Since writing papers is pretty much a way of life for an academic, I like to have tools that let me concentrate on the content, yet make beautiful documents with minimal effort on my part. The solution to this is LaTeX. While it gives me beautifully typeset documents, it doesn’t handle bibliographic data management. That job is left to BibTeX. This is a widely used plain text format for bibliographies.

Since I work mainly in Emacs, coupled with AucTeX it makes for a very comfortable writing environment. However, dealing with bibliographies involves more than just choosing the right reference from a list. I’d like to pull references from PubMed or SciFinder. I’d like to create groups of references. I’d also like to store PDF’s and tags. This calls for a bibliographic data management system. There are many such systems, both Open Source (JabRef, pybibliographer) and commercial (EndNote, RefWorks etc). See here and here for comparisons between various systems.

Being a Mac user I chose to work with BibDesk. This is a very nice GUI tool for managing references, with very responsive developers. It’s oriented towards BibTeX and LaTeX but easily exports to RIS, EndNote XML, RTF, HTML and RSS. It has built in search capabilities for a variety of databases (PubMed, Library of Congress, SciFinder), support tags, PDF storage and indexing and overall made my life much easier.

The only problem is that I haven’t been to persuade all my collaborators to use LaTeX. As a result I still have to use that monstrosity called MS Word. And along with that, EndNote. This was a pain since I had to make sure that I kept everything in sync (and the EndNote UI sucks!).

However, Derick Fay on the BibDesk mailing list pointed out BibFuse, which is a set of AppleScript‘s that allow you to drag citations from a BibDesk window into Word and then format them all at one go (with appropriate numbering). If you delete an in-text citation, a reformat will remove it from the bibliography and so on. It’s certainly not “cite while you write” – but that doesn’t bother me, coming form the LaTeX world. It uses a BibDesk template file to format the bibliography – so if you need a differently formatted reference list you have to understand the somewhat arcane template language that BibDesk uses.

It’s certainly not a point and click solution – but it does let me use BibDesk with Word for those times that I need to use it. And it lets me do away with EndNote (unless a collaborator decides to insert an EndNote formatted bibliography!)

Overall a very handy solution for integrating BibDesk with Word.