After reviewing several reference management software (Wikipedia, WISC.edu, Imperial.ac.uk, Columbia.edu) I opted for Zotero. It’s simple to use, free, and open source. It has a 300 Mb limit with the possibility to buy extra space. Although 300 Mb doesn’t seem like a lot, it’s fine for the moment.
Zotero has a Firefox plugin that’s in constant connection with the server. You can also chose to have it installed locally, on your machine.
The following steps apply for a Zotero 4.0 standalone package on Ubuntu Studio 12.04 LTS, 64 bit.
1. Which package should I download?
Most of the time, zotero.org will propose a package that suits your system. If you’re not sure whether your computer runs on 32 or 64 bit chips, type this in the terminal window.
uname -m
2. Download
-> Go to https://www.zotero.org/download/ and download Zotero standalone with the browser extension of your choice.
-> extract the archive from its tar.bz2 compressed format
-> move the folder to your /opt directory, alongside other programs. You can do this in two ways
a) open a terminal window and type:
sudo mv ~/Downloads/Zotero_linux-x86_64/ /opt
This will move the Zotero extracted directory from your Downloads location to the /opt directory
b) open your Home folder -> press ALT+F2 -> *type gksudo nautilus -> click Run -> type your password -> OK
Navigate in the newly opened window to File System -> Opt
Paste here the Zotero folder you extracted in your Downloads location.
3. Make a .desktop file in usr/share/applications in order to make the system recognize that you have installed Zotero, and to be able to find it in your Applications Menu
-> open gedit or other text editor and type:
#!/usr/bin/env xdg-open [Desktop Entry] Type=Application Name=Zotero GenericName=Bibliography Manager Icon=/opt/Zotero_linux-x86_64/chrome/icons/default/default48.png Exec= /opt/Zotero_linux-x86_64/zotero %f Categories=Office Terminal=false
Be sure to change the Icon and Exec lines if you run on 32 bit
Icon=/opt/Zotero_linux-i686/chrome/icons/default/default48.png Exec= /opt/Zotero_linux-i686/zotero %f
-> save the file as zotero.desktop somewhere on your computer and then paste it in usr/share/applications. Be sure to do this in the window of Step 2/b, that gives you root access.
Done.
I would like to reference http://anterotesis.com and his original post Installing Zotero standalone on Ubuntu 11.10. I used his steps and page comments to install version 4.0, changing somewhere along the way from terminal use to folder view.
* you might need to type kdesu konqueror or gksudo thunar if you have Kubuntu (KDE) or Xubuntu (XFCE) – read more here – http://www.psychocats.net/ubuntu/permissions
Adrian Dobre 
I see now that I had not done step 3 right, i just pasted into the file system instead of going ahead to the opt folder, I have tried to redo this but some how it is not working. how do I access the applications menu?
In this case, I’d suggest looking at the links at the end of my post. It’s where I got the information in the first place, and they achieve the same thing, just a bit differently.
About the applications menu, it’s the menu where you access your installed programs. It might be on the top-left corner of your screen, the top button on the left sidebar etc., depending on the desktop environment you’re using. Look here: http://3.bp.blogspot.com/-UUJapIGHjB0/T5juJZMAKkI/AAAAAAAACsE/bVFkKQtbyIo/s1600/Ubuntu+12.04+Precise+Pangolin.jpg
Let me know how it works out.
Thanks Adrian, I have followed the steps and installed Zotero, how do I get it on the launch bar and start to use it?
Hi, Mary! I’m glad the installation process went well. If you did step 3 right, then you can see the Zotero icon in your applications menu. Just drag and drop the Zotero icon to your launch bar. I assume we’re both talking about the left, favorites side-bar.
If you cannot see the Zotero icon in you applications menu, then something went wrong in the process of creating/ placing the .desktop file in usr/share/applications/ Write a comment here if you need help, I’ll help as much as I can.
Here are also some links that might help:
How to add program to left bar manually (won’t pin) – http://ubuntuforums.org/showthread.php?t=1948574
And, in case you upgraded: A guide to the Unity Launcher in Ubuntu 13.04 – http://myubuntublog.com/unitylaunchertutorial/