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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How to Make Better Plots in MATLAB: Plot Wrapper

This is third and final of a series of posts on plotting in MATLAB. This series is focusing on suggestions and considerations to get your plot looking “just right” for your paper or presentation. In the first post, I talked about how to improve the look of curves. In the second post, I talked about fixing up the text, including axis labels and legends. Here, I will talk about using a plot wrapper to automate most of your work. I will also talk about exporting your figure to whatever format you need.

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How to Make Better Plots in MATLAB: Text

This is the second of a short series of posts on plotting in MATLAB. This series is focusing on suggestions and considerations to get your plot looking “just right” for your paper or presentation. By the end, you will have a plotting function that will do most of the tweaks automatically. In this post, I’m talking about text in figures. These include axis labels, legends, and other annotations.

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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 Make Better Plots in MATLAB: Curves

This is the first of a few posts on plotting in MATLAB. I’ll be describing more than the mechanics of calling the plotting (and related) functions. This series will present suggestions and considerations to get your plot looking “just right” for your paper or presentation. By the end of the series, you will have your own plotting function that can automate as much as possible. I’m focusing on 2D plots generated by the MATLAB “plot” function, which is the most common in MATLAB, but most of the ideas also apply to the other plotting functions, too (like “histogram”), or even to plotting in general (via MATLAB or elsewhere). In this first post, I’m talking about improving the curves themselves. The next post describes annotations and other text.

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Deadlines and Academic Writing

There’s a love-hate relationship between deadlines and research. If open research is really open, then unrealistic deadlines only get in the way. Does it make sense to have a submission deadline if you haven’t figured out what problem to solve? I definitely don’t recommend pushing out an incomplete paper just to have your name on something. If that’s the case, then the deadline is being more of a stick than a carrot.

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Being Up Front in the Abstract

The abstract holds an odd place in a research paper. It’s not really part of the paper itself. It’s more like the elevator pitch. The abstract is usually the last section that you write, but it’s the first part that people will read. Obviously, you want to write an abstract that entices the reader to keep reading. But what if they don’t read beyond the abstract? I recently asked myself this question, and it has fundamentally changed my perspective of abstracts, both as a reader and as an author.

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Wrapping Functions in MATLAB

If your research relies on simulations, then you typically have parameters that you need to change for every simulation you run. If you use a software platform like MATLAB, then you can try getting away with changing parameter values directly via the command line. Generally, though, it’s a lot more flexible if you assign parameters in a function or script that runs your simulation. An even more flexible strategy is to use a function wrapper. This post is an introduction to using function wrappers in MATLAB.

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Diligence in the Author Proof Process

It’s always satisfying to see your paper get accepted by a peer-reviewed technical journal. You have recognition of your work, both of your research and the writing itself. You’ve satisfied the expert reviewers who were asked to assess what you’ve done. If you’ve gone through a few rounds of revision, then you’re familiar with the process of addressing concerns and suggestions. This takes a lot of diligence, since every critical point made by a reviewer should be accounted for. While it’s a good reason to celebrate, it’s not the end of the road. After a paper is accepted, and before it is finally published, there’s the proofing process. The publications team will finalize your paper in the format required for the journal, and they will send you a proof for your approval.

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