Writing Tips: Methods Overview

What are the interesting computational ideas underlying a new computational method?  What are the intuitions behind the method?  How is the method related to other methods?  These are the key question that papers which describe new computational methods should be answering.
Unfortunately, most papers describing new computational methods don’t explicitly address these questions due to constraints of the journal styles.  Introduction of methods papers often have a only few sentences about the method.  The Methods section typically has many more details but has very little discussion of the underlying ideas.   Understanding what is interesting about a method is left completely to the readers imagination.  Often, the journals request that the Results section precede the Methods section which then makes understanding the results very difficult without the reader reading the sections of the paper out of order.  Authors can appeal to the journal to have the Methods section first, but this is also not a good solution since there are many details in the Methods such as descriptions of the datasets which take away from the flow of the paper.
In order to avoid these problems, in our papers, we make the first subsection of the Results section of the paper a “Methods Overview.”  In this section, we describe the method in terms of the high level ideas and typically include as a figure a small example which we utilize the help the reader understand the example.   The goal of this section is to give enough details that the readers can then follow the rest of the Results section without requiring looking at the Methods section.  A well written Methods Overview will make it much easier for the reader to follow the actual Methods section.
These sections and examples are designed to be self contained and should be in a language appropriate for a general audience.  In fact, some of the blog posts are almost verbatim copies of the Methods Overview sections of some of our recent papers.  For example, see these blog posts on GRAT and Genome Reassembly.
Another way to think of what to put in the Methods Overview section is what you would explain in a talk about the method.  Often presentations on computational methods have excellent slides showing intuitions and very clear examples.  The place to put that kind of material is in the Methods Overview.  Remember, in your paper you must give a compelling argument as to WHY your method is interesting. If your readers don’t understand the intuitions underlying your work, they will never appreciate it.
I’m sure you may be asking, “Isn’t this a little redundant?” What I’m proposing here may be a bit repetitive, with a methods overview section and a methods section later in the paper.  But they serve different purposes.  With a well written Methods Overview section, a reader can stop after the Results section and understand most of your paper.  The Methods section then only becomes important for someone who wants to understand all of the details.