(Modified 2014 Feb 17)

Reference managers
or bibliography databases

Basically, my goal is to avoid copying and pasting from PubMed and formatting by hand.

Bibus 1.5.2 incompatibility with LibreOffice 4

LibreOffice 4 uses Python 3.3 (somewhere), while Bibus uses Python 2.X, such that Bibus doesn't work after upgrade. An explanation, but not a solution, for the problem was given at Bibus's SourceForge page. I got the general strategy for getting around this problem from LinuxG.net, although the listed tarball doesn't exist anymore. So for lack of a better idea, I downloaded the binaries individually from Ubuntu Packages Search, and had to resolve dependencies the hard way, like I had to do in the Dark Ages with RPMs. (I searched the 'Quantal' release specifically for LibreOffice 3.6 binaries.) There was a lot of trial and error involved, but essentially, you'll need to uninstall the existing version of LibreOffice, plus any other package that might conflict. If you miss one, the installation will be unsuccessful, and when you try to uninstall the package that caused the conflict apt-get/Synaptic will tell you to repair things, which will re-install packages that you'll need to turn around and re-uninstall. It was a big pain.

In any case, here's a list of all the packages I needed to download and install (Keep in mind I'm using a 64-bit system.):

Did I mention it was a pain?... At least I didn't need to install the files one-by-one. The command was simply (assuming those are the only *.deb files in your directory):
sudo dpkg -i *.deb
Pay close attention to the failed installations or configurations.

<rant on>
I see questions online about this topic going back eleven months, during which no one had solved the problem. I'm sympathetic towards the Bibus people, since it probably isn't a trivial change to keep up with, but I'm less sympathetic to the Ubuntu people, who made LibreOffice 4 the default, while not addressing the incompatibility with the version of Bibus that they chose to include. I like Ubuntu, but my brand loyalty doesn't extend to accepting loss of functionality. I took a short trip to Distrowatch to see if there's an alternative I might try.
<rant off>

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