Defeating Bedlam - Olivia Judson Blog - NYTimes.com

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Several pieces of software are now being developed to address this problem. I want to look at two of them here. The first is called Zotero; the second, Papers. Both are in version 1 and are still a bit buggy; but each has the potential, I think, to become a valuable tool for research.

Zotero aims to let you build a library of useful books and articles that you encounter while surfing online. It’s an extension of the Web browser Firefox, and as you’d expect, it’s free to download and easy to install.

Once you’ve installed it, each time you visit a Web page that contains items — books, newspaper articles, soundtracks, films, etc. — with bibliographic information, it extracts that information and allows you to save it to your Zotero library if you want to.

So, suppose you’re interested in books about the psychology of war, and you go to Amazon and type “On Killing” into the search box. A list of books appears; Zotero collects the information for all of them and allows you to select the ones you want to keep. These are then put into your Zotero library. Once they’re there, you can make notes on them, put them into folders with other items that are related, and so on. If you ask it to, Zotero will see if it can find a given book in a local lending library. And, supposedly, you can also pull bibliographic information from Zotero into documents you’re writing, but I haven’t tried that part yet.

It’s a powerful piece of software with a lot of capabilities, though not all of them work as well as they could. For instance, it’s hit-or-miss with newspaper articles — sometimes it recognizes them, sometimes it doesn’t — and it can’t interpret information from, alas, my local lending library. It does, however, allow you to screen grab, so you can still collect such information if you want it. The screen grab also allows you to add interesting Web pages to your Zotero library. (This is different from storing the link to a Web site. The screen grab gives you the page as it was when you looked at it; clicking a link gives you a site as it is today.)

A minor quibble: if you use a small laptop, as I do, you may find the Zotero window occupies too much of the screen. But I shall certainly keep using it, though not, perhaps as its conceivers intended. For me, it’ll be a scrapbook of interesting stuff — books to buy later, press releases on subjects I think I might write about one day, magazine pieces about cities I’m thinking of visiting.

For the bulk of my researches, however, I shall use Papers. This software has been designed for the Macintosh by two avid fans who call themselves Mekentosj; it only works on the Macintosh platform. It’s not free, but it is quite cheap (20 pounds sterling; 40 U.S. dollars) and, for me, it’s been worth the money. For it solves the problem I started out describing — how to keep on top of scientific articles. How to know which ones you have, where they are, and what else you’ve got on the same subject.

The makers describe it as iTunes for .pdf files, and that’s broadly right. (For anyone who’s never encountered these things, a .pdf file is a type of document file that any computer can open using a free downloadable piece of software. This is the form electronic journal articles come in, and it means they look just as they would have done if you were reading the journal the old fashioned way. iTunes is a piece of music management software.) The idea is that, when you download an article, it goes into your Papers library. The bibliographic information immediately appears; so does, if you’re lucky, the “metadata” — like the abstract and the list of subjects that the authors thought their article touches on. (I say “if you’re lucky” because this doesn’t always happen automatically.) The document itself gets neatly filed in a folder on your hard drive, and renamed by authors and year. Gone are the days of 456330a.pdf and sd-article121.pdf. Hallelujah.

And that’s just the beginning. Not only can you read the papers, annotate them, find them and create folders of papers on related subjects, you can also use the software to search the big scientific databases like PubMed and the Web of Science. (Such databases are where you go to find out what’s already been published on the subject you’re interested in; it’s where most scientists find out about the papers they want to collect.) It doesn’t (yet) replace bibliographic software such as Endnote

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Papers does have some teething problems. As I said, it’s still buggy, so not everything functions as it should. Moreover, the way it works is not always intuitive, and there’s no formal “help.” Instead, if you have a question, you have to wade through user forums to try to see if anyone else has had the same question before — and, more to the point, whether anyone has answered it. But after a couple of days of experimenting, I got it doing exactly what I need.

Organizing materials is always idiosyncratic. I have one friend who organizes the novels he owns by the year in which the books were published; another goes by the color of the spine. (The first accused the second of having the soul of an interior decorator.) But the important thing is not how you do it, but whether it works — whether you can find what you’re looking for. These bits of software open up possibilities; for some people they will be useful, for others they won’t. Some will use both, others neither. For me, well, a few days after discovering Papers, I put 20 sacks of real paper into the recycling bin. At last, I’m back to knowing what I have and where it is.

Bedlam has been defeated.

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