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