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Much like a previous question on keeping research notes organized, my question is how people keep their pile of papers organized. I've got a stack of about 100 in my office, most of them classifying as "want to read", a couple "have read", and lots in between.

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I've found JabRef, http://jabref.sourceforge.net/ , to be the best tool (for me) for organising a BibTex database, and linking / organising all of my downloaded pdfs.

The biggest advantages of JabRef are that it is genuinely cross-platform, being written purely in Java, and that the native format for the database is BibTex, which means that if I decide to change my methodology then I can straightforwardly use my database with other programs. Storing the database as a BibTex file also means that I can directly edit the database, e.g. doing search and replace with an editor.

It has all of the functionality I need, and in particular it is possible to apply labels to each paper for categorisation, either manually or via keyword searches.

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Yes, it's extremely useful that you don't need to export Bibtex files and then worry about all kinds of problems in the conversion. Your database is a Bibtex file (+ a directory that contains the PDF files). –  Jukka Suomela Aug 15 '10 at 12:25
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Let me add my "+1" here - and stress that JabRef is really superior to just maintaining a bibtex file, and a directory of downloaded papers, by myself. E.g. you can enter an arXiv identifier, generate the bibtex entry, then press a button to download the .pdf, which is then saved and automatically linked to the bibtex entry. Or if your bibtex entry contains an url/doi fields (as most entries on mathscinet do), there is a plug-in that can automatically download the .pdf from the journal's webpage (if it is accessible from your domain, of course). –  Arend Bayer Sep 6 '10 at 14:08
    
I've only started using this recently, and I've found it pretty useful. I actually have a lot of papers or books as djvu files, so I was concerned by what seemed to be an overemphasis on the files being a "pdf" or "ps" format. But it looks like you can pretty much link any files to the entries in the database. –  BrainDead Nov 15 '10 at 18:30
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I use Bibdesk, and it works quite well. It's free (as opposed to Papers). I haven't tried Mendeley, but I've heard good things. I also use CiteULike to bookmark papers that I'm interested in.

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As I wrote in my comment to Scott, I've been using Papers to organize my PDFs, and Bibdesk to manage my bibliography files. Papers just doesn't do a good enough job with BibTeX, whereas Bibdesk can't find, store, and display PDFs. –  Theo Johnson-Freyd Oct 28 '09 at 5:42
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I'm not sure what version of Bibdesk you were using, but on my Mac it has a very nice interface for storing and sorting PDFs. It allows a custom script for sorting the papers and a drag-and-drop interface for depositing them. –  Steve Flammia Oct 28 '09 at 13:05
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Although I just started using it, Mendeley Desktop seems like a very good tool to organize papers. How to organize the hard copies in the office is still way beyond my knowledge ;)

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For the hard copies, back before we had PDFs I used to just number them consecutively and keep them in a drawer in my file cabinet in strict numerical order. Then I used a simple text file to keep track of author, title, and number. A quick search with a text editor would reveal the number, and I could withdraw the paper from my file cabinet. With the advent of electronic copy this system has fallen into disuse but I think this may have been a mistake. –  Harald Hanche-Olsen Oct 28 '09 at 0:43
    
i just downloaded it and tried to start working with it. it seems awfully slow at creating the collection and i can't have it do an initial scan, as far as i can tell. –  Sean Tilson Apr 18 '10 at 2:55
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Mac users might find the program "Papers". I tried it for a while, and didn't end up excited about it (maybe I don't read enough papers?) but I've heard good things from many people.

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I like it. I don't love it, but I like it. My current complaint: it exports BibTeX, which is nice, but it does a fairly bad job at it. In particular, I would rather that it simply store the MathSciNet BibTeX. One advantage is that it interfaces reasonably well with a number of citation/paper sources (Archive, MathSciNet, etc.), but it does not do so with WorldCat. So anyway, I've been using Bibdesk to manage my bibliography files, and Papers to sort the actual PDFs. I wish they were merged. –  Theo Johnson-Freyd Oct 28 '09 at 5:41
    
My solution to this problem was to only import published papers using the MathSciNet plugin, so that it would store their MR numbers. Then you can export BiBTeX, use something like grep to pull out all the numbers, and pull the correct entries off of MathSciNet with a huge query (make each field "MR Number", connected by "OR", and retrieve BibTeX citations from the results page). There's a thread on the Papers support forums that's over two years old now where people have been requesting BibTeX support for things that aren't journal articles; maybe it'll happen in version 2.0. –  Steven Sivek Oct 28 '09 at 13:14
    
I've got a huge directory full of papers downloaded from the arxiv. I can search it well enough with Spotlight, but it would be nice to be able to browse as well, so the main thing I'd want is an interface with the arXiv to obtain metadata and automatically rename all these files. At first Papers looks like it'll do this, but if I'm not mistaken, (a) it seems to want to go paper-by-paper and obtain my confirmation of matches, when I'd like something that does this in batch, and (b) sometimes it fails to match anything. Am I wrong about this? If not, is there anything that does better? –  D. Savitt Oct 28 '09 at 15:42
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As for physical papers:

I have two coexisting systems. The first is a file cabinet organized by author. Organizing large numbers of papers by subject or date or whatnot ravels out of control. The second is a series of magazine racks labelled by project, which contain papers directly relevant to the corresponding projects.

As for electronic papers:

I used to put them in folders by author, with helpful filenames like

Fukaya-FloerHomologyFor3ManifoldsWithBoundaryI.pdf
HatcherLawson-StabilityTheoremsForConcordanceImpliesIsotopyAndHCobordismImpliesDiffeomorphism.pdf
KustermansRognesTuset-TheModularSquareForQuantumGroups.pdf

but maintaining this got old. I tried Papers, and thought it was going to be fabulous, but like Scott, wasn't won over in the end.

But now search has gotten good enough there is much less need for explicit organization. You can just put the pdfs all together in a ginormous folder, and whenever you need something just search for it. It's the google way. (And if you use Google Desktop, then literally so.)

Here is the one thing I would like to be able to add to this system: it would be great to be able to add tags to papers, which would even further facilitate targeted retrieval and browsing. Does anyone know an easy way to do this?

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I use Jabref for exactly this purpose; it also lets me attach notes to papers. On the other hand there's some overhead... –  David Zureick-Brown Oct 28 '09 at 4:48
    
How many files are we talking about? I was considering doing something like this. All files in a single folder, but I have around 14000 files (do not ask why), amounting to around 14GB. Do you reckon this may make the OS go crazy? I use Windows 7, but this idea may be used by someone who may be in Unix or even windows 95. I am aware this maybe goes a bit off topic. Apologies if so –  Jesus Martinez Garcia May 11 '11 at 12:03
    
I don't know at what stage the finder begins to have trouble. Certainly a thousand files in one folder is no problem. My guess is that ten thousand is okay too, but I haven't tried. –  cdouglas May 11 '11 at 17:38
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There's a Firefox plugin called Zotero, which is supposed to help organize online research. It can even automatically grab data from sites like jstor, springerlink, amazon etc. I have just started using it, does anyone have any experience with it? Is it usable for mathematical research? Edit: There's a video demonstration on their homepage which really looks impressive!

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I use Zotero. As with 'Papers' above, it could do a better job exporting to BibTex. Otherwise, I'm pretty happy with it. –  HJRW Aug 15 '10 at 15:59
    
Oh, right, as Nicholas Jackson mentioned, Zotero now allows you to keep your database on a central server, which is a great feature. –  HJRW Aug 15 '10 at 16:04
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I use a modified version of RefBase. It's an online bibliography database that can also store copies of papers. Useful features include:

  1. Multi-user capabilities
  2. Import from arXiv by identifier
  3. Tagging and grouping of articles
  4. BibTeX and other formats exported
  5. Links to webpages and so forth
  6. Import from a BibTeX file (so you can pass it your bibtex file from a paper) with automatic grouping

My modifications include:

  1. More mathematical fields (the main developers are geologists)
  2. MathSciNet import by identifier
  3. It gets the daily arXiv listing and I can choose which articles to add to my collection

My version is available as a BZR repository at http://www.math.ntnu.no/~stacey/code/RefBase

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Andrew, I would have liked to try your version of RefBase, but that link seems broken. –  Zavosh Apr 4 '10 at 18:24
    
That's because it's a bzr repository so you are meant to download it using bzr, not a web browser. If you'd rather have a tar ball, I can create that for you - just ask. –  Loop Space Apr 5 '10 at 11:27
    
It works beautifully. Thanks very much! –  Zavosh May 25 '10 at 7:57
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This is something I've been musing about for a little while, without very much progress. Wikipedia has an article comparing various different reference management systems. I'd like something that I can access no matter what computer I happen to be using (sometimes I work at home, sometimes I work in the department) so although the Firefox extension Zotero looks pretty good, and is properly extensible, it didn't look like it was going to be particularly easy to use on more than one computer (unless I kept a copy of all the local files on a USB key and remembered to take it with me). Having said that, the official website says that version 2.0-beta has the ability to synchronise via a central server, so maybe I should take another look at it.

I had a look at a few web-based systems, and experimented with Bibsonomy, CiteULike and Connotea, and vaguely settled on Bibsonomy, but I haven't entirely taken to it. The social networking aspect appeals - accurate recommendations for relevant other papers would be great - but I'm not sure it's quite there yet. Perhaps I should follow Andrew's lead and install RefBase on my home webserver.

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Try this tool.

EDIT: The program is called citeulike. It is a free service (at least as in beer, not sure about speech) sponsored by Springer. It appears to allow you to store, search and tag PDF's and to search others tags. Edit by David Speyer

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It's nice to give people some clue what you're linking too, without asking them to hover or click... –  Scott Morrison Oct 28 '09 at 0:59
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thanks for the tip! –  Proportional Oct 28 '09 at 21:07
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There is a new tool called colwiz, which seems to have some advantages for mathematicians. In particular, it has MathSciNet support, unlike Mendeley. I wrote a summary of why I like it here.

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I just installed it. How do I use BibTeX with it? Do I need to export everything into a BibTeX file? –  Deane Yang Jul 12 '13 at 3:15
    
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