Commenting scientific papers

This article is originally published at https://lcolladotor.github.io/

I’ve been thinking about commenting papers in blog posts. I did a few some long time ago, but now I’m thinking of doing this activity more systematically. There are several reasons why I’m thinking of doing this, say for 1 paper a week. It has the obvious advantage of forcing me to read a paper in depth per week. At the same time, I want to learn more from others. See what I like in other papers and maybe avoid some mistakes. There are two main lines of papers that I would be posting about. Anything that is somewhat close to my research (genomics, RNA-seq, biostatistics, bioconductor, visualization) and anything done by my undergrad peers from LCG-UNAM. I don’t think that there is a compilation of papers from LCG students despite many of us doing research all over the globe —Mexico, US, Canada, Denmark, France, England, Germany, Switzerland, Austria, Australia to name a few countries. Maybe compiling a list of papers with contributions from LCG students is a task for Más Ciencia por México which seeks to promote science in Mexico. But I would be happy to learn what others are doing and in a way keep in touch academically. 

Another reason in favor is that blogging helps me practice my English. And writing helps me organize my ideas.

But, the question remains, if you systematically comment papers, what would you comment on?

I think that I should state my opinion of the paper in different areas. Kind of like doing a review. First, try to summarize the paper. Next, was the scientific objective clear? They did answer the main question? Then, given the nature of my Ph.D. program, I think that I should try to comment on any statistics used in the papers. This certainly includes the plots and reproducibility. If they included tools (software), I could take a quick look at it. Then, I can end with stating the main things I liked. Maybe I could come up with some scoring mechanism to rate the paper.

You can think of other aspects to talk about of a paper. For example, in what way did it help it’s field? But, I don’t think that I can answer this for many papers outside my research area. It would all be speculation. I guess that I could use Google Scholar to see who cited the paper and maybe comment on it’s impact that way. For the LCG papers, I could point out how the LCG students contributed. 

Or maybe I could take the more educational route. But that’s very time consuming as I can see from La Ciencia explicada's highly detailed posts.

Anyhow, if I have something clear in mind is how I would implement it. I’m thinking of making a GitHub repository and writing my comments using Rmd and knitr. Then posting them here using Markdown. It should be easy to then have a template post and fill in the gaps after reading the paper.

The risk of using a template is that the comments will start to look boring. That’s why I might add a more free section, or change things up a bit.

If you have any ideas, let me know!

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This article is originally published at https://lcolladotor.github.io/
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