Mendeley free extra storage

Author: Simone Labels:: , ,

Mendeley is a wonderful piece of software. If you are even remotely doing something that requires you to have a digital library (and you don't own a mac...), then Mendeley is what you need! It is a digital documents organizer for scientists, or, as they put it, "an academic reference management software for researchers". Mendeley is available for linux (Ubuntu), mac and win. While mac and win have valid alternatives to it, for linux Mendeley represents "the" academic reference resource.

With Mendeley you can keep track of your papers and organize them in groups, arguments, etc, and make them public or private. An interesting feature of Mendeley is the possibility of storing your library on a dedicated server. The papers are always synchronized with every machine on which the program is installed. So you can have your library wherever you go. The program gives the end user 500Mb of free space and 500Mb for shared groups, which you can create to share important paper with a group of collaborators. Practically, this becomes a 1Gb storage, because it is not mandatory to share your shared group with anybody but yourself. Mendeley also is able to rename your file and categorize them in different folders according to names, journals, years, etc. There is a "Watch a folder" option which scans recursively a directory of your choice and updates your library as new pdf's are added. Very nice, works quite good.

But... Well, just after few years of active research, it is practically guaranteed that the size of a scientific library will easily exceed that quota (my library is over 1Gb). Of course, Mendelely allows you to buy extra storage for a low monthly fee. While I am not against this kind of "premium" system, I think 1Gb of free space is not enough for the average end user, which, in my opinion, (almost) defies the "free" part in "free software". But that's just a small rant.

So here it is what I did (and credit goes to the discussion on Mendeley forums about external servers storage). I am going to use a different server to store my papers, which will allow me to turn off the "online syncing" feature of Mendeley, but still keep my library synchronized across all my computers.

There are a few services one can use to store documents online, personal clouds which, for free, give you the possibility of having always you most important documents, wherever you go. Dropbox is one of them. It allows for 2Gb of free encrypted cloud space. It is easy and fast to install. Once it is installed, it will create a Dropbox folder, which you can place wherever you like (mine is in my home directory).

Since Lucid 10.04, Ubuntu ships with Ubuntu One, a free 2Gb storage on an Ubuntu server. What I am about to write should apply to it to, even though I am afraid there might be a few caveats due to the syncing frequency of the service. If anybody is willing to try and report back, please give me a holler. Just a side note, Microsoft has not invented anything new with its "To the cloud!" ads....

Before starting the process, please make a backup copy of all the files that are involved, including you Mendeley library folder, so that you can revert to them if anything goes wrong. On the good side, the worst that has happened to me has been that my mendeley database needed to be rebuilt. This means that you will lose all the manual changes you have done, and if you had any paper that was deleted from your library but not from your folder, it will be put back in your library. It took me about half an hour to do that, but it was not so bad.

Everything can be done either by command line or by nautilus. The latter is simpler, so I will stick with it. First, make sure Dropbox is not running. You can stop it from the icon in the panel. Then, open Mendeley, go to Tools, then Options. In the "File Organizer" label, make sure that the "Organize my files" option is ticked and take note of the folder. Let us say, that is /home/yourusername/Mendeley Desktop. Close the options dialog, then go to the main window, above all your documents, and click on "Edit Settings". Untick the "Synchronize attached files" button. In this way, the program will no longer upload your files to the mendeley server. Close Mendeley, then move your mendeley library folder to your Dropbox folder (cut and paste works fine).

Go to your Dropbox folder and create a link to your Mendeley library folder (right click -> Make Link), then move it to where the Mendeley library folder previously was (the path you noted in your Mendeley options, to be clear). Be sure to rename it, removing the "Link to..." part, so it is identical to the "Organize my files" folder. If you like, you can actually make this your "watched" folder, even though I prefer to have them separated. In this way, I don't need to make periodic backups of my library ;)

Now we have to synchronize the Mendeley database. For linux, the database is in the directory:

~/.local/share/data/Mendeley Ltd./Mendeley Desktop/

Nautilus hides by default hidden files and directories. In order to find the .local directory, open nautilus, then select View -> Show hidden files (or Ctrl-H). Find the aforementioned directory, then move the .sqlite file which has the email address you used to register to Mendeley to the Dropbox directory. In my case, this file is www.newcolour78@gmail.com@mendeley.com.sqlite . Go to the Dropbox folder and make a link to the file you just copied (Right click -> Make link), then copy the link back to the directory where the database file was ( ~/.local/share/data/Mendeley Ltd./Mendeley Desktop/ ). Be sure to rename it, removing the "Link to..." part in front it.

And we are magically done! Start Dropbox and go get yourself a coffee while it syncs your massive library to its server. One note of caution: Dropbox syncs files in real time. This may create conflicts between different databases which are open at the same time on different machines. In order to avoid this problem, I follow this protocol:

  1. Start from Dropbox and Mendeley closed in all your machines
  2. Open Dropbox on machine A and let it sync your database
  3. Close Dropbox and open Mendeley on machine A. Do your work for your 10 hours (right?)
  4. Close Mendeley, open Dropbox on machine A, let it sync your database, then close it
  5. Open Dropbox on machine B, let it sync your database and your files changes
  6. Close Dropbox and open Mendeley on machine B. Your database is now up to date, including your notes and highlights
...And that's all. This is really just a workaround until Mendeley will allow the end user to choose the server on which store the files. As I said in the beginning, be careful when dealing with the database, as you can mess around and will be forced to rebuild your database. I won't take responsibility :) Again, a lot of credit some of the people in the Mendeley feedback forum and to this blog for some of the input.

13 comments |
  1. Mr. Gunn January 23, 2011 at 3:17 PM

    I would recommend you not do this. Not only can you really mess up your database this way, as you've noted, but you lose out on the added features provided by Mendeley web. Personalized recommendations are provided by the information you upload to the Mendeley servers, and sync with the web makes the research catalog better for everyone who uses the service. While free, your hack still costs in time, convenience, & reduced functionality.

  1. Simone January 23, 2011 at 3:38 PM

    Hi Mr. Gunn, thanks for commenting. I agree with you that this hack can mess up the database, and I warned about that (it can still be easily rebuilt, if you keep backups of the db and the papers). About the rest of your comment, I don't really see where the problem is. Not syncing the database with Mendeley is already an option the program gives you. Nobody forces you to put your papers on line. Before installing Mendeley, my papers were already on Dropbox, so that I could access them from all my machines. I want to use Mendeley only to organize them, there is no rule that forbids me to do that. This is what my workaround does. My hack does not cost any time, convenience or functionality, or they would not give me the possibility to opt out. Peace.

  1. Mr. Gunn January 24, 2011 at 9:33 AM

    Simone - You're right that it doesn't cause any problems for you if all you want is access to your papers on different computers. If that's all you need, that's fine and that's why the option to not use Mendeley Web is there.

    However, syncing with the web does provide you some useful features such as the online CV and it makes it possible for Mendeley to provide article recommendations that are personalized to you. In addition, when you sync your library with the web, the corrections to the metadata you make help others who later add the same document to their collection.

    So while you certainly can use Mendeley in standalone mode, I hope you'll consider syncing with the web as well.

  1. Simone February 7, 2011 at 4:53 PM

    Mr. Gunn, what you say is actually incorrect, but it stems from an imprecision of mine. I can sync my library to mendeley (I actually do it at regular intervals). What I do not do is to upload my files to the mendeley server to avoid... well, being cut of part of my library. In this way, every modification I do on my files, including corrections to metadata and whatnot, goes online, making me a "contributor" to the community.

  1. Paolo Sifredi June 23, 2011 at 3:01 PM

    so what if you want to add new pdf files in machine B. How do you synchronise then?

  1. Simone June 23, 2011 at 3:11 PM

    Hi Paolo,
    the procedure is actually symmetrical. Syncing the db with dropbox makes it easy to swap machine B with A. This is how I do it: Imagine that yesterday you did all the steps like I did in the post. So you have now a synced db on dropbox for all your machines. Today you are out in the park and you want to download your paper in B. Open mendeley and let it recognize your paper. Once you are finished, shut down mendeley, fire up dropbox and let it sync your new db. Shut down dropbox on B and open it on your machine A. It is really that simple, whilst cumbersome. BTW, even if you forget one of the steps, dropbox makes backup copies of your documents, so you can revert to an old db and let mendeley take care of the rest again :)

  1. Paolo Sifredi June 23, 2011 at 3:24 PM

    yeah. but imagine that you are working on machine B and you discover a new paper which you up to now do not have in your paper. You have to manually rename the pdf and copy it to the dropbox folder first. right? And then you proceed by dragging the file to the mendeley which will input the reference in its db. It really is ok ... i was just looking for an alternative to the tedious renaming of new pdfs etc :) Would have love mendeley to do that part for me...

  1. Paolo Sifredi June 23, 2011 at 3:25 PM

    should have read:

    yeah. but imagine that you are working on machine B and you discover a new paper which you up to now do not have in your LIBRARY. You have to manually rename the pdf and copy it to the dropbox folder first. right? And then you proceed by dragging the file to the mendeley which will input the reference in its db. It really is ok ... i was just looking for an alternative to the tedious renaming of new pdfs etc :) Would have love mendeley to do that part for me...

  1. Simone June 23, 2011 at 3:34 PM

    Hi Paolo,
    no, this is not what I do. Mendeley does the work for me. This is the way it works for me: mendeley watches a particular folder. In my case it is a folder named "library". If you go to Options -> File Organizer in Mendeley, you can have it copy your new files to another folder, which sits in your dropbox shared folder, like I described above. In the same tab, there is the option of having mendeley rename the file in the way you like. So, you download your file in your "library" folder, mendeley renames it and copies it in your shared folder, actually doing all the work. In this way, I always have a backup copy of all my papers outside dropbox. I know, these papers will be divided among all my machines, but it is just a safety measure. On the other hand, you could even have mendeley watch your shared folder, and rename the files in that same folder. I have not tried it yet, for I really want backup copies of my papers (some of them are soooo difficult to find :) ), but you can try, if you like.

  1. Paolo Sifredi June 23, 2011 at 3:49 PM

    thanks for that! but you are not really getting my question. What if I am working on B when I find a new paper. How do you synchronise that with A?

  1. Simone June 23, 2011 at 4:11 PM

    Hi Paolo,
    I think I have understood your question, and it is really my fault (or rather, of the way I wrote my blog post), but please hit me again if I am wrong: once you sync your database, Mendelely knows that your paper is in a particular folder. Mendeley on machine B has written to the db "Simone's new paper is called *this* and it is in *that* folder". When you sync your db, machine A will see the same thing, so it will believe that "Simone's new paper is called *this* and it is in *that* folder". In practice, this means you should use the same absolute paths for your database and shared folder on every machine. In this way, once you sync your db on your machine B and do the dropbox stuff, mendeley on your machine A will know where the new file is, because it will be in the (new) database, and the path to the new file will be correct. So it will find it. Or, rather, for the program on machine A it has been there since you modified the db on machine B, right? ;) Was that what you asked?

  1. Simone June 23, 2011 at 4:12 PM

    Or, maybe, more simply, you were asking how to sync you db in A while you are working on B? :)
    In that case, you can ssh your machine A and fire up your dropbox from the terminal. I have never tried, but I do not see why it should not work.

  1. Paolo Sifredi June 23, 2011 at 4:39 PM

    ok that's great ... i wasn't using the same paths. It was something I had considered when I was setting mendeley on my machines but am being quite cautious with all this ... don't really want to lose all the stuff I got on it. Thanks and well done for the post!

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