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.

Writing Tips: Introduction

In this blog post, I would like to “introduce” you to our introduction style. Writing the introduction is the most daunting part of the paper writing process, especially for students who are not native english speakers. To help structure the introduction writing process, in our lab we have developed a standard style or template for writing introductions. Since the majority of the papers that we write are papers that describe new computational methods, many of our papers naturally fit into this style. We usually publish our papers in Genetics journals which have very high standards of writing and are read by researchers with a wide range of backgrounds. The difference between a paper getting accepted and rejected is often determined by the clarity of the writing.

Our introduction style is a very specific formula that works for us but obviously there are other ways to structure an introduction and each experienced writer will have their own style. However, the truth is, you NEVER start out as a good writer and new writers need to start somewhere. It takes practice, consistency and effort to write well. If you are a new writer apprehensive about writing an introduction, we hope that this structure can help you.

Our introductions are typically four paragraphs long with each paragraph serving a specific role:
1. Context – First, it is important to explain the context of the research topic. Why is the general topic important? What is happening in the field today that makes this a valid topic of research?
2. Problem – Secondly, you present the problem . We typically start this paragraph with a “However,” phrase. Simple example: We have this awesome discovery in XYZ… However, using former methods it will take us 10 years to run the data. Each sentence in this paragraph should have a negative tone.
3. Solution – By this point, your readers should sympathize with how terrible this problem is and how there MUST be a solution (maybe a little dramatic, but you get my point). Paragraph three always starts with “in this paper” and a descritpion of what the paper proposes and how it solves the problem in the second paragraph.
4. Implication – The last paragraph in your introduction is the implication, which describes why your solution is important and moves the field forward. Typically, in this paragraph is where you summarize the experimental results and how they demonstrate that the solution solves the problem. This paragraph should answer the readers question of “so what?”.

An example of the 4 paragraph introduction style is in the following paper:

Mangul, Serghei; Wu, Nicholas C; Mancuso, Nicholas; Zelikovsky, Alex; Sun, Ren; Eskin, Eleazar

Accurate viral population assembly from ultra-deep sequencing data. Journal Article

In: Bioinformatics, 30 (12), pp. i329-i337, 2014, ISSN: 1367-4811.

Abstract | Links | BibTeX

Most of our other papers in their final form do not follow this format exactly.  But many of them in earlier drafts used this template and then during the revision process, added a paragraph or two expanding one of the paragraphs in the template.  For example, this paper expanded the implication to two paragraphs:

Kang, Eun Yong; Han, Buhm; Furlotte, Nicholas; Joo, Jong Wha J; Shih, Diana; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar

Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice Journal Article

In: PLoS Genet, 10 (1), pp. e1004022, 2014, ISSN: 1553-7404.

Abstract | Links | BibTeX

and this paper expanded both the context and problem to two paragraphs each:

Sul, Jae Hoon; Han, Buhm ; Ye, Chun ; Choi, Ted ; Eskin, Eleazar

Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches Journal Article

In: PLoS Genet, 9 (6), pp. e1003491, 2013, ISSN: 1553-7404.

Abstract | Links | BibTeX

For methods papers, sometimes what are proposing is an incremental improvement over another solution. In this case, moving from the context to the problem is very difficult without explaining the other solution. For this scenario, we suggest the following six-paragraph structure:
Problem 1 (the BIG problem)
Solution 1 (the previous method)
Problem 2 (Why does the previous method fall short?)
Solution 2 (“In this paper” you are going to improve Solution 1)

An example of 6 paragraph introductions where the 3rd and 4th paragraph were merged is:

Furlotte, Nicholas A; Kang, Eun Yong; Nas, Atila Van; Farber, Charles R; Lusis, Aldons J; Eskin, Eleazar

Increasing Association Mapping Power and Resolution in Mouse Genetic Studies Through the Use of Meta-analysis for Structured Populations. Journal Article

In: Genetics, 191 (3), pp. 959-67, 2012, ISSN: 1943-2631.

Abstract | Links | BibTeX

There it is… the beginning to a great paper (at least we like to think so!). Will this work for you? Have other ideas? Let us know in the comments below!

Writing Tips: How we Edit

This is an example of our edits.  The red marks are directly edits and the blue are high level comments.

This is an example of our edits. The red marks are directly edits and the blue are high level comments.

In our last writing post, we talked about how our group of a dozen undergrads, four PhDs and three postdocs (not to mention our many collaborators) stays organized. This week we would like to focus on our paper writing process, and more specifically, how we edit.

Believe it or not, each one of our papers goes through at least 30 rounds of edits before it’s submitted to be published. You read that right… 30 rounds of edits. Each round is very fast with usually a day or two of writing, and we try to give back comments within a few hours of getting the draft. Because we are doing so many iterations, the changes from round to round often only affect a small portion of the paper. The writing process begins in week one of the project. This is because no matter how early we start writing, at the end of the project, our bottleneck is the paper is not finished even though all of the experiments are complete. For that reason, starting writing the paper BEFORE the experiments are finished (or even started) leads to the paper being submitted much earlier. Some people feel that they shouldn’t write the paper until they know how the experiments are finished so they know what to say. I completely disagree with this position. I think it is better to start at least with the introduction, overview of the methods, the methods section, the references etc. If the experimental results are unexpected then the paper can be adapted to the results later. However, getting an early start on the writing substantially reduces the overall time that it takes to complete the paper.

To jump start the students writing, I sometimes ask them to send me a draft every day. We call this “5 p.m. drafts.” Just like we mentioned in our very first writing tips post, the best way to overcome writer’s block is to make writing a habit. What I find is that if I get a draft that is one day of work or a week of work from a student, it still needs the same amount of work. This is what motivates our writing many many many iterations.

This is an early edit where we did a lot of rewording. For this, we use notes or text boxes.

This is an early edit where we did a lot of rewording. For this, we use notes or text boxes.

Editing in our lab is certainly not done in red ink on paper. That would be WAY too difficult to coordinate the logistics. The way we do it is via a PDF emailed from the students. I edit it on my iPad using the GoodReader app, which can make notes, include text in callouts, draw diagrams and highlight directly on the document. GoodReader also lets me email the marked PDF back to the students directly. It typically takes 30 minutes to an hour to make a round of edits. This inexpensive iPad app has increased our workflow and decreased our edit turnaround significantly. Keep in mind that I don’t always need to make a full pass on the paper, but just give enough comments to keep the student busy during the next writing period (which can be one day).

Since my edits are marked on the PDF, the students needs to enter the edits into the paper. This is great for them as they get to see the edits and this improves their writing. Previously, when I would make edits on the paper directly, they wouldn’t be able to see them. When I edit, I make direct changes in red and general comments in blue.

Like our method? Let us know!