Thursday, November 19, 2009

Managing pdfs with Mendeley

Recently, I've been playing around with Mendeley, a pdf file manager. It does have some very neat features: it allows one to catalogue their pdf files in one database, it keeps a copy of the catalogue (and files, up to 500 MB) online, it inludes an internal pdf browser and provides nice search & filtering options, it allows one to share groups of pdfs with up to 10 other people; it is also possible to comment on pdfs and share those comments as well. Another nice feature is that the package includes a file manager which (if you want) can organize copies of imported files, so that you end up with one organized folder with all your pdfs and positions in your catalogue are linked to them. You can also decide to generate a bibtex file (or bibtex files) as you go, if you like to use LaTeX. When you add files, you can automatically do a google scholar search for file details, it works pretty well. Overall, I think the authors have done a pretty good job. I decided to import all my pdfs into the database. The whole thing, however, is in its beta stage and there are some minor issues - here are some remarks:

  • There is no explicit "work offline" option, and if you change the library and restart the program, it connects automatically with the server and uploads the changes. Sometimes, I'm connected with internet only by a wireless stick, and I don't want my library to automatically synchronize with the server while adding pdfs and editing pdf intro.
  • The program crashes once in a while (in my case, it's more like 3-5 times a day). Luckily, no data loss occurs.
  • The bibtex file that the program generates is kinda weird, you have to take a look at it and correct it by hand. File links in Bibtex don't work when you open the file with JabRef. In the original database it's difficult to make a distinction between those capitalizations that are to be preserved in Bibtex. If you imported your files from a bibtex database, in the new database most likely the entries will get new keys. Still, it's easier to correct the entry and copy it to your "real" bibtex file than to create a new one, so I rather enjoy the bibtex-related features.
  • The internal pdf browser isn't too elaborate - I wouldn't mind having at least "go to page", "go to next page", "go to previous page" buttons. Also, it would be nice if the browser supported bookmarks.
  • The file organizer options, even though they include organizing files into folders by journal, author or year, don't allow you to organize files by collection.

I do think, however, that overall this is a pretty cool stuff and I'm sure, given some time, it will become even better.


snowiswhite said...


I was wondering if there is anything here that improves on BibDesk? Is it the syncronisation?


Rafal Urbaniak said...

I think, mostly, synchroniziation and the possibility of sharing pdfs and comments online. Plus the availability of this stuff from anywhere once you upload the papers. Also, I don't think Bibdesk actually organizes files, automatically renaming them and copying to appropriate folders.

Colin said...

Have you used the program "Papers" by a company Mekentosj? It looks like Mendeley is very similar, I am wondering how they compare in terms of functionality and stability.

Rafal Urbaniak said...

Hi Colin,

I don't use a mac, so I haven't. But it does look similar. Mendeley, I think, is platform-independent. Not having played around with both, I can't comment, though.

snowiswhite said...

BibDesk does do the organisation and sorting, although not as nicely as Papers. Papers doesn't output BibTeX nicely.


Rafal Urbaniak said...

I stand corrected, then, Tom. As for BibTeX, I don't think anything apart from JabRef or bare code editing outputs BibTeX nicely.:) Do you have any comments about the difference between how Mendeley and Papers organize files?

SciPlore MindMapping said...


if you like mendeley, our software "sciplore mindmapping" might be interesting for you, too. sciplore mindmapping is a mind mapping application that allows you to integrate your pdfs and references with mind maps. the big advantage of this approach is that you do not have only a list of your PDFs but a mind map in which you can add additional information and arrange PDFs more flexible. And in case you really like Mendeley, you can even use Mendeley in addition to SciPlore MindMapping.

For a short demonstration of sciplore mindmapping see

To try the software (open source, Java):

and to read about how to write a phd thesis (or academic papers in general) with sciplore mindmapping see