Tag Archives: pdf

arsenal of research: organizing citations, PDFs, notes, brainstorming, and drafts

Post title courtesy of the tyrannical Brian Vivier.

Although I post about the content of my research quite a bit (when I do post), I thought I’d take a step back and talk about the research process today. I’m going to write about a very specific aspect: the ways in which the computer helps me organize and engage in my research.

Obviously, there are things like databases and library catalogs, which are a topic for another day. Many people I talk to don’t know the first thing about WorldCat, so it needs to be addressed! But let’s pretend I already have my sources. Now what do I do?

When I read, I’m very traditional. I take notes with pen and paper when I have a book or a photocopied source. In fact, I used to print out PDFs too, and highlight and write in the margins. Well, that turned out to be a terrible idea. Your highlights and margin notes are not very accessible when you’re coming back to the document later to brainstorm, outline, or write.

My lesson learned – learned after many difficult situations – was to take notes like I’m never going to see the source again. My advisor recommended I do this with primary sources, but if you take long notes that involve mostly direct quotes from the sources, there’s no need to buy the book or really even check it out again. There’s no need to keep binders and binders of printed-out PDFs. So that’s the kind of note-taking I do with pen and paper, first.

The next step is to get them into the computer, because I want them to be 1) stored somewhere safe (I do daily external HD backups, plus sync, more later on that), and 2) searchable, and also 3) copy and paste-able. But where to keep them? How to organize?

I have gone through several pieces of software trying to figure this out, and I’ve settled on Mendeley. I first used Scrivener even for note-taking, which is a great program, but bad for citation management. I then tried Zotero, but that turned out to be bad for PDF management. What I really wanted was a good database that would save my citations, any PDFs I happened to have (I’m currently digitizing all of my sources from my dissertation so they don’t get lost or damaged, and so I can free up my filing cabinet for other things), and ideally let me take notes and even annotate or highlight the PDFs.

Well, despite Mendeley being owned by the devil (Elsevier), it’s free and it actually does everything I need with only a few minor nitpicks, and does it in a way that makes me supremely happy. (My nitpicks are no nested bulleted lists in the notes, and no shortcut keys for bold/italics in the notes.) If you have a PDF attached to your citation and it has OCR, Mendeley’s search function will search not only your citations, notes, and annotations, but also inside the PDFs. It can be overkill at times, but it’s pretty amazing.

So step two of my research organization process is the painstaking, mindless, thankless task of typing my pen-and-paper notes into Mendeley under the appropriate citation. It’s boring but worth it. As I mentioned above, it searches all my notes, and I can copy and paste them into Scrivener, which I will address next. As I type my notes, at the very least I copy and paste them into brainstorming documents as appropriate (usually full quotes), and if I’m up to it, I do some free-writing to brainstorm how the source informs my topic and what I could write about related to it. This usually brings up new ideas I didn’t know I had.

What happens after I get all the notes typed in, PDFs organized and annotated if I have them? I next move over to Scrivener. I’ve been using it for over five years, for both research and creative writing, and can’t sing its praises enough. It’s a word processor that creates a database for your project, where you can store your reference materials, brainstorming ideas, notes, and draft. And more, if you can think of other areas you need to record notes in. Unlike old Scrivener (when I first started using it), you can now add footnotes and comments that port straight to MS Word when you compile your document for it, making the transition to final draft in Word very easy. (Sadly, publishers seem to prefer things that are not Scrivener databases when reviewing.) The typical things I store are the draft itself (of course), a research diary of brainstorming that I update periodically, brainstorming specifically about sources and particular concepts or points, and also under the “Notes” section the comments and suggestions and draft corrections I receive from others. So I keep my full writing process, except for mind mapping/concept mapping (another post), all in one place. It’s amazing.

I’m extremely happy with these two pieces of software; my only complaint is that neither of them does all of what I want, and I have to use two different things complementarily. Well, the situation is still significantly better than several years ago, when I used Mendeley Alpha and it deleted my entire library of citations multiple times. Yikes. Now its syncing works perfectly and I haven’t had a library failure yet. (Fingers crossed).

Next posts will include mind mapping software, how I take notes, how to effectively find and import source citations, and how I deal with multiple languages in my citations.

finally: vertical text and aozora on the kindle!

Trying to figure out how to a) display vertical Japanese text on almost anything, and b) get Aozora texts on my Kindle in a way that makes for pleasant reading, has been driving me mad for some short time now.

One reason I bought a Kindle, in fact, was to have a convenient way to read books in Japanese. My options are either to order paperbacks from Japan at exorbitant shipping costs, or (especially if the books aren’t available in paperback anyway) carry around thick photocopies or bad PDF scans of works from large reference anthologies. Neither of these is a pleasant way to read a book. I love my 文庫本 just as much as the next person, but I think they’re the major factor in my continually worsening eyesight. If I keep reading them, I’m sure I’ll be blind within 5 years or so at this rate.

I was going to write a whole post here about how I wish I could get vertical text going (because this is much more comfortable for me to read), and how I was trying to devise some system for automatically converting books to Kindle-sized PDFs or even .mobi format.

Well, someone has – thank god – beaten me to it! I give you the simplest, free, web-based system for converting any Aozora book to Kindle-sized PDF, by pasting a link from Aozora into a box and downloading the PDF. It preserves ruby (furigana) and lets you choose a text size. (I recommend 大 because even 中 was giving me eye strain. Trust me, you don’t need the 文庫本 aesthetic on a Kindle screen.)

And with no further delay, here is the post from the friendly blogger at JapanNewbie who explains it all:

How I Use My Kindle

Please give him a big thanks when you visit!

Here’s a direct link to the PDF conversion site too:

http://a2k.aill.org/