Striving for greatness

Thoughts on emerging tech, open source, and life

Academic papers in Linux

We’re beginning to put an academic paper together, and of course I’d like to do this using open-source software if I can. My PI (principal investigator, the head of the lab) uses Word — so whatever ends up getting used, it needs some capability to at least export to .doc or .rtf. A critical aspect of any solid academic paper is citing your reference in a bibliography. does have some basic bibliography capabilities, but that’s what they are: basic. Work is underway to fix that, but it’s not expected to get anywhere for a year or so.

After some research, I’ve come across a few promising packages:

Zotero: A Firefox 2.0 extension, public beta started less than 2 weeks ago. No integration with word processors yet, but you can copy and paste a formatted bibliography across, and export and import the actual data. “It lives right where you do your work — in the web browser itself.” As a result, adding references from online searches such as PubMed is as simple as a single click. Every other package needs explicit support added for online searches.
Bibus: Uses’s Python functionality, also integrates with MS Word. The build system sucks — it should use distutils, but instead it’s got some custom Makefile and weird shell scripts and configuration files. Its functionality comes highly recommended, however. Will do PubMed and eTBLAST queries.
Pybliographer: The development version (1.3) integrates into OO.o and LyX. The 1.3-series GUI is alpha-quality and just had its first release. Will do PubMed, Web of Science and CrossRef queries.
bibutils: Command-line filters to convert between a variety of formats, including EndNote (which is currently in use under MS Word). Also handles RIS and BibTex, so that provides for OO.o import and export as well.

Update: As of now, bibutils and Bibus are both available in Portage. Try ’em out.


Written by Donnie Berkholz

October 16, 2006 at 11:35 am

Posted in Uncategorized

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