The Open Source Dissertation

My university has done a wonderful thing, in accepting only PDF files for deposition of a thesis or dissertation with the graduate school. Gone are the days of printing 5 copies of a 300-page document on acid-free paper that costs 20 cents a page (and then finding out that one of the margins is 0.1" too wide, so please correct and resubmit before the deadline in three hours). The transition is a wonderful step forward, and also means that it is much easier to distribute the dissertation.

As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).

Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.

Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.

Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.

Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.

Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.

Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.

Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.

Do Your Presentations Impress?

Pretty much everyone has to give a presentation at some point, whether in class lectures, conferences, public lectures, or as part of a class assignment. Microsoft PowerPoint has swiftly taken over from the old days of slide projectors, overhead transparencies, and chalkboards. It's a point of debate whether or not this is entirely a good change, but it's the world within which we now live.

When I switched to OpenOffice.org from Microsoft Office, I was delighted to see a fully functional presentation program within the open source office suite. I've since used this program, Impress, to put together several new presentations, as well as edit some old ones. In this post, I'll briefly review my experiences.

Interface: The switch to Impress from PowerPoint was an easy one, interface-wise. Many features closely parallel those found in PowerPoint, and features that don't are logically arranged and pretty easy to find.

Software Features: I can do pretty much everything in Impress that I could do in PowerPoint. There are enough slide transitions, special effects, drawing tools, text formats, and other goodies to put together a truly hideous presentation, if one desires. One possible downside is that the default installation doesn't include a lot of prepackaged slide templates. This may matter to some folks, but I don't use templates often as it is.

Importing PowerPoint Presentations: I've found that my old PowerPoint files import nearly flawlessly in most cases. I hear that sometimes the really fancy special effects don't always import well, but should you really be using those in a talk that colleagues and potential employers might see?

Export PowerPoint Presentations: This can be a little more finicky. I like to build multiple bullet points on a slide, and have them fade to gray as I move on to subsequent points. This works fine in Impress, but for whatever reason the exported PPT files fade the text to a bluish gray. Annoying. I haven't found a workaround for this (other than creating multiple slides for the fade in and fade out of each point). Fortunately, this has been the main quirk I discovered.

Video Clips: This is the one area where Impress has consistently let me down - its support for embedding video clips within presentations stinks. It won't let you put an AVI file directly on a page, and I haven't even gotten the supposedly supported MPEG or MOV files to embed properly either. So, I've had to develop a work-around. Specifically, I create a hyperlink that links to the video file I want to play. Click on the link during the presentation, and up it appears! Of course, this might lead to trouble if you have to run your presentation on a computer other than the one which housed the video file originally.

Practical Realities: There isn't anything that would make me bail on Impress to return to PowerPoint. The program does what I need it to do, and does it pretty well (for the most part). If I can run off my own laptop, I can - this eliminates the problems of file export. If I have to export as a PowerPoint file and run it from PowerPoint, I make darned sure to test the file out beforehand. I haven't run into any true disasters in export, but there are occasionally those little quirks that annoy the perfectionist in me.