-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathhowto_write_paper.qmd
94 lines (64 loc) · 6.27 KB
/
howto_write_paper.qmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
# Writing papers
## How to write a scientific paper once we decide that you have one or more interesting results
*Start by discussing with me what the paper is about!*
### Figures and Tables
- Create a draft of your ideal set of *Figures* & *Tables* (in addition to supplements) that can tell an interesting, coherent story.
- Write detailed figure/table legends to help understand what piece of the story each figure/table will convey.
- Get feedback on the entire story draft from colleagues / collaborators / committee.
- Based on these interactions, keep revisiting & revising this draft.
### Introduction & Discussion
- Read widely and deeply. Read often.
- Remember that this exercise is going to entirely feed your *Introduction and Discussion* sections.
- Record all the papers in a *Zotero* library, starting with Slack shares and periodic PubMed searches.
- Create a single *Google Doc and make notes about each paper* along with its title & link. The purpose of the notes is to make the points you will write in your manuscript to cite each paper.
- Based on these readings and discussions during project meetings, *pick a target journal*.
### Supplementary data
- Make all main and supplemental *Figures and Tables* along with declarative titles & detailed legends.
- Run many controls and sanity checks.
- Rapidly iterate with me & colleagues and do additional analyses needed to fill gaps & round-out the story.
- Prepare for & do code review.
### Methods & Code+Data
- Write a very detailed *Methods* section and prepare *Code & Data* to be released.
- Decide (w/ me) what *Code & Data* need to be released with this manuscript.
- As you write each sub-section of *Methods*, organize and document the pertinent code, data, and results.
### Results
- Write the *Results* section and rapidly iterate with me & colleagues to make changes/improvements.
### Tying them together
- Start with the story line.
- Make the Figures/Tables (you will keep iterating over these until submission).
- Write the Methods since that's the easiest one to tackle.
- Then, write the Results describing your Figs/Tables.
- Finally, write the *Introduction and Discussion* sections, and add *References* (*e.g.,* Zotero + Google Docs integration).
- The Introduction section should lead up to the main questions and results of the manuscript.
- The Discussion should put the new results in the context of existing work, describe novelty & potential impact, and conclude with opportunities for future work.
- Perform any additional analyses/comparisons needed to make these sections airtight.
### Title & Abstract
- Write *Title and Abstract*, and get feedback from me/colleagues/collaborators on this full document.
### Last Steps
- While others are critically reviewing the manuscript:
- Create a well-organized & documented companion *GitHub repo* for the manuscript.
- This should contain all the *Code & Data* (from Step 4) that will be publicly released.
- Write the *Cover Letter*.
- Submit on bioRxiv, share on social media, and submit to journal! 🎉
## Resources
> Much has already been written on how to think about and go about writing good papers. This doc contains pointers to great resources on these aspects.
#### Getting Started -- General Thoughts and Principles
1. [How to write a first-class paper](https://www.nature.com/articles/d41586-018-02404-4) -- Six experts offer advice on producing a manuscript that will get published and pull in readers.
2. [Ten Simple Rules for Writing Research Papers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003453) -- Principles and attitude that can help guide the process of writing in particular and research in general.
#### Writing the Paper -- Sections and Structure
1. The [CommKit](http://mitcommlab.mit.edu/broad/use-the-commkit/) is a collection of guides to successful communication in the biological sciences. It contains an entire section on writing Journal Articles with annotated real-world examples. Highly recommended!
2. [Ten Simple Rules for Structuring Papers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619) -- Clearly laid out structure for papers. <br> <img src="https://journals.plos.org/ploscompbiol/article/figure/image?size=large&id=10.1371/journal.pcbi.1005619.g001" height="300"/> <img src="https://journals.plos.org/ploscompbiol/article/figure/image?size=large&id=10.1371/journal.pcbi.1005619.t001" height="300"/>
3. [Writing Scientific Papers --- Structuring, Drafting, and Revising](https://www.nature.com/scitable/ebooks/english-communication-for-scientists-14053993/writing-scientific-papers-14239285/)
#### Nailing Key Sections and Fine-tuning
1. [The 5 pivotal paragraphs in a paper](https://dynamicecology.wordpress.com/2016/02/24/the-5-pivotal-paragraphs-in-a-paper/) -- There are five really pivotal paragraphs in any paper. If you get those five paragraphs right, you are likely to have and communicate the story arc in a way that grabs attention.
2. [How to write paragraphs in research texts](http://blogs.lse.ac.uk/writingforresearch/2017/07/17/how-to-write-paragraphs-in-research-texts-articles-books-and-phds/) -- Essay on crafting solid paragraphs.
3. [How small changes to a paper can help to smooth the review process](https://www.nature.com/articles/d41586-019-01431-z) -- Aspects of presentation that make it as easy as possible for editors and reviewers to focus on the work's scientific content by avoiding confusion or misinterpretation (generate substantial delays in the review process).
4. [How to write an effective abstract](https://www.nature.com/documents/nature-summary-paragraph.pdf) -- An excellent annotated abstract from *Nature* detailing all the components & flow of a good abstract.
### Reading, Writing, Reviewing, Sharing Data, Creating an R pkg \| from Jeff Leek
- [How to read papers](https://github.com/JRaviLab/readingpapers)
- [How to review papers](https://github.com/jtleek/reviews)
- [How to write your first paper](https://github.com/jtleek/firstpaper)
- [How to share data](https://github.com/jtleek/datasharing)
- [How to write an R package](https://github.com/jtleek/rpackages)
### Acknowledgments
Cited sources above + KrishnanLab.