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!

Writing Tips: Getting Organized (and Staying that Way)

Up to this point, I’m sure most of you are saying, “That’s great, but what about YOUR lab? What do YOU do?”

Following the advice in the book How to Write a Lot by Paul Silvia (see our blog entry about the book here), I (and everyone else in the lab) set aside time exclusively for writing.  Given that at any time there are over a dozen papers in various states written in the lab, how to allocate that time across the different projects is not that obvious.  This piece of advice is probably more appropriate for someone running their own lab, and not a student.
What I do is inspired by the book’s advice to create a priority list of our writing projects based on how close each paper is to being completed.  Our lab has been tracking our papers and projects in Evernote monthly since October 2012 and continued to the present.  Overall, this approach, as well as setting aside dedicated time for writing, has significantly increased our lab’s overall productivity. We finish our papers much faster and spend less time being “stuck” without making much progress for long periods of time.
Here is exactly how we organize our Evernote notebook.  Each month I create a new note (this month’s note was called “Paper Organization February 2015”).  It starts as a copy of the previous month’s note and is updated as things change throughout the month.
The Evernote document has several lists of papers in order to how close they are to be completed.  Each paper entry in the list has a short title as well as the key student authors working on the paper.
Submitted Papers:
These papers are currently under review.  They are in this list because we don’t need to do any actual writing work, but periodically, we should check with the editors to see what is going on with the review process.  In the note, I keep track of where the paper is submitted.  Even when a paper is accepted,  I still keep it on this list until it appears in print and in Pubmed.  This way we can keep track of the paper through the proof editing process, uploading copyright forms, etc.  The reason these papers are listed first is that it only takes a few minutes to check in to see if anything needs to be done with any of these papers, but if something needs to be done, it is usually urgent.
Revise and Resubmit Papers:
This category is to track the papers when they have come back from review.  Regardless of whether the paper was accepted/rejected or whether or not the journal is willing to review another version, what we need to do is revise the paper taking into account the feedback and get it resubmitted as quickly as possible.  If the journal is willing to take a revision, then we also need to write the response to reviewers.  Since these papers are so close to being completed and published, any paper in this category takes priority over the remaining. During my allocated writing time, I usually spend the time writing the response to the reviewers and helping organize with the students what edits need to be made to address the reviews.
Active Papers:
This category keeps track of any paper that is currently being written by someone in the lab as their primary project.  I check in on these papers regularly and hopefully whenever my scheduled writing time comes around, I have a draft of one of these papers from a student who works on it, and I can make a pass on the paper and send back the edits.  If I don’t have any edits, I have the list of the students who I can send a reminder to ask for them.
Future Papers:
This category keeps track of the papers in the lab that we plan to work on or were working on before but the student who was working on the paper is no longer pushing it forward.  The reason we keep them separate from the Active Papers category is to keep it from distracting us when we are setting our writing priorities.  Anything in this category isn’t being actively pursued.
A few other categories that we have experimented with over the years is keeping track of “Collaborator’s Papers” where we are involved in the analysis, keeping track of “Grants” that we are writing, and keeping track of “Collaborator’s Grants” where we are responsible for contributing sections.
Our lab is pretty big right now and currently, we have eight submitted papers, seven papers we are revising after reviews and 14 papers which are currently being actively written by a student. Many of these papers will be completed and published in the next six months, but for a select few, we may be working on them for the next two years. Unfortunately, this is typical, as a paper which was just published from our lab was originally submitted for the first time in December 2012.  Keeping track of these papers in this way helps us keep organized and to prioritize our efforts.
Have any methods that work for you? Would you like to comment on what you’ve read so far? We’d love to hear from you!