Scholarly Papers - tips?

[fcoulter]

I had an epiphany about an hour ago. I'm a graduate student, and I've been collecting PDF files of scholarly articles from many of my various classes. They've ended up scattered among various computers and various folders, and are impossible to find when I need them again a year or two after last I've seen them.

I have no idea how I'm going to be able to catalog all of my old articles since I don't know where most of them have gone, but suddenly realized that using Calibre to store all of the new articles would be a great idea, especially since it appears that I can maintain several libraries on my computer.

My thought is that I would set up a separate library for the scholarly articles. Each article would be a separate book, with authors, etc. The description (free form text field) would be a copy of the abstract. I'm sure I can store all the information needed for APA citations within calibre, using custom fields if neccessary. I could tag the article with the class that referred to it, as well as any times I've used it as a source in one of my own articles.

I wouldn't bother converting any of the documents to another format. Although I like to read on my Kindle, Calibre's conversion from PDF isn't very good, and Kindles really don't like tables, even if converted properly.

So the question is -- has anyone already done this? Do they have any tips or suggestions?

[chaley]

I suggest you look at something like zotero, which is a scholarly paper bibliographic manager. Managing such papers presents very special needs, especially if you are building a citation database, and calibre is not designed for that. Examples: difference between author & editor, difference between journal and conference paper and book chapter and conference presentation (to name a few), presentation location, and the various dates. In addition, good biblio managers handle formatting for different venues, which calibre doesn't even touch.

[fcoulter]

I hadn't realized that Reference Management Software could also maintain a library of the actual papers. I thought they all worked like the citation manager for Word; just a list of possible references. Thanks for the tip.

Now, of course, I need to go through all the software listed on the Wikipedia site to see if any of the other software might do a better (or even an as good) job as zotero. Half way through the list, and I found another possibility -- Qiqqa.

Zotero has (at first glance) one big plus and one small minus. The plus is that it will store PDF's in the cloud and sync between multiple computers. This means that when the inevitable happens, all of my references are still saved out there and I can work on multiple computers. The minus is that it requires Firefox. I've heard a few complaints about the latest version, as well as it's attempts to take over a computer during installation. (But then again, so does Microsoft Office and iTunes...)

At any rate, thanks for the tip.

[gotreef]

While Calibre would be useful for pushing your papers to your ereader, it would be a terrible for library maintenance and I would also vote +1 for using a real reference program.

Zotero is great as a free option but I wouldn't use it if I was anything other than a undergrad; personal opinion of course. I would recommend using endnote as it is widely considered the standard in reference managers, at least in the scientific community. It integrates well with MS Word (Without making assumptions on what type of grad prog you're in, if you write papers with 30+ references, you'll wonder how you ever lived without this feature), ensures proper formatting, and most journal repositories support direct exporting.

Of course it's not free and that sucks. Assuming you're not morally flexible enough to find a free copy somewhere, keep in mind that endnote is almost considered a mandatory program (at least it is in my discipline). Most universities offer this program at a steep discount to students (It costs $25 at my school). However, many departments also have site licenses you can tap into and as it's also degree relevant, it's not too hard to tap your grant to spring for it.

Like the "cloud" aspect of zotero? Then have endnote store all your files in dropbox, a program that installs a "folder" onto your computer(s) that's really just a gateway to a free cloud-based storage service. The previous link gets me extra 500mb if you decide to install, if you don't want me to get extra space or simply don't trust me, just head over http://www.dropbox.com. I've moved all my school related data to my dropbox as it allows for seemless integration and filesharing between my home computer, my laptop, my work unix box, and if it's a "not-so-smart day" my android device.

Still somewhat paranoid about losing your meticulously maintained collection of papers? No problem, since dropbox is just a "folder" all you have to do back it up is hardlink that folder if you use *nix or a mac (I think macs can do it, don't own one though) or, if you use windows, have it set to backup that directory or install Mozy (once again a reference link, click http://www.mozy.com if you don't like me).

My personal setup is endnote and dropbox on all my computers. Endnote imports to a specific folder in dropbox. This allows all my .pdf papers and my endnote database to be consistent and accessible across all my platforms. Additionally, I have mozy installed on my main computer since I have stuff on there (tax returns, personal photos etc.) that I want to keep backed up anyways so I have it also keep my journals safe while it's at it.

Lastly, the new firefox 4.0 (and the 5.0 betas) are fantastic, I would question the sanity of whoever told you otherwise. If you don't want it to be your default browser, it's a simple matter of clicking 'no' and unchecking a box when it first runs.

Hope this helps

[Stampercam]

I also use endnote for scholarly referencing, it can't be beaten. However I do also have all the journal articles in calibre for ease of transferring to my ipad (via itunes). For me the combination works well. I have a separate library in calibre just for academic titles, and have a few custom columns for details like journal name, date, publisher. Calibre handles multiple authors well, so that makes searching via researcher or acadmic easy. I read on the ipad, but if I want to reference from the article I pull the reference from endnote. Oh, and dropbox is definately the way to go with endnote storage.

[Manichean]

Just to give my two cents on the issue: Personally, I use Mendeley for managing my papers. It has cloud synchronization as well as a pretty good autodetection of metadata if you dump PDFs into the program. I use it in conjunction with LaTeX, which works very well.

[fcoulter]

Originally Posted by gotreef

Zotero is great as a free option but I wouldn't use it if I was anything other than a undergrad; personal opinion of course. I would recommend using endnote as it is widely considered the standard in reference managers, at least in the scientific community. It integrates well with MS Word (Without making assumptions on what type of grad prog you're in, if you write papers with 30+ references, you'll wonder how you ever lived without this feature), ensures proper formatting, and most journal repositories support direct exporting.

Of course it's not free and that sucks. Assuming you're not morally flexible enough to find a free copy somewhere, keep in mind that endnote is almost considered a mandatory program (at least it is in my discipline). Most universities offer this program at a steep discount to students (It costs $25 at my school). However, many departments also have site licenses you can tap into and as it's also degree relevant, it's not too hard to tap your grant to spring for it.

Still somewhat paranoid about losing your meticulously maintained collection of papers? No problem, since dropbox is just a "folder" all you have to do back it up is hardlink that folder if you use *nix or a mac (I think macs can do it, don't own one though) or, if you use windows, have it set to backup that directory or install Mozy (once again a reference link, click http://www.mozy.com if you don't like me).

My current masters program in in Public Administration. My previous one is in Accounting, and my next one is will (probably) be in Management Information Systems. After that, I'm aiming for a Ph.D. in Public Affairs.

I don't know if there's a "standard" piece of software for either Management Information Systems or Public Affairs, but according to the professors I talked to, no such standard exists for Public Administation. (I wrote almost no papers in the Accounting program, so it didn't matter.) However, they did say good things about EndNote, too.

The problem I have with EndNote is the UCF licensing agreement. EndNote is free, but only as long as I'm a student at UCF. Since I'll be graduating by the end of the year, I see a large payment in my immediate future as I loose the academic license. Which, as you say, sucks.

I have no problem getting you a commission, except that I already use Mozy for my backups. If I decide to use DropBox for any other purpose, I will definitely click on your link.

Thanks for the info.

[fcoulter]

Originally Posted by Manichean

Just to give my two cents on the issue: Personally, I use Mendeley for managing my papers. It has cloud synchronization as well as a pretty good autodetection of metadata if you dump PDFs into the program. I use it in conjunction with LaTeX, which works very well.

My employer (for some reason) blocks the Mendeley site, so I had to do my research on my phone. That's just weird.

It does look like Mendeley and Qiqqa are going to be my two finalists. Unfortunately, for those who like comparison charts, Mendeley doesn't compare itself to Qiqqa, while Qiqqa does compare itself to Mendeley and comes out aheard on the comparison. (This shouldn't surprise anyone, since no one is going to make a comparison chart that makes the competitor look better.) I'm not sure which way I'm going, but (again), thanks for all the help in pointing me in a better direction.

[Manichean]

Originally Posted by fcoulter

It does look like Mendeley and Qiqqa are going to be my two finalists. Unfortunately, for those who like comparison charts, Mendeley doesn't compare itself to Qiqqa, while Qiqqa does compare itself to Mendeley and comes out aheard on the comparison. (This shouldn't surprise anyone, since no one is going to make a comparison chart that makes the competitor look better.)

I picked Mendeley because it was recommended to me by a coworker as well as preinstalled on my work computer. As far as the comparison goes, I cannot comment on most features, since I mostly just use the categorization and export BibTeX files, but one comment as to the "web library" feature: I don't know what Qiqqa understands a web library to be, but when I log in on the Mendeley website, I can access my library including attached files. That would pretty much be a web library to me