Thesis tools

Not that anyone cares of course, but I’ve now started to write up my PhD. I spent a long time agonising over whether to use Word or LaTex. In the end the lack of decent reference management tools for Word persuaded me that I should just learn LaTex and get on with it.  Yes I know Endnote exists, I also know there’s citation available with in Word now and yes I’m also aware of Bookends and Zotero. I’ve not used Bookends in real anger nor Zotero and Word 2008’s reference management is rather limited and frustrating to use. 

So LaTex uses Bibtex for reference management and it’s fairly simple. Bibtex generates a flat text file with all you references formatted the way you want and then merges them into LaTex for you.. well it’s typeset LaTex, Bibtex, LaTex, LaTex. The nice thing about it is that unlike Endnote it’s simple and you don’t find the interface crashing or refusing to let you edit things. But still things aren’t idea. My workflow currently looks like this.

• OS is Mac OS X 10.5.3 with MacTex 2007 installed
• I’m currently using TexShop for editing my LaTex files because it’s nice and simple. Output is pdftex.
• I’m managing all the journal papers I need with Papers, which is in essence iTunes for journal papers. I’m using it to export the references to Bibtex.
• However papers doesn’t fully support all the features of Bibtex so I’m also using BibDesk. It’s be nice if you could use just papers.
• I’ve also installed Skim to enable commenting on PDFs similar to what you can do with Zotero. 
• I’m using VectorDesigner for my vector graphics, it’s not as powerful as Illustrator, but it is easier and quicker to use not to mention cheaper. Plus I’m not sure I want to spend ages drawing really beautiful figures.
• Pixelmator is sitting in the sidelines for the odd bit of raster work. Again it’s a cut down version of Photoshop. So far I’ve not needed it.
• Plotting is taking place in Origin 8 which means I also need Windows installed. This is under Virtual Box which unlike VMware and Parallels is free. The interface isn’t as refined though. Origin definitely isn’t the ideal plotting program but a lot of my data is already in Origin and it’s very quick to use.
• MacPython with numpy, scipy, matplotlib and ipython is there for generating some plots and more importantly simulating various things. The output is often saved to text files and then plotted up in Origin. Partly because re-plotting all my data in matplotlib would be too time consuming.
• I also have GraphClick there for lifting the odd bit of data from someone else’s paper.
• Finally my entire set of thesis files is under version control using Mercurial. This allows me to commit regularly and revert if needed. It’s also pushed onto a web server so I can sync across my home machine and college machine.

So that’s it at the minute. I should note that everything was also under Time Machine, but due to a lack of spare hard drives currently isn’t. Though that will be resolved shortly. It’s quite a lot of software and that’s before you include the everyday tools such as the web browser, pdf viewer, mail client and of course Office as a lot of my older papers and conference presentations are in Word and Powerpoint.