Computer desktop with Zotero and Instapaper open

An updated reading and referencing geek-out

About two years ago, on my old blog, I posted a description of the technology I use for managing and reading various types of articles. I re-post it below. It is largely still accurate, with some minor changes that are worth noting. For one, I’ve started using LiquidText for my pdfs. Underlining and other annotations seem to work more smoothly, and I also like the ability to combine several sources in one document, connecting notes across such sources in one document, pulling quotes out from the documents, and then exporting everything in a word document. That’s quite helpful for literature reviews. The downside, as I note below, is that LiquidText integrates less smoothly with the iCloud than Goodreader. You can’t always get what you want!

I still use Instapaper, even though taking unlimited notes now again requires a paid subscription, with the owners providing only minimal development of the system, even only minimal updates of the iphone/ipad apps. I don’t mind the modest price (about $3 per month), but some of the functions can be a little buggy, particularly the text-to-speech playlist function. Still, it’s the only app that I’ve found lets me easily take and export underlines and notes on web articles, and the playlist function, buggy or not, is quite amazing. I commute a lot, and listening to class readings, even if read by Siri (or “Samantha”), has been a real time saver on occasion.

OK, here is what I wrote in January 2018, after the jump.

Time for the confessional: When it comes to academic reading, record-keeping, and note-taking, I am a mess! When I find interesting articles online, I may save them to Instapaper for later reading, or if they come in pdf format, I may save them to Dropbox, send them to GoodReader on my iPad, or save a reference to Zotero with the tag “Read” (yea, right!). The result: a sizable Instapaper database, a mess of files in GoodReader, and random references in Zotero. The worst thing: I have a pretty bad memory, and if I don’t underline thoughtfully, take good notes, and use a well-organized database, I could just as well stop reading. So, over the last year I’ve been trying to come up with a way to keep track of academic readings, make note-taking more efficient, and be a bit more organized in my lit databases. It’s not necessarily the best way to do these things. There are other apps, tools, methods to keep track of reading (and read) materials, notes, and the like. But it works for me, and I’ve been able to keep it up for a while. Here’s what I do:

Time for the confessional: When it comes to academic reading, record-keeping, and note-taking, I am a mess! When I find interesting articles online, I may save them to Instapaper for later reading, or if they come in pdf format, I may save them to Dropbox, send them to GoodReader on my iPad, or save a reference to Zotero with the tag “Read” (yea, right!). The result: a sizable Instapaper database, a mess of files in GoodReader, and random references in Zotero. The worst thing: I have a pretty bad memory, and if I don’t underline thoughtfully, take good notes, and use a well-organized database, I could just as well stop reading. So, over the last year I’ve been trying to come up with a way to keep track of academic readings, make note-taking more efficient, and be a bit more organized in my lit databases. It’s not necessarily the best way to do these things. There are other apps, tools, methods to keep track of reading (and read) materials, notes, and the like. But it works for me, and I’ve been able to keep it up for a while. Here’s what I do:

Zotero’s the home base for academic reading

I know that Zotero is not the only game in town. I still remember Papyrus, which was a neat little DOS program back in the 1990s. I’ve used EndNote as well as various BibTeX managers in the past, and then at some point switched to Zotero, since it was cheap and generally worked well. When I decided that I had to review my literature file keeping, I looked into Mendeley, in part because that’s what Raul Pacheco-Vega uses, and he’s one heck of an academic productivity guru. In the end I decided to stick with Zotero, not so much because it’s free (in fact, I pay for cloud storage to automatically sync references as well as pdf copies of articles) but because I already knew how to use it. Furthermore, I had a sizable number of references on file, and I found that it could do everything I needed it to do quite nicely: I can import references automatically from the literature databases that I commonly use (EBSCO, JSTOR). I can tag, search the database in a flexible way, and attach all kinds of notes and files. In the past, I’ve found that Zotero works well with Word, OpenOffice, and other word processing options. I recently made it work with Google docs. Though I haven’t used LaTeX in a while, the Better Bib(La)TeX add-on makes Zotero fairly easy to use in that environment as well.

And I discovered the magic of ZotFile. More on this below.

(Note: If you’re thrifty, you can easily find the Zotero database on your computer and keep it manually in sync across machines. Then Zotero is actually free.)

GoodReader is good (er, good enough) for my academic reading

The last time I moved houses, I realized how heavy (and by implication pricy) paper is. Therefore I try to keep more of my academic reading in electronic format. Not necessarily my pleasure reading: I love books and all that comes with them; in particular, I like the connection between reading time and the thickness of a book that cannot really be replicated in e-readers. Also, I am worried about longevity of locked-down e-reading formats: Will Amazon forever maintain its Kindle reader? What about Acrobat Digital Editions? What if one of those major companies goes under? I am old enough to remember Enron… I guess it won’t matter for fairly short-lived academic books, but can I tell before reading whether something is a classic to be kept?

For pdfs that I can use without DRM restrictions, my app of choice is GoodReader, on my iPad. There are others out there, equally good or maybe even better and smoother, but I find that GoodReader works for me: I can easily underline and highlight, use free-hand drawing and writing, type comments, and have all the other annotation tools available that are by now standard. Annotations can be saved in the pdf or in a copy of it. I use iCloud to transfer pdfs from my computer to my iPad. Even though it’s a bit slow, iCloud is a cheap cloud space, and the iCloud drive appears as just another folder in GoodReader: I can save pdfs from my computer to a dedicated iCloud folder; these files then appear in GoodReader; all annotations that I make in GoodReader are automatically saved to the files on the iCloud. (Of course, this requires me to be connected when I read, so I may need to make local copies in GoodReader if I want to do some offline reading.)

ZotFile connects Zotero and my iPad

ZotFile is a magic little Zotero add-on that does a number of highly useful things: First, it renames pdfs that I’ve uploaded into Zotero, based on reference metadata. Second, it makes it easy (right-click easy, that is) to send pdf files to the iCloud folder where I keep all the readings that I want to access from GoodReader on my iPad. (After ZotFile has sent the pdf to my iPad, it adds the tag _tablet to the Zotero reference.) Third, once I’m done reading, highlighting, underlining, and annotating, I can tell ZotFile to re-import the file to Zotero and extract the highlights or underlined text and my typed annotations to a separate note. This process works particularly well if the pdf is well-OCRed; if the pdf consists only of images or badly scanned text, extracted highlights may appear scrambled and require some cleanup (or I may just deal with bad notes and use the pdf itself in my work).

Sadly, a few months ago, Zotero introduced a major update that essentially broke ZotFile. As a result, I’ve been using the older Zotero version and have held off updating to Zotero 5. But recently I’ve seen that Joscha Legewie, the creator of ZotFile and an Assistant Professor of Sociology at Yale, has completely rebuilt the add-on to make it work with the new Zotero version. (Thanks, Joscha!) I haven’t had time to update yet and don’t know how well it works, though.

News and magazine articles go to Instapaper

Goodreader is great for pdf files, which in turn are useful if what you read relies on tables or graphics and if you have to keep track of page numbers for citation purposes. But pdfs are problematic: They are not always accessible, frequently large and therefore slow to open, and inflexible with respect to font size and type. They tend to be unreadable on small screens, such as phones. So, for texts that I do not have to read in pdf format—in other words, most newspaper, magazine, blog texts—I use Instapaper as an app to save, read, and create reading lists that help me quickly access those things that I need to keep track of. The phone and iPad aps download a reasonable number of articles for offline reading, in case I’m away from wireless, and the fact that most of the formatting is stripped from the articles reduces their file size considerably. I can change the font size and the background lighting (black on light color, white on dark color). Underlining works pretty smoothly, and once I am done I can upload the underlined text to an iCloud drive for later import into Zotero.

One fun aspect of Instapaper is the ability to create playlists of articles and have your phone (or other device) read them to you. In other words, I can get Siri (or Alex, or any other electronic voice du jour) to read my readings to me during my commute. Only on special days, though. On normal days, Crap From The Past will have to do.

What I fail to do with this setup is sharing. For highlights and comments that are to be worked on communally, or that should be shared, Hypothes.is is wonderful—but it is a pain to export highlight and comments into a semi-readable format (and this format still has lots of distracting meta-data gobbledygook). So, for now I am selfishly taking my own reading notes and underlines and keep them in my Zotero database.

via GIPHY

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