PhD Tools: DevonThink for File Storage and Discovery

[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]

Discovering similar notes in one of my DevonThink databases

I first heard about DevonThink in the same breath as Tinderbox. They go together, though they serve different purposes. Some people want to make an either/or decision about which to use. I see them as sufficiently different to assess them on their own merits and as per your usage scenario.

As with all tools, you should come to the decision table with a set of features that you're looking for. Don't just shop around for new things for the sake of newness or for the sake of having a really great set of tools. These programmes are not cheap. Luckily almost all of them come with generous trial versions or periods, but I don't recommend 'newness' as a feature of any particular merit.

Devonthink (I use the Pro Office version) is a place to store your files and notes. It can, I think, take any file you can throw at it. It comes with software for processing PDFs into fully-searchable documents (OCR software, in other words) which is part of the reason why the license for the Pro Office version of the programme is so expensive.

If you're anything like me, you're drowning in PDF documents. They all come with helpful names like "afghanistan_final_report_02_16.pdf" and unless you have a rigorous file hierarchy and sorting system, you'll probably be unable to find one file or the other. And using the basic file hierarchy system for storage doesn't help you with situations like when you want to store the same file in multiple folders (i.e. what if a report is about Afghanistan and Tunisia). (DevonThink has a feature which allows you to store the files in multiple locations, but without saving two copies of the file. Any changes or annotations you make in one file will automatically be transferred to the other).

You might ask yourself why you would need DevonThink and Tinderbox (see this post for more). The short answer is that they store different kinds of files/data, and that DevonThink is less about thinking than about storage (to a certain extent) and discovery.

One of the key features of DevonThink Pro Office is its smart searching algorithms, its ability to suggest similar texts based on the contents of what you are looking at, etc. It does this by means of a proprietary algorithm, so I can't really tell you how it works, but just know that it does. It works best on smaller chunks of text. In this way, I was reading through a particular source from the 3 million-word-strong Taliban Sources Project database and then I clicked the "See also" button and it had found a source I would never otherwise have read on the same topic, even though it didn't even use one of the keywords I would have used to search for it. It uses semantic webs of words to figure this stuff out. Anyway, beyond a certain database size, this power becomes really useful. It can also archive websites, store anything including text, do in-text searches on e-books etc etc. (Read more on how I use DevonThink for research in general here.)

I also used it a little as an archive for substantive drafts / iterations of the writeup process. That's another important part of the process: making backups of many different kinds. I never found any use for them, but at least they were there (just in case).

If you're a data and document hoarder at heart, like me, you'll soon have a Devonthink database (or several databases, split up by topic) that is bigger than you can fully comprehend it, or remember what was inside the files. At that point, search becomes really important. Not just a straightforward search, but the ability to input 'fuzzy' terms (i.e. if you search for "Afghanistan" it'll also find instances where it's incorrectly spelt "Afgahistan"), and boolean language, into your query is really powerful/useful. DevonThink is an amazing search tool. The company that developed the database software also make something called DevonAgent, which is basically a power-user search tool for the internet. Google on steroids, if you will. Fully customisable, scriptable... you can really go crazy with this stuff. I use it, but my PhD wasn't really about searching things on the internet, so I didn't use it much for my research or writeup. But it's a great tool, too.

In short, DevonThink is a research database tool that will help you store and find the documents that relate to your research, and do smart things to help you find sources and texts that maybe you'd forgotten you'd saved. Highly recommended for anyone working with large numbers of documents.

PhD Tools: Think better with Tinderbox

[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]

Tinderbox is a tool for writers and thinkers that can handle most things that you throw at it. Anything to do with thinking, it can probably do what you want. That said, there is a slight learning curve to the programme, and it may not be to everyone's particular style. With those caveats stated, let's dive in.

Any PhD student generally takes a lot of notes. Notes on books or articles you're reading, or notes about points you want to make in the argument of your text / writeup. There are purely text-based / database-style systems that can handle these kinds of notes (like DevonThink, about which more soon) but none with the flexibility or visual features of Tinderbox.

A list of notes, for example, can be transformed into a visual / spaced-and-linked map of meaning like traditional 'mind maps'. You can switch back and forth between outlines and maps easily (or even display both on the same screen/window) and display notes as well.

It's fast, it doesn't break or crash or slow down your computer, and it helps you think things through in the way that is best suited to your needs. Too often, software forces you to think in a particular way (i.e. the way of the software creator), but Tinderbox adapts to the way you were thinking and allows you to draft notes and structure accordingly.

I've written elsewhere about some things I've done using Tinderbox, so no need to mention all that here, but some things I found specifically useful for my PhD:

1. Small databases, constructed on the fly, while taking notes from books. An example of this is a database of key players or individuals from within the Taliban who occurred at various places in my notes. This grew to a pretty extensive document, but Tinderbox allows you to make these kind of structured data sets without needing to think too much about how the data might eventually be presented or used. Changing things is easy.

2. Timelines -- Tinderbox can display lists of events with start and/or end dates on a timeline. I used this to create the TalQaeda timeline, for example, or the list of moments where the Afghan or international military forces claimed to have killed or identified a Chechen fighter in Afghanistan (chechensinafghanistan.com).

3. Working through 'unstructurable' ideas -- There's often a gap between the ideas you think you have in your head and the ideas as they are expressed on the page. I have found Tinderbox extremely useful in allowing me to find a way to make the two align closer together, or to figure out a structure or a sequence to parts of an idea in a way that makes most sense.

You can also use Tinderbox as a day-planner or a task outliner (like I discussed in my post about Trello), though I think it might be less suited to this task when compared to Trello.

The forum for Tinderbox and related products is a great place to discuss method, process and different ways of structuring ideas. Users are a mix of complete beginners and others who have been drafting books, novels and essays using Tinderbox for years. I find the discussions in the forum are often stimulating; asking questions there is an interesting way to rethink a particular mental quandary you might find yourself in.

BONUS: Listen to my podcast interview with Tinderbox's creator, Mark Bernstein, for more on the vision behind the software and for some practical tips on structuring ideas.

PhD Tools: Visualise Structure and Kanban Flow with Trello

[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]

What was leftover by the end of my PhD submission process...

I used Trello for structuring my PhD argument and for tracking my progress during the drafting and redrafting of the final text.

Trello is primarily associated with the Kanban workflow / movement and as such it offers a fast and easy-on-the-eyes way to visualise structure, the passage of tasks through a particular workflow and so on.

It only works with an internet connection, however, which makes this a somewhat qualified recommendation. The mobile apps associated with Trello also lack an offline mode.

Tasks are split up into lists, and these are organised in a sequence. Thus for me, my lists at one point were my different chapters. It's easy to email things (links, notes to yourself, or anything else text-based) into your lists from outside Trello, so it can function as a useful 'bucket' where you can deposit things you want to research in the future, or just tasks that need to be performed for a certain chapter.

It's a way of seeing what needs to be done, or what you want to add to a particular chapter, at a single glance. Not essential, but I found it useful at certain junctions of the editing process.

PhD Tools: Beeminder

[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]

I feel like I've mentioned the end of the PhD several times in recent posts (PHD IS OVER!). It occurred to me that it might be useful to go through some of the tools and principles that I found most useful in completing the doctoral thesis, the research and the work in general. Part of this is by way of giving thanks to the application or methodological creators, and the other part is me thinking that others (future / current PhD students?) might find this useful.

It took me many years to finally settle on these tools. It would probably be unwise to adopt my entire writing style and process for yourself, because everyone's unique. I read a lot of books, blogposts and discussed things in forums and at meetings with others. This is all the product of a lot of procrastination (some active, some just resulting from hanging out on twitter or subscribing to a bunch of productivity-related blogs in my RSS reader).

Each post will vary in size. For some I'll go into a bit more detail because the principle will be somewhat unknown. Others are mega-players in the tech world so I'll just tip my hat in their direction.

Minding the Bees

My first pick is, of course, Beeminder. (I've written about Beeminder before here.) The principle behind this service is pretty simple: you commit to doing a certain thing (or things) by a certain date (or regularly each day etc) and if you don't do them, you're penalised with money taken from your credit/debit card. The amount of money taken depends on whether you're a first-time offender (free, or $5), but then it increases exponentially. Pretty soon you'll be facing $270 or even higher fines.

Needless to say, this is a pretty strong motivator. You can hear about some of the nitty-gritty details in a podcast interview I did with Matt Trevithick and the founders of Beeminder, Bethany Soule and Daniel Reeves.

I have used Beeminder for a really wide variety of things -- not just for my work but for my personal life, too -- but in terms of my PhD, I had three main goals it supported:

1) tracking the amount of time I spent writing. You can hook up RescueTime (a passive activity tracker on your laptop) to feed into Beeminder. I can then say that I want to make sure I do a minimum of 1 hour of writing in Scrivener each day (for example), and Beeminder keeps track of the rest. This is a good thing to track because, ultimately, the PhD is all about keeping writing. You can get lost in the research, but after a certain point you just have to deliver it and ship the damn thing. This keeps you honest about the writing part, the sitting down in the chair and putting words on the page.

2) words drafted -- this one's a bit more delicate, since often when you're starting out, drafting a new section or chapter, the words that come out are useless drivel (or replace with a far less charitable way of describing their quality, and say hi to my inner voice while you're there!). At the beginning, doing basic drafting, it's hard to get started because you feel everything has to be perfect. The best antidote to this is to work on a 'shitty first draft'. Here, the idea is simply to churn out enough thoughts to fill the blank space in the outline, or book, or chapter or wherever.
A specific example: I flew to Karachi in late 2012 to hammer out the first draft of my dissertation. I setup a Beeminder goal of having 100,000 words of text (approx the maximum word count allowed for submission to the university) and a date 6 weeks in the future, and I got writing. Beeminder calculates and tells you how many words you have to get done each day in order to stay ahead of the curve. (There are graphs. They are awesome). As long as you keep writing, you're ok. And I did it. Most was horrible, and some of it was inner conversations between myself and myself about the subject under consideration, almost all of which I had to rewrite in some shape or form later on. But... it was words on the page, and it was me thinking through the issues. It was essential.

3) Sources Read -- this might be unique to me, but at some point I had to return to the newly-gathered sources of the Taliban Sources Project. I looked in my DevonThink database (about which, more to come in a future post) and saw I'd flagged 1000+ articles to reread, catalogue/tag and integrate into the main thesis argument. So I plugged those numbers into Beeminder, gave myself a workable daily rate (50 or 100, I think) and then it calculated the rest and kept me honest.

So, to sum up:

• Beeminder forces you think backwards from your goal if you have a specific endpoint in mind. This is extremely valuable as it makes sure you're not being overambitious.
• Beeminder gives you accountability. It keeps you honest. This is what I initially found was most valuable, but later on I needed this less. YMMV.
• The community of Beeminder users is wonderful. The forum is a great place to get ideas, discuss approaches / failures etc.
• It works! Many people have had great results using Beeminder.

I'm not going to say I couldn't have written my PhD without Beeminder, but I'm almost saying it. Go check it out!

Real People as Agents

I was reading in the first volume of Taruskin's history of music -- all right, procrastinating from overdue PhD chapters -- and came across this useful and timely reminder:

"Statements and actions in response to real or perceived conditions: these are the essential facts of human history. The discourse, so often slighted in the past, is in fact the story. It creates new social and intellectual conditions to which more statements and actions will respond, in an endless chain of agency. The historian needs to be on guard against the tendency, or the temptation, to simplify the story by neglecting this most basic fact of all. No historical event or change can be meaningfully asserted unless its agents can be specified; and agents can only be people. Attributions of agency unmediated by human action are, in effect, lies -- or at the very least, evasions. They occur inadvertently in careless historiography (or historiography that has submitted unawares to a master narrative), and are invoked deliberately in propaganda (i.e., historiography that consciously colludes with a master narrative)." (Richard Taruskin, The Oxford History of Western Music, vol 1, p.xviii)

It's good to be reminded of this when thinking about most things, but especially when discussing ideology and influence with regard to the war in Afghanistan and the identity of the various groups fighting. People have thoughts; ideas do more than just 'emerge'. I'm just as guilty of this as anyone else, but I think writing on the nature of the Taliban, for example, could become a lot clearer if we stuck to the agency of real people rather than abstractions.