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Biblatex and arXiv: A Simple Workaround

I’ve written before on using arXiv (see why I post to it and watching out for posting delays) and I rely on it to share preprints for most of my work. It’s usually fairly easy to share a paper by uploading the LaTeX source files. But recently I hit a snag due a conflict between a journal’s requirements, arXiv’s backend, and the LaTeX install on my own machine. I wasted probably a couple of hours on trying to identify the problem (mostly tied to the biblatex package) and get a clean solution, but in the end I did the simplest thing I could think of and wanted to share it here.

A brief summary:

Problem: I needed to use the biblatex package to properly format my references for IEEE Transactions on Biomedical Engineering (TBME). biblatex is very finicky with version numbers and it was recently updated. arXiv won’t compile a source whose bbl file (i.e., reference list) was generated from a different version than its system.

Solution: Disable use of biblatex in the version uploaded to arXiv, since they don’t have TBME’s formatting requirements.

For more rambling about how I stumbled into this problem, read on …

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Fixing Bibtex Files Made by Mendeley

Mendeley is a popular citation manager but it doesn’t properly export bibtex files. Bibtex files (with a .bib extension) are used to add your references to papers compiled in LaTeX. You can find many reports of these problems, including the Mendeley support page. Some of these problems haven’t been officially fixed for over 6 years! In this post I will share some code that addresses these problems, including:

  • Constraints on what you can write in the “year” field
  • Extra curly braces around titles
  • Incorrect format of “month”
  • Ability to select what types of entries include the URL (instead of only webpages)

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How to Cite Yourself

In my last post, I offered some guidelines on choosing citations. The very first guideline was to avoid conflicts of interest, which generally refers to citing yourself (but also applies to your close collaborators). Now, I’m going to describe how to cite yourself. I’m not changing my mind on this topic, but I believe that there are scenarios when self-citations are justified. Here, I’m going to list when it’s ok to cite yourself and how you should do it. Read more

How to Choose Citations

Choosing papers to cite is a key step in preparing a manuscript, but you shouldn’t take it lightly. Consider that a highly cited paper is often assumed to be a great paper. I don’t believe that this should be automatic, but I recognize the value of this (relatively) objective metric for judging someone’s work. With this in mind, this post offers some general tips on how to choose citations.

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