In an earlier post I mentioned that I’m using MutliMarkdown to write my honours thesis. A critical component of any academic writing is the bibliography. This is how I’ve integrated the bibliography into my writing workflow.

First I’m using Zotero as my primary bibliographic management and article repository. Mainly due to the ease with which I can import items from the myriad of websites, online databases, and publishers websites from which I’ve been sourcing material.

What makes using Zotero a little awkward is that the current non beta version only works with the Firefox browser and my primary browser of choice is Google Chrome. There is a beta release of Zotero that I may look into further when I have some more time.

Second I use BibDesk to manage the bibliography for the thesis, this is so that when I use the LaTeX format produced by MultiMarkdown as a means of getting a PDF file I can use the LaTeX applications to do all of the heavy lifting in managing the bibliography and reference list. Importantly not everything in my Zotero library is going to end up being referenced in my thesis. So the migration from Zotero to BibDesk also helps in filtering out those items that I don’t need. Fortunately Zotero makes it very easy to migrate data out of Zotero and into BibDesk.

Third I use the MutliMarkdown standard metadata fields to associate the document with the bibliography.

What confused me for some time today was why when I seemed to have all of the pieces in place why my bibliography wasn’t appearing in the final output. The reason, I eventually discovered, is because there was a step in my workflow that I was missing.

My new workflow is as follows:

1. Use Byword to edit the source files, I have one file for each chapter
2. Use the mmd_merge.pl script to merge my source files together
3. Use MultiMarkdown itself to create a LaTeX file using the merged source file
4. Run the pdflatex application
5. Run the pdflatex application again
6. Use the bibtex application to create the bibliography using the aux file created by the second run of the pdflatex application
7. Run the pdflatex application a third time
8. Run the pdflatex application a fourth time to create the final version of the PDF file which includes the list of tables, list of figures, and the bibliography

It’s becomming a lengthy process, and one that I’ll have to script at some point, but the output is exactly what I need which is the most important thing.

The “Bibliography” photo was uploaded to Flickr by Alexandre Duret-Lutz and used under the terms of a Creative Commons License.