In a previous post I discussed some of the benefits I discovered in using LaTeX with LyX as a front-end. Another extremely useful tool to learn how to use is a Bibliography manager. If you are like I was, and often develop a new bibliography for each paper you write, this is something you might want to consider. On the other hand, you might be used to Microsoft applications and already be familiar with bibliography managers (such as Zotero) that integrate pretty well with the MS Office family.

As I started my PhD and began writing more papers, I noticed that many of my citations were the same. Rather than copy-pasting from previous papers and then adjusting the formatting for each submission, I realized it would be much easier to have a centralized location for all the papers I wanted to cite, and have the computer deal with the formatting according to the style sheet I needed to use.

Fortunately, support for this is ‘baked-in’ to LaTeX/LyX. There are various good tools that integrate with BibTeX (as the bibliography manager in LaTeX is called), but the one that I found to be most useful for my purposes is BibDesk. Rather than explain how I do it, I’ll point you to this excellent tutorial for Mac, which describes how to set it up. In the rest of this post I’ll simply give my reasons for using BibDesk.

1. It centralizes bibliography management.
   
     Using BibDesk allows me to have a single repository for all the details of every publication I will ever need to cite. I keep this single (small) text file in a cloud folder, so I will (ideally) never lose it. All of my academic writing accesses this same text file database.
     As I read new publications and decide that I want to cite them, I add them to my main bibliography database. I will never face the problem again of having to build a completely new bibliography, unless I decide to change fields completely.
   
   
2. It forces me to be more exacting about my workflow and citation data.
   
     Previously, I might let one citation slip through that only had a first initial, or another minor error. Since I’m forced to fill out the same form for each citation, I also have to be more precise about the details of the reference.
     I now try to find each author’s full names (sometimes this is impossible, unfortunately), because I know some bibliography styles require full first names, etc. The same goes for full names of journals or a series - the particular style will define how things get abbreviated, if at all. And this has actually led to some interesting discoveries - by forcing myself to find the full names, I have been led to other relevant publications that were ignored by previous writers on a particular topic.
   
   
3. It allows me to annotate and auto-file relevant documents.
   
     Annotations such as notes to myself (of quotable quotes, page numbers, keywords, etc..) make a particular publication much easier to find. Not only that, but if I can attach a relevant document like a webpage or a PDF, I can much more easily re-read the article. Having a searchable database is incredibly useful, particularly if the article itself is open-source and machine-readable. BibDesk can take an existing document and re-file it for you according to conventions defined by you (the user), which means that you can have a single folder housing all relevant publication documents.
     I work with quite a number of old documents that are out of copyright, and it is extremely useful to be able to download an old scan (from Google or Archive.org) and have it re-named and re-filed simply by dragging it onto the relevant bibliography entry in BibDesk. If I have an OCR’d version, then searching for keywords in the BibDesk search bar can bring up entries that I didn’t realize were even relevant.

Each of these reasons alone are worth getting your act together and creating a single bibliography repository. You can likely think of other good reasons, which just means there is no excuse to not do so.

Another issue that I am thinking about is how to make my library of citations/documents available on any computer with internet access via the cloud. This would ensure at the very least that I wouldn't worry as much about losing it if my computer dies (though I'm still going to make backups regularly). A fellow academic and friend of mine has managed to integrate all of his citations and PDFs with Zotero, and make it available on his phone in an app like Google Drive, so that at conferences he can remember a publication or search for one in a conversation and pull up the reference and/or associated document to show people. This is super cool and super useful - I’ll write about it if I can figure out how to pull it off on my own, or maybe I’ll get him to write about it.

​One of the first things I did after passing my PhD confirmation exercise (like a qualifying exam in the USA) was to research the best way to write my thesis. As a side note, I use the word 'thesis' to refer to any large written work, including a PhD, while other English speakers might use the word 'dissertation' to refer specifically to the work that a PhD student produces. In any case, the relevant information here is the term "large", since I knew I was going to be writing a lot. I now consider the tools I'm writing about here to be essential for a productive workflow, and so this post continues the theme of an earlier post on linguistic tools.

In researching how to write my thesis, I asked friends and fellow linguists who had written grammatical descriptions. Most of them had used MS Word, and told me horror stories of lost work, un-editable documents due to the sheer size of their files, difficulties formatting and printing the thing, etc.. So that was out of the question for me, at least at the time (2011; I think more recent versions of MS Office may have fixed some of these issues). But one of them mentioned a program called LaTeX (the funny capitalization is actually part of the name), and that it made typesetting and organization a breeze. And it's free! Which is pretty important to students (if not everyone).

So I checked it out, and ended up spending the next few months learning how to set it up on my computer and how to use it (I use MacTeX as the backend). I am fortunate that I have a little background in coding, because LaTeX is essentially a markup language. You write the text of what you want, formatting parts of it by using special combinations of characters and commands (or 'tags') that tell a program how to format them. Then you run a 'compiler' that outputs everything in the correct layout in a PDF. This is pretty brilliant, because it lets you (the writer) worry mostly about the content rather than the format. But learning how to fiddle with the code is rather time-consuming, so if you're not a hardcore programmer (and I still don't really consider myself one of the hardcore types) there is quite a learning curve. Worth it, but steep.

This is where a visual editor like LyX comes in. LyX is, pretty much out of the box, a simple way of interacting with your LaTeX code. It hides most of the code and offers formatting options, similar to MS Word or other word processors. Unlike them, however, you choose the general formatting parameters and let the backend handle the layout. You can also fiddle directly with the code if you need to, or add code to the front of the document for particular use cases, like a PhD cover page, interlinearized glossed text (IGT) examples, and more. Basically anything you need to add has probably been coded or figured out by someone, and if you're a troubleshooter like me you can run a Google search and find forums (and contribute to some yourself) that deal with your particular problem or at least something similar. And the assistance you get can be pretty phenomenal.

LyX does take a bit of configuration, and I might write another post that explains how I set it up for my use case(s). But for now, I’ll just say that using LaTeX/LyX was one of the best decisions I made as a PhD student. It really simplified my writing process and allowed me to do so much more. Rather than spending the final month on formatting my thesis, I was writing and making final changes all the way up to the deadline. I probably wrote more, and re-organized the structure more, in the last month than I had in the previous three. And the text file that contains my 700+ pages of analysis, examples, and appendices is only ~6 MB. Possibly the greatest benefit was that LyX kept track of all my linked example sentences, and formatted them all properly. Once I got it set up this saved me days and weeks of man-hours. The learning curve was totally worth it.

In closing, if you are seriously considering using LaTeX/LyX, there’s lots of good articles about this online. Here’s one, and here’s a discussion on the topic, to get you started.

I finally submitted my PhD thesis last week. It has been a crazy final month. The reason I had that deadline was that here in Singapore (at least at NTU) all PhD students are given 4 years of funding in which to research and write their thesis. If your four years end before your thesis is completed, you are required to pay tuition for the remaining semesters that you continue writing.

Additionally, part of the requirement for the linguistics division (I think also for some of the other divisions in Humanities) is that you have to take 6 courses, which I did in my first year. So I only started doing research on Pnar 3 years ago, which is not much time in which to write a grammatical description of a language. Despite that fact, I managed to write a grammatical description of Pnar that totals about 550 pages of description and 100 pages of texts and appendices. So I'm pretty proud of that - though the description still needs a lot of work to clarify analyses and fix mistakes.

I used LyX/LaTeX to write and format the thesis, and I thought it might be useful to other students at NTU or those who use LyX in general if I included some of the files that I created for formatting purposes.
So here is the LyX file that you could use to write your thesis: NTU_PhD_Thesis_template.lyx
And this is the PDF that it can generate: NTU_PhD_Thesis_template.pdf

Of course this doesn't include my actual PhD, but that's partly because it's under examination. The next step in the process is to wait for comments from the examiners and then work furiously to incorporate them into the document, before I can resubmit and hopefully set a date for defense and confirmation of the actual degree. At least at the moment I'm feeling much more free!