Writing a PhD in the modern world — Tools of the Trade

I previously wrote about the dire state of writing for science.

But this post aims for a more positive bent — in this year of 2015, how can a fresh-face postgrad take advantage of the joys of modern computing? Personally I’m sad to admit there is no fully-baked solution — but I hope I can make some sane suggestions. These are entirely biased, opinionated suggestions, and for good reason. Any web search can throw up dozens of options, what’s most interesting is which ones work!

Writing in Markdown

Most of us learned to write documents in a word processor (most likely, MS Word). These programs come with stacks of functions, buttons, graphical interfaces for all sorts of things. It can seem backwards and barbaric then to want to write the most complicated documents you will ever write in a plain text. And yet, this is what I recommend, for a few reasons.

Firstly, there is a aesthetic elegance to writing in plain text, free of the jittery distractions of a Word. Admittedly, this argument on its own won’t appeal to too many people — although some will appreciate a few less distractions. More prosaically, text files offer a high level of stability (no unexpected formatting mess-ups), don’t suffer issues when documents get very long, and allow much more flexibility in editors — there are stacks of excellent text editors on every platform (including mobile) that are guaranteed not to make a mess of your files.

It would have been at this point that, a few ago, we would introduce LaTeX. In fact, LaTeX remains inescapable for one reason: PDF. The PDF file format is pretty darn complicated and over the decades LaTeX has remained one of the most reliable free tools for generating these files. Today however a new challenger has appeared: Markdown. Originally conceived as a simple format for writing content for web pages, inspired by the conventions people use in emails, it has bloomed into a diverse collection of conventions and power conversion tools.

The most useful of these to the scientist is pandoc . This utility can convert a flavor of Markdown to a huge variety of formats — including word documents. That’s right — you can write plain text and switch to a Word if you must. It also supports tables, bibliographies, and more — consult the extensive documentation on the site. Most usefully, it can generate Latex files for you and thence produce PDFs — giving you the power of LaTeX without the clunky syntax and boilerplate.

A caveat however — this is the cutting edge of writing technology. There are some pieces missing to the puzzle. Most critically, references for Tables, Figures, and Equations are missing — in their place the LaTeX syntax can be used (though its ugly). Promising developments suggest this feature will land this year, until then it’s a bit of a workaround. Even with this caveat however it’s more of a pleasure than dealing with LaTeX.

A Good Text Editor

Sublime Text has for some years been the text editor of choice for many programmers, and for good reason. It provides a clean, fast interface with all the power of some of the more “hardcore” editors. Crucial to its success is the huge library of add-on packages which add support for all kinds of file formats. With a few packages, this programmers’ editor can be turned into a powerful text editor for regular documents.

For my writing work I depend heavily on the AcademicMarkdown and Citer packages, and to a lesser degree the WordCount and Table Editor. These provide very elegant themes. Citer allow rapidly inserting references for a .bib file, which can be generated from most reference managers. If you use Mendeley, it will keep one updated for you.

Manage references with Mendeley

Mendeley has been my go-to reference manager for many years now. After trying a variety of free and commercial alternatives, I have yet to find anything better. That’s not to say its perfect, but it rarely lets me down. Once upon a time the only real option was EndNote, frankly that product costs a lot of money and fails to offer much value in exchange.

Where it doesn’t quite come together

I personally love my markdown-to-pdf workflow. I get to write in a clean, readable format in an elegant, powerful editor. But it was work to get there. For one thing, achieving this result involved installing and configuring three separate programs (latex, pandoc, sublime text)— hardly plug-and play.

While there are no inherent limitations in using Markdown to write papers, in practice there are key bits of the conversion tool which aren’t quite ready, requiring workarounds. Something I was happy to work with in exploring better writing tools, but again not the plug-and-play experience you want to see.

The write-preview-correct cycle is frankly the most clunky part. Generating a PDF remains slow (frankly shocking these days), and viewing it means a trip to another program. Although Markdown makes your document much more readable than LaTeX, it’s still a sore point.

My Vision is that one day, you will be able to download and install an editor that will come with everything you need. I think that is not so far away. My worry is that there just isn’t enough incentive. Academia is plagued by the ad-hocness of its processes. Everyone solves the same problems over and over, without those solutions building on each other because the individual’s goal is the production of research, not research tools. Furthermore with no budgets for these kinds of tools, there is no motivation for a company to jump in with a product to fill this gap. I can only hope that the open-source community will, over they years, manage to fill it.