Entries from June 2005 ↓

Zen and the art of PhD: Part 1

I thought I’d try my hand at a useful post explaining what organisational tools and systems I’m using to try and get through my doctoral study. Mainly I wish I already knew about these systems so I could have been using them from the beginning instead of floundering for the first 12 months.

Unlike other more general guides to do with research, supervisors and miscellany, I’m going to focus on the tools and systems that have allowed me to record some kind of permenant record of what I’m doing.

Reference Names

What ever you do, you’ll inevitably have to cite other people’s work and more than likely you’ll have to cite insane numbers of articles. Trying to keep track of them all is madness – but eventually I settled into a standard suitable for myself.

I use LaTeX for document production – this (generally) takes away the incentive to muck around with styling and lets you focus on the content. More about this later, however it has a nice system to reference articles: “\ref{Jones99}”. This is what you type in the document and LaTeX (more specifically BibTeX) will turn this into (Jones, et al. 1999) or whatever format is appropriate. What I suggest for naming articles is to use the last name of the primary author and the last two digits of the year of publication. If you have an author publishing more than once a year then append letters of the alphabet to each. i.e. “Jones99a” and “Jones99b”.

Now this isn’t anything amazing in itself, but it is important to have a standard method of naming for it to fit with the other tools.


These days you’ll mostly likely get journal articles as PDF files. Which is great, although I ashamedly still like reading from a paper copy (really would like to save natural resources though). I keep a repository of all the articles I obtain and name the files based on the above system. So I’ve downloaded Jones’ 1999 paper on goose wrangling and I name it “Jones99.pdf”. Now, you can either shove all your article files in one directory or in sub-directories indicating the area of research. It is up to you since the next tool can deal with either system…


A kick ass reference management tool, it can import and export to a wide number of formats but is bibtex native. It is written in Java so you can use it wherever you are, this is good for me because I juggle between windows and Debian linux all the time – although not by choice.

Basically this tool is very simple but you can set it up to point to a article directory and search all subdirectories for a pdf with a filename matching the bibtex key. This means when you enter the Jones99 article into bibtex in automatically can find the pdf in you articles directory. You double click on it and it pops up your PDF viewer. Brilliant!

That’s all for now, since I should actually be doing PhD work rather than explaining how I’m doing it. Next post on it will be about Zen and the art of PhD wikis.

Graphic Novel madness

A while ago I finished a bunch of graphic novels that a friend lent me. I don’t really have time for a comprehensive review of each – plus it has been while since I read the first so these will be short and sweet.

Astro City – Kurt Busiek

A superhero comic where the main character is actually just a normal kid who has had some martial arts training. He moves to Astro City from the country after his father passes away to seek his future – which he hopes will include being involved with the super heros in some form. He gets taken up as an apprentice by a strange and shadowy benefactor with a dark past – and although the colouring and art is quite bright there is quite a dark undertone to the novel’s theme.

All in all I like.

The Hedge Knight– Georgre R. R. Martin

A short one which is a prequel to the “beloved fantasy saga” called A Song of Ice and Fire. I haven’t read the series, so I wasn’t sure what to expect – but it reads well by itself. Really nice artwork and inking in it, and I liked that the story wasn’t about some heroic amazing guy. It is about a squire taking the place of his deceased master and trying to claim victory in a tournament. He is quite pig headed to begin with too, which can be infectious but in the end you just know he is going to be taken down. All though it is all not quite as you’d expect.

From Hell – Alan Moore

I’ve really enjoyed the other Alan Moore stuff I’ve read and this is no exception. Quite a different style from what I expected and long (>450 pages). And yes, this is the basis of the movie that came out a few years ago (although I’m told the plots differ quite a bit because I can’t remember the movie too well) so like the movie it is all about the Whitechapel murders (AKA Jack the Ripper) .The art is quite rough, black and white sort of sketchings but fits the mood and tone of the story perfectly – so no complaints form me there.

All in all, very dark and disturbed – but the story and underlying truth is also dark and disturbed, so perfect if you have the stomach for it.

Top 10– Alan Moore

Well what do you know, another Alan Moore novel. I forgot that he did this one too. Another crazy super hero reality in which most people have some form of power, so this story is from the side of a new recruit to the law enforcement agency in the city. Very humourous, I giggled lots, but like all Alan Moore stuff it has a deepness to it that makes it so good.

Marvel 1602 – Neil Gaiman

Well this was a suprise to see Gaiman to do Marvel superheroes thrown back in time in an alternate universe. Not something that seems to really fit the other things he’s done. However, it works – for me at least. And since I can vaguely recall it since it was the first I read I’m not going to say much more – although I do wish there were some other marvel characters in it…