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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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Compiling and linking netlib

Author: Simone Labels:: compiling, g77, gfortran, netlib, slatec

Ok, so here is the deal. I just got this awesome new computer at work. A slick Dell workstation, i7 double core, a load of ram and hard drive space.

So, first thing first: wipe out windows 7. Great. Got the new Ubuntu 10.10 Maverick to do it. It took literally 5 minutes. No kidding. I spent some time installing my programs: flash and skype, all the way down to my little programs. But, as I said, it is my work computer. I have to use it to actually produce something. And to do so I might just need a compiler. Fortran, C, C++ and so forth.

A few years ago, when I started, g77 was the deal. Gnu made that, it was free, it had good performance, it was it. A couple of years ago, Gnu decides to change to gfortran. Installing gfortran is just a matter of apt-get and such, no problem. However, to actually linking it to libraries that are over a couple of years old turns out to be a problem, ending up in an actual nightmare for a stubborn ass like me.

There is a large set of math libraries which is called slatec, from netlib. It used to come standard with linux a few years ago, and ubuntu had its version. This was until gnu decided to change its compiler to gfortran. I remember, back in my days of college, that building a library was not the worst thing in the world. It was just a matter of writing a makefile and properly linking everything.

Well, that was before today. I have to admit, I have not done it in some time, but - hey - I thought - if anything else I got smarter with age, not dumber. Facts proved me wrong.

This slatec library has been built against g77 for years (starting actually from f77). It has no business with gfortran, and it does not want to obey. So I download the sources (about 1000 fortran files) and build my little make program the way I learnt years ago and guess what? The library does not work. It does not want to work. Not only that, it refuses to compile, it refuses to give me any real advice on what to do. Thanks for nothing, gfortran.

So I think: I better give up now that the day is still young, install f77 and build the library against it. But... Now there is gfortran. g77 is no more. There is an f77 program which is just an interface for f2c, which converts fortran to c and then compiles. You can do the math.

Here it is what actually happens when building slatec against gfortran. Through the makefile you actually get a library which you will need to move to your /usr/lib or /usr/local/lib. And when you compile your fortran code - believe it or not - the code compiles with no problems. When you test it with one of the many programs that comes with it, it does not work. It gives weird messages. I tried it with one of my old programs (I have used it so many times that I just know it works), which integrates a simple set of ordinary differential equations. Nothing fancy, nothing stiff, something you could do with matlab without issues. I got nothing. And the weird thing is that, when I used the single subroutines instead of the library, the program works.

Ok, long story short: I installed another compiler. Yeah, that's it. Thanks gnu for helping. One day lost. 10 hours in the can. And I flushed.
Another day, another rant. I start to resemble Adam Carolla.

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Why gwibber sucks

Author: Simone Labels:: facebook, gwibber, microblogging, social networks, twitter, ubuntu

Ok, this is kind of a rant. However, after hours and hours of struggling with it, I have decided that gwibber sucks.


But let's start from the beginning...

Gwibber is a little microblogging program which currently supports a wealth of services, from twitter to flickr, to digg. It is the first choice for Ubuntu, and it ships with it. You get a little icon in the Ubuntu messaging menu that says "Broadcast", which opens it, if you click on it.

The problem with Gwibber is that it lacks most of the functionality you actually need for a useful social network application. When you use it, you get the weird feeling it stops right before something you may actually need, in between "I don't need this crap" and "It is really useful".

It is something like "I can live with it". But not quite. You got the feeling, right?

But while it may be ok for twitter (even though there is plenty of better alternative around), where it really sucks is with facebook. Big time.

First of all, there is a known bug (which has been there practically forever) that prevents you to authorize the program with facebook in a simple way. You want to add your facebook account to gwibber? Well, just click on Edit -> Accounts and you will be prompted with a window that has a scroll down menu. If you select facebook, you are then sent, from within the program, to a login page, where you will need to tell facebook to allow gwibber, etc. etc. Once this is done, you should get a button telling you to add your facebook account to gwibber.

This is where it gets completely random. From what I have been able to figure out, if gwibber is somehow already in your applications (like, maybe you were able to authorize it with facebook from another computer), then you will not be able to authorize it again. So, you will get a very annoying (I swear, after three times I wanted to smash my laptop against the wall) and very long window where there is nothing to push which says "Authorized" and "Success". But is it? Yeah, it is, but only if you remove this piece of useless software. A trick (which also works randomly) is to go to your facebook page, click on privacy settings and edit applcations. Then remove gwibber and try again. But, hey, try to do that from multiple computers! If you remove the authorization, gwibber on the computer you already authorized will stop updating and you will get nothing but days old friends messages reminding you that your favorite soccer team lost the last game. It sucks, right?

If you are able, somehow, to get the program running with facebook, things do not get much better. Gwibber lacks a few simple, but important features. First of all, it does not seem it can distinguish between the messages and the wall posts. So when you click on "Messages", you actually get the wall posts. This feature works slightly better with twitter. Moreover, if there is a post with several comments, only some of them are displayed. Are they the last ones? Well, that would be reasonable, would it? No, you get comments in a totally random order. Well, but that would be fine... if we could actually see all of them. But you can't. You just see those two or three messages, and that's all. And, of course, you cannot "Like" a specific comment, but only the main message. Which, by the way, does not work all the time, of course.

I am stunned. I am actually hoping this program gets nuked from Ubuntu as soon as possible. The real problem is that, while for twitter, digg, flickr and such there are a few alternatives, there are not so many for facebook (apart from prism, which is a trick). There is one little, very nice piece of software, which is called yoono. It works great, but it does not have a full integration with Ubuntu. This means that you need to compile it, you don't get an icon for it anywhere, it lays in your desktop somewhere and, of course, it does not go in your message menu. You cannot minimize it (you can use alltray, but this is a trick). There is no integration, I repeat. Which sucks, because it let you waste time. And it does not work after suspend or hibernate. You need to restart it, which is, again, a few clicks. But this is another story....

I told you this was a rant...

1 comments |

Program focus: Ailurus

Author: Simone Labels:: Ailurus, linux, tweaking, ubuntu

Ailurus is a nice little program that allows you to tweak your Ubuntu installation. It is thought for the Linux newcomers, but it has very interesting feature that will appeal also the more experienced users. The most important feature of Ailurus is the possibility of accessing several layers of optimization.

To install the program, go to Ailurus webpage  and download from the right tab the version that fits your Ubuntu flavor.


Once the package has been downloaded, double-click on it or type from command line

sudo gdebi <ailurus_package_name>

Follow onscreen instructions. The program will be accessible from Applications -> System tools. 

The program has a few interesting features a new Linux user will certainly appreciate. First of all, under the Systems Settings tab there is a very useful automatic configuration button for Mozilla Firefox. One may play a little with the settings the author of the program has chosen, which are certainly optimal for some configurations but may be sub-optimal for you. 


There are several other interesting options this little utility brings to the Linux user, from a simple program installation tab to a tab that allows one to choose the fastest repositories based on the location.


A very interesting feature that may be attract also the more expert user is the possibility of taking snapshots of the programs installed (through apt) on the system. In this way, you can easily keep track of the system's performances while installing new programs. It is unclear to me if that would include also the programs installed through gdebi, but it is indeed a simple and yet useful idea.

The program also allows one to get rid of useless stuff, like unused kernels and config files for uninstalled programs. Furthermore, the memory can be freed, as well as some disk space through cleaning the apt cache and the recent documents list.

Finally, a feature that I really liked: Linux tips & tricks and the chance (that I personally took) of downloading a free copy of the Ubuntu pocket guide and subscribing to the magazine "Full Circle".

In short, Ailurus is a very nice program, very useful whether you are a Linux guru or a newb. Give it a try!

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