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Mendeley free extra storage

Author: Simone Labels:: database syncing, Dropbox, Mendeley

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.

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Installing Ubuntu Netbook Remix 10.10 on Acer Aspire One D150

Author: Simone Labels:: acer aspire one d150, Ubuntu netbook remix

I just got a nice, little piece of hardware, the tiny, tiny Acer Aspire One D150. It shows a shiny 10.1 screen, 160Gb of hard drive, 1Gb of memory, and a few other nice features, including integrated mic and webcam.

It is, of course, ultraportable, which makes it very desirable for almost everybody, including my wife :) The processor is an Intel Atom, which delivers decent performance. Not stellar, but good.


This particular unit had the (in)famous Ubuntu Netbook Remix 10.04 on it, which I actually put myself. Not sure if you are asking yourself, but this was my mom's computer. She upgraded to a new Dell, and so...


Anyway, I wanted to stick with Ubuntu, but UNR 10.04 was very buggy and had something I considered very annoying, namely a very much reduced desktop space. So I decided to upgrade to the 10.10 version of UNR.


I always prefer a fresh new install to an upgrade and this case was no exception. Installation was quite fast and uneventful. Unfortunately, the wireless does not work during installation because of the proprietary firmware, and so one is forced to update the system later. The firmware is installed during the installation and so the wireless works out of the box. Actually almost everything does, which is always a good news and shows how much linux has evolved in the last few years.


The appearance of the new UNR 10.10 is great. The unity sidebar, which is very similar to the mac dock, is really cool, even though it has still a few glitches. Since unity is going to be the default in the new 11.04 Natty, I am expecting it to be much more stable and, above all, customizable. That is the big drawback of the sidebar: I have not been able to spot where the settings are for it. Thanks to the Ubuntu forums, I have figured out that I can add programs to it by right click on the icon when the program is running and select "Keep on the launcher".


Yeah, the right click... It looks like UNR has banned the right click from the whole environment. This is an open attempt at becoming more mac-like, but I am not sure I like it very much. The reason is that it takes now a few clicks to do things or access menus that were only a click away. This is not strictly a right click issue, in the sense that it does take now a few clicks to do almost everything. Why is it so, I have no idea. But for somebody that is used to optimization like I am (heck, my most accessed program is gnome-do, which, by the way, does not work very well) this may become a big waste of time.


UNR 10.10 performance is average. It is not snappy (10.04 wasn't either, I doubt the desktop edition would be better), but one can live with it. Notifications are reduced to the minimum, which means that you will find yourself wondering for several seconds if you really clicked that icon before the program appears. This happens notably with the ubuntu software center, which is awfully slow to open. Yeah, the little icon of the program wiggles on the sidebar, but this happens only when the program appears, not before, which completely defies the point.


Down to the dirty, here there are the post-installation issues I had to face.

• The mic has a very high level of noise. This is due to pulseaudio thinking the mic is two channel stereo and it is very noticeable in skype, less in other programs. There is an easy fix: Install pulseaudio controls (sudo apt-get install pavucontrol), then unlock the input channels. Reduce the volume of the right channel to zero, keep the left channel high (75% works for me). The noise will be reduced, even thought it will still be present. In some cases, this also solves the problem of muted mic. This problem impacts also the new gmail "Call phone" feature. Once you install the plugin and try to make a call, the plugin will reset both mic channels to the original setting, muting the microphone (and screwing your conversation). In order to solve this problem do the following:
  
  cd ~/.config/google-googletalkplugin
  gedit options (If the file does not exist, create it)
  
  And insert the following in the file:
  
  audio-flags=1
  
  Save, reboot and make sure the microphone channels are decoupled and the right one level is at 0. Enjoy your free conversations!
  

• A big issue I still have is with power management. Out of the box, unplugging the power causes the unit to go on standby. This is, of course, unacceptable. The cause is that power management recognizes the event "unplugging the power" as "lid closing", and so it suspends the netbook. There is a simple workaround for this issue. Open gconf-editor by typing gconf-editor from the terminal (BTW, did I mention that Alt-F2 does not work? Too much mac is not so good, man!). Go to Apps -> Gnome-Power-Management -> Buttons. Where you see lid_ac and lid_battery, click on "suspend" and replace it with "nothing" (write it, with no quotes). Reboot (or restart power management) and it will work. Unfortunately, the netbook will not suspend when you close the lid, which my wife hates! The only way of solving this issue is to update the bios to the version v1.11 at least (the v1.13 is out at the moment I am writing). However, this operation is not very easy to do on this computer, since it does not have a floppy or a cd drive. There is a little utility called flashrom that can be used to flash the bios from within the operating system, but at the moment it has been reported to brick the unit, so I am not going to a attempt. I am at the moment looking at ways of flashing the bios through a usb stick, but I have not found anything yet.

So now you have your new little toy with a shiny Ubuntu on it. While the desktop 10.10 was great, this UNR 10.10 looks like a transitional release. Hopefully, in a few months most of the problems this release has will be solved in the new Natty 11.04.


Credit for the tweaks goes to various sources, including several posts in the Ubuntu forums (the first place to stop for help) and the google help forum. All the rest is mine! :)

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