Non-scientific software that helps me get science done

This is a shout out to all the software that helps my science happen despite not necessarily being developed for scientific purposes.

Fair warning, the list skews toward Linux programs since that’s what I use in my day-to-day work.

Tmux

I spend a lot of time at the command line. Or rather, command lines (note the plural). I often have four open at once. And I want to see all four at once, and jump back and forth between them all. Separate terminal windows or tabs don’t cut it. But Tmux does.

Here’s a pared-down example of how I might typically use Tmux: two panes, with one for editing text and the other exploring exploring directories.

Not gonna lie, Tmux is awkward to start with. The default keyboard shortcuts aren’t intuitive, simple things like copy/paste functionality don’t necessary work as you’d expect them to, and many online resources are outdated because older versions of Tmux used configuration commands that are no longer compatible.

But Tmux is well worth the learning curve.

Autokey

There’s a lot of trial and error and boilerplate in my scientific workflow. Autokey lets me automate much of this repetition. Over the years, I’ve created about 100-odd scripts for quick little tasks that run whenever I press a keyboard shortcut or type a specific abbreviation.

One of the reasons Autokey works for me is that uses Python, a language I’m already using in my scientific work.

I use Autokey to

  • Easily type symbols in any program
  • Interface between programs, such as Sublime Text and my Python console
  • Use a few keystrokes rather than type out long stretches of text
  • Open or shift focus to my most commonly used programs: web browser, terminal, python console, email, etc
  • Copy and paste a title while removing title caps (Title Caps Looks Like This)
  • Copy and paste while removing new lines
  • Autocorrect the same set of typos that I always seem to make
  • Create extra macros and shortcuts macros for various programs

Zim is a good example of the final bullet. Within Zim, I type ‘/no’ and Autokey converts it to −1, or I type ‘eq’ to trigger the equation editor.

What’s Zim, you ask?

Zim

There’s all kinds of note-taking programs out there, and you may well already have a favourite. If not, consider Zim. It has all the features a scientist likely needs (images, LaTeX equation editor, tags, subpages) without any bloat.

I keep my notes for every scientific paper I’ve read within one Zim notebook, which is separated into about 10 topics. Being in a single notebook, I can search across all my notes at once.

Sublime text

Keiran Healy says ‘get used to using a good text editor and then just learn the hell out of it’, and I’ve certainly done that. I’ve been using Sublime text for seven years now.

Two months I ago, I decided it’s time to buy a license. Though I thought of my payment less as a purchase and more as a donation to a good cause. You see, despite what its website says, you can use Sublime Text as long as you like without ever paying for it. The only difference between the licensed and unlicensed versions is that the latter occasionally has an easily-ignored pop up telling you to buy.

Despite its free version having all the features, Sublime Text is worth its $99 USD price tag. Given how much I’ve used it to date, my $99 works out to a couple of cents per hour!

WebPlotDigitizer

This post is meant to be about software not specifically designed for scientific purposes; WebPlotDigitizer does not fit this description. But I’m gonna let it slip in, if only to keep you from making the same mistake I did.

I used WebPlotDigitizer sporadically for several years without realising it has an Automatic Extraction tool. I had been extracting data from graphs within old papers by manually and tediously clicking on dozens of points along the lines. WebPlotDigitizer can do this for you automatically. How did I miss this for so long?

uBlock Origin

I’m gonna assume you’re using an ad blocker. But are you using all of its features? Are you blocking the distracting content that doesn’t count as ads?

The best example is Hot Network Questions sidebar on the Q&A series of StackExchange websites. Here’s what it looked like on August 12, 2022:

Without fail, this ever-changing sidebar always has at least one or two questions that pique my curiosity. Which leads me astray from the task at hand. So I have my ad blocker hide them.

I also block the sidebar on YouTube. And, if I were to use Twitter, I’d block their sidebar as well.

Ag—The Silver Searcher

Ag is a command-line tool to find specific words across a bunch of files and directories in seconds, if that. I’m reminded how good Ag is every time that I SSH onto a remote computer that doesn’t have Ag installed and I’m stuck wondering how I’m meant to find what I want to find.

dtrx—Do The Right Extraction

Whenever I download something will a file extension of .tar, .tar.gz, .zip, or something similar, I rely on the command line tool dtrx. There’s no need to remember the proper command.

Albert Launcher

Albert is, I believe, equivalent to Apple’s Spotlight search. It’s a little tool that lets you find and open files and applications instantly. If, in 2022, you’re still opening all your files by clicking through a hierarchy of folders, or opening apps from a start menu, you’re doing it wrong. Go check out Albert, Spotlight, Launchy, Synapse, or whatever works best for your operating system.

Inkscape

Inkscape was the subject of the first ever post on this blog. Seven years’ later, I still use it multiple times per week, if not per day.

PDF shuffler

PDF shuffler does one job and does it well. It manipulates pages of a PDF file. I usually use it to pick out a subset of pages from a longer file, but it can also be used to combine multiple files and shuffle and rotate the pages within.

Tranquility Reader

There are many choices when it comes to browser extensions to improve the experience of reading on the web. Firefox (my go-to browser these days) even has a built-in reader view, but it didn’t work exactly as I wanted. Tranquility Reader did work as I wanted. And in the past, especially when using Chrome, I found Just Read to work well.

Remarkable

Remarkable is a Markdown editor (not to be confused with the paper tablet reMarkable). I’ve left Remarkable to last as I’ve not yet thoroughly used it. From a quick play, it seems like a nice Markdown editor with live preview. Though I have used it enough to know it’s missing Find (Ctrl + F) functionality.

Author: Ken Hughes

Post-doctoral research scientist in physical oceanography

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