Tag Archives: software

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.

software installs that make me smile

Here’s two today that cheered me up. I’m installing a lot of software for workshops that I’m going to in the next couple of weeks (causing a minor panic attack over my laptop possibly not running any of it – turns out to be false attack). I also installed a great little application to help me clean out my hard drive. Face it, 40 GB seemed like a generous amount in 2005 but somehow it ran out fast.

The first is from a visualization package that I’m using this weekend. I love it because – well, you can’t go wrong no matter what system you have! They accommodate just about everyone.

Screenshot of an installation menu.

Second, there is the truly awesome license agreement for OmniDiskSweeper, which I also really recommend. It discovered that in my Volumes directory there were 3GB of total nonsense left behind by one of my external hard drives. I haven’t used that one in a year – so that’s how long this has been clogging up my computer! That explains a lot. I know 40GB isn’t much space, but given that I don’t store much of anything on this laptop except for text documents and applications (my music and photos are all on other drives), it was a little suspicious that I couldn’t delete enough things to get even more than 2GB free. Now I have 8GB, thanks to Omni. Now check out their call for feedback on the license agreement:

OmniDiskSweeper License Agreement

google dropping app support; molly has PPC angst

A decision I made over five years ago has ended up making me quite unlucky these days.

iBook G4 photo

I intentionally bought a PowerPC Mac, the iBook G4, when my iBook G3 succumbed to the infamous logic board defect a year or so after Apple stopped fixing it for free. My first winter semester at Michigan had just started, so I was stuck: I needed the data from my G3’s hard drive even more than I needed a computer, and I knew that Apple would soon drop PowerPC in favor of Intel. Like the idealist I can be, I went for the PowerPC instead of waiting a while for the new hardware, because after taking some computer architecture courses and having done a little assembly programming, I had come to the conclusion that RISC architecture is superior to CISC – meaning that I favored PowerPC over Intel.

Little did I know how ghettoized the PowerPC is out there in the real world. Naive, I had no idea that most operating systems and software are not ported to PowerPC – not even Linux.** In the first few years this wasn’t a problem and wasn’t anything I noticed beyond having a matte screen instead of a shiny one. I still love my G4, with its plucky reliability and long battery life.

Starting about last year, however, more and more software makers dropped PowerPC completely, as OS X only went up to version 10.4.x on PowerPC and many required 10.5, which is Intel-only. Even the software that is still released for 10.4 stopped supporting my laptop, including OpenOffice.***

I resigned myself to having a laptop that is circa 2009 in terms of what it runs. I am okay with running a Japanese version of OpenOffice 3 that will open .docx files for me, and running Adobe CS3 and Word 2004. Honestly, I don’t need the newer versions of these programs for a base model iBook that only has 40GB of hard drive space. What I need is the reliability, toughness, and 5 hour battery life (with the ability to buy new batteries) that my 5 year old friend provides. I have a desktop for everything else!

I have a sinking feeling about it now, though. We have a problem. Google is going to gradually drop support for older browsers, which includes pretty much every browser that I can download for my PPC Mac. While I applaud their strict use of HTML5 (I use it too!) and refusal to cater to legacy browsers that don’t understand it, I realize that I am basically screwed. And how much I rely on Google, frankly.

Here are things I would like to use a laptop for: Web browsing, Gmail, Google Docs, a little word processing, PDF reading and editing, writing, and possibly a little Photoshop. And some Twitter. If I suddenly can’t access or use Gmail or Google Docs, that is a huge blow to using my laptop to be productive – it’s the point of carrying something around that will let me access my files remotely to begin with!

“Get a MacBook,” a voice pleads in my head. They are so shiny, fast, small, and nice. They’re still only 13″ but have a wide screen that makes it seem so much bigger than the 12″ iBook. They have long battery life. I’m kind of in love with them despite myself. Admittedly, I resent the non-removable battery that will allegedly last for the average life of a laptop. But if I wasn’t suddenly losing all software support for my peculiar architecture, I wouldn’t even consider a new laptop.

I just bought the laptop a new battery. It has 5 hours of battery life, does everything I need it to, and is very hardy. It’s relatively small, light, and convenient. It has some very expensive software on it. Most importantly, it simply still works fine and has nothing wrong with it. I abhor wasting things. I am fond of this laptop. If it weren’t for the uncertain nature of old hard drives and impossibility of replacing that without breaking the case, I’d argue that it probably has many years of good life left in it. It’s the Volvo of laptops.

So even if I bought a new laptop (which I can’t exactly afford now), I’d want to keep using the iBook for as long as I can. Why waste it? But why have two laptops, one running Linux?^ (Seriously, I already have a netbook running Linux.) They’re the same size. It makes no sense to keep the iBook around for anything other than preserving my installation of many pieces of CS3. And because I heart the damn thing.

I’m at a crossroads: my PPC laptop is soon not going to just be dated, but unsupported. I don’t want to waste a perfectly wonderful laptop that has seen me through an entire PhD program. I have good software on it. Why buy a laptop the exact same size and type? Because it will save me from Google no longer supporting my laptop, and Web browsers that are actually implementing new W3C standards from not running on it.

Lesson learned: Even though I want superior architecture and don’t jump at trends (like oh, x86?) that I think are not worth it, I have to just go with the crowd, because sooner or later it will leave me behind. I am still not getting an iPad though. How long do you think I can scorn touch screens before I become officially old?

* (Yes, that is how old the G3 was. About three and a half years. Not bad for a laptop with a manufacturing defect that I was very hard on.)
** There are a number of PPC Linux distributions, but specific software may or may not be ported. Usually not.
*** Weirdly, there are a few local language versions of OpenOffice that do still support PowerPC architecture. Since one of those is the Japanese-language version, I now happily use a Japanese word processor and try to keep my language skills current, at least in terms of menu choices.
^ If I could get it to run for the newest AmigaOS I would run to it without hesitation, but I have only gotten reports of it running on a Mac Mini. Don’t think I haven’t considered getting a Mac Mini solely for this purpose. The lack of a monitor is mostly what’s stopping me.