This weekend, I prepared a survey paper for a Japanese Symposium (which, incidentally, will become the basis of the bibliography chapter of my thesis :-P). I decided that it would be a great opportunity to leave the stone age and start using some bibliography management software. Following suggestions from friends, I tried out Mendeley, Zotero and Jabref – these are my impressions:
Mendeley is developed by some people from last.fm and skype. It has many very sexy features, including the ability to drag a PDF into it, which will create a new entry and pre-fill it with information gathered from the PDF. Mendeley can also update an entry’s fields by searching for its title on the web (google scholar), and the accuracy for this one is very good. The interface was clean and very intuitive – I could easily find all functions that I needed to without having to think/click too much about it, specially the addition of tags/comments to and article.
But (unfortunately, there is always a big But), Mendeley had some pretty big problems. The first one is that it would crash too often – After adding just a dozen or so entries, I would find the desktop application crashing without notice – and worse yet, without error messages or memory dumps that would help me track the problem down. In one of these crashes I lost my entire database (fortunately I was just trying the program at the time, no real data was lost). A secondary problem was that the search function was a bit buggy – If I added a keyword, say, finance, to 6 papers, searching for this keyword would only return 3 or 4 of them.
I hope that they fix those bugs eventually, but until they do, Mendeley is unusable for me :-(
Zotero is a firefox add-on that also claims to be able to search for paper details on the net. This is already one letdown (at least for me) – I want a standalone program, not something riding on a Firefox instance (specially because Firefox is SUCH a memory hog!). Zotero won’t even reside inside a tab, it must occupy the root screen of FF. Also, because it is an add-on, its data (including stored pdfs) is saved in a bizarre location inside the hidden mozilla folder – it would be cool if this was configurable, since it would make things easier to back up. These aside, it had many of the same features that I liked in Mendeley, like searching for paper information on the web, and getting info from PDF’s – although they were a bit clunkier to use – for instance, if Zotero couldn’t find the info from a PDF you dragged into it, you couldn’t just enter the info yourself in the entry, you had to create a new one, and drag the pdf into it. They also had a cool feature to link entries as “related” between themselves.
However, all of the above is pointless when Zotero simply chocked on my bibfile. Not sure if it was FF or Zotero’s fault, but trying to import my references file into Zotero would result in FF locking. Next.
Jabref is a java based bib management software. After installation, it read my bibliography file immediately, without glitches. The program was stable, with powerful options to select/search/group papers. However, the interface was very obscure – it took me a while to find the button I had to click to edit an entry (couldn’t just double click it), and there is no option to add tags (I can add keywords to a field and text-search it, but it is just not as easily automateable). Jabref can only search on IEEExplore, and can’t read PDF metadata (it can, interestingly enough, WRITE pdf metadata though – I wonder what is the point of it).
Anyway, after playing with it for about one hour or so, I got the hang of where most of the functions are. It could really use a “search the net for details of this paper” function that searched more than IEEExplore, or a “read PDF metadata function” for convenience of use, but other than that, jabref is functional enough to last me until the other options get their act together.
Hi Klaus,
thanks for trying Mendeley and writing up the review! Very sorry for the trouble you experienced. As we prepare to leave the “beta” status within the next two months, increasing the stability is our main priority – the next release should eliminate most bugs that lead to crashing.
In order to avoid any potential data losses, the next release will automatically create local backups of your database, as well as include a “restore from/to server” functionality.
Regarding the keyword search bug: This was a known bug in 0.9.2, but should have been fixed in the current version 0.9.2.1 – is that the one you were using? You’re on Ubuntu, right?
Thanks again and best wishes,
Victor
Zotero does let you configure your data directory
(Gear Menu –> Preferences –> Advanced –> Data Storage)
What type of file did you try to import? Did you look for help on the forums?
A lot of this also has to do with what word processor you want to use – if you’re not writing in LaTeX, using jabref is a bit of a weird choice, because it doesn’t give you any word-processor integration.
If you’re writing in LaTeX, jabref with bibtex is probably your best choice, although you may still miss Zotero’s ability to get references quickly of the web and use its bibtex export.
You can customize the location of the zotero storage folder. Gear icon->Preferences->Advanced->Storage Location.
What do you mean by it choking on your bib file? How large was the file and how long did you wait?
JabRef’s ability to write metadata proves useful when you use other programs to search for PDFs.
Hi Claus! We’re working very hard to improve stability for the next release. From what we can tell, it seems to be worse on some platforms than others. I wrote my entire dissertation with it on my Vista machine with no crashes, but sometimes I did have problems with the built-in PDF viewer.
We’d really like to be your reference manager of choice, so would you please get in touch with support@mendeley.com to see if they can get to the bottom of your crash problems?
Thanks for the comments!
@Victor
Thanks for the comments – I’ll certainly give Mendeley another try once you get out of Beta.
As for the version, I was using version 0.9.2.1 for Ubuntu – So I guess the bug is not quite fixed yet.
@Sebastian
Thanks for the configuration hint. I just tried to import a regular bibtex file.
To be honest, I didn’t play with the configuration menu, or search the forums, because after Zotero locked, I went on Jabref, and since it worked out of the box I decided to go finish my paper that day instead of trying to fix the problem.
I agree with you that the best solution depends on the setup. I’m using just the default latex + bibtex, so I guess I’ll stick with jabref for a while – when I have some downtime I’ll try to find what went wrong with Zotero :-)
@noksagt
Thanks for the configuration hint!
By choking I meant that zotero showed the “loading” bar, and then it (and Firefox) became unresponsive – I think the longest I waited was 5 or 10 minutes while doing other stuff. My bibfile is not large (I think), about 200-300 entries.
Thanks for the explanation about the utility of writing metadata. Now it makes a lot of sense.
@Mr. Gunn
Like I said on the report, Mendeley did not generate an error message or an error log, so I’m really not sure what I could say to the support department. I tried to use v.0.9.2.1 with Ubuntu 8.04 and Gnome 2.22.3, if that helps any. If there is any other information that you might need, feel free to ask :-)
Hi Claus,
Our of my experience, JabRef combined with BibTex is a good combination for writing scientific articles.
Cheers and see you one of these days!
Antonio