergraduates and postdocs how to write and publish their papers, as well. All without the stress, writer’s block, endless iterations, or numerous rejections.

So what type of article do you want to write? You should think about this at the beginning because this will really define HOW you will write the paper. There are research articles, short articles, methods papers, review articles, protocol captures, data set papers, case studies, commentaries, editorials, and more.

Each of those different types of articles have a very different style and length. Thinking about this before you start writing is crucial because it determines how you're going to write it and what the writing style is going to be. The article types and names differ by journal.

Check out the journal’s author guidelines (for example for Scientific Reports) for the types of articles and their formatting requirements.

And keep in mind that not all article types are unsolicited, some are invited or commissioned. For instance, Nature has many commissioned sections, meaning that you cannot just submit an editorial because it will be decided internally by the journal who is going to write this and what this is going to look like.

Research articles, which what we’re covering in the IDEAS framework, describe new research findings. This could be a particular system, let's say, a biological system, a new database, an application of a method to a new system, or a new methodology.

When you think about what the goal of the paper is, you need to think about your audience. Who is going to read your paper? We write papers to communicate our science, and in scientific publications, we do that in written form, which is the paper.

Let’s think about communication in a different way for a minute. Let's imagine you talk to a friend who is not in the same lab, who really has no idea what you're doing. When you're explaining your science to them you can see how much they understand depending on their reaction, their facial expression, and their body language.

Unfortunately, this type of feedback is absent in a paper. However, when you write your paper, it actually makes it a lot easier to write if you shift the focus from yourself to the reader, simply because you're asking yourself: How do you need to write something to make that understandable for somebody else?

What often happens when you start writing your first few papers, you think about mostly about yourself and how you get your thoughts from your head onto the page. But that's not the question you should be asking yourself. The question you should be asking yourself is:

What does your reader need, for them to be able to understand what you are doing? This mindset shift often makes a huge difference in improving the clarity of your research paper. You want to be clear, you want to be brief, and you want to be quantitative.

Defining your reader and your audience will set the tone of the paper. It will define how much detail you will want to add for specific sections. It will determine how the story will be written. And different types of subject areas write things differently.

This is something that a lot of people don't think about, but it can save a lot of time in the long run if deciding on that before you start writing. One major way of keeping your draft moving later, is to use shared documents or a shared workspace. This saves time because you don't have to send back and forth a Word document or having to integrate edits from multiple people into a single document.

When using shared documents, you can just share the link to the document and people can edit asynchronously into the same draft. If you have a large number of authors, this is the only way to keep your manuscript moving (I’m talking from expertise here because I've written articles with 50 or even over a hundred authors).

When using a shared workspace, you need to think about what you need. You need to easily see the outline of your document. You need ways to comment, you need ways to edit, but it would be nice to also see the history of the edits. And ideally, you would want a shared workspace where you can share figures in an editable format.

Dropbox is great simply because, you can create folders and you can have all of your documents in one place, whether it's manuscript draft, the supplement, the figures, or anything else. The only downside I think it has is that sometimes the syncing results in them creates an additional document that you would have to integrate. And you're not necessarily editing a document live. You're opening a document that is then synced with Dropbox.

This one is my favorite because, even though there are disadvantages in using it, I have found writing manuscripts in Google Drive and with Google Slides and Google Docs is the easiest, simply because you can see live edits from your co-authors, you can edit the document with your co-authors simultaneously, and you don’t have to integrate any documents into one another. Plus, I usually share versions of the figures in Google Slides as well.

Overleaf is highly used in the mathematical and physics and computer science area. It's great for equations, but it requires compilation, meaning that you have to hit a button to compile the written document into a PDF. It’s not my favorite because you see two documents: the raw text document and the compiled PDF, so you don’t see the final version in the document you write. Still, a lot of people are using Overleaf and many journals provide templates to write your manuscript in.

So which journal are you trying to submit your manuscript to? This really requires some thought, simply because it's very easy for your paper to get rejected if you pick the wrong journal. Identify the journal based on the aims or scope, which you can find on the journal website - this should match your goals for the paper.

The impact factor is computed by the number of citations in a specific year divided by the number of publications within the previous two years, indicating the average number of times an article was cited within two years of publication.

You can Google the impact factor or you can often find it on the journal’s website (example HERE). The impact factor should match approximately the research that you're trying to publish. For instance, if you have a three-month project and you're trying to submit this to Nature, which has a very high impact factor, your paper is not going to get accepted simply because the match between the impact factor and your research is too large.

And last but not least, also think about some of the features of the journal. What brand does it represent? Is it open access? Who is on that editorial board? Sometimes these are decisions that can be easiest made by your PI. You can also ask your co-authors or talk to people in the lab where they usually publish their papers.

If you're writing a mathematical paper and you're trying to submit this to a biology journal, it's likely not going to get accepted. Thinking about this ahead of time really avoids rejection in a lot of cases.

Why NOT, you ask? Because you’re making it more difficult on yourself than it needs to be and this will result in more iterations of manuscript drafts.

So then: in which order are you going to write the sections and why?

Start with a preliminary title! To beat writer's block, start out with ANY title, and then revisit the title later. What we want to avoid is overthinking your title when you have nothing else on the page, as that would prevent you from moving forward.

Similarly, start with a preliminary author order without overthinking it too much at this point. This often changes slightly throughout the writing process. You want to have something on the page and then later on throughout this evolution of your draft, you can adjust this.

The methods section should be the first section for you to write because it’s the easiest starting point. You know the experimental details, or you can design your experiments that way, including all the specifics. You will revisit those details before submission but at this point, that should be the fun part. The benefit of this approach is that your experimental design, including the details, will essentially become your To-Do-list for your experiments.

This is the meat of your paper. But before you get into that, you need to create a storyline. What is the storyline of your paper? And how are you going to write it? We’ll go into more detail about that in part 4 of this series [LINK]. Once you have that, then you can write your results and discussion. After that, really the biggest parts of your paper are done.

Once the biggest parts of your paper are done, it's easy to write the abstract. Don’t write the abstract at the beginning of your paper writing process, because you won’t know at that stage what the storyline of your paper is going to be and what the main parts are to highlight in your abstract.

The same applies to the conclusion: the conclusion is easy to write once you know what your paper is going to be about. The abstract introduces the paper and the conclusion leads out of it.

Now it’s time to create the perfect title that matches the contents of the paper and is understandable.

Then, add references using one of the reference managers available and add the

Organize your supplement, make it follow the story of the paper so that it's not just like a dumping ground of random information.