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Using MoinMoin to keep track of research notes and references as part of my PhD.

h2. Introduction

I started a PhD in January 2005 and needed a way to keep track of all my notes, the papers I’d read, the quotes I’d like to remember etc. Initially, I spend (far too long) writing a Java outliner to keep track of my thoughts. This quickly snowballed into a complicated project but wasn’t giving me what I wanted, so I abandoned it. Next, I thought an existing framework would help me to concentrate on the real issues – I tried using “NetBeans”:http://www.netbeans.org as a base but it was, again, far too complicated for a quick project. Recently, I’ve been using a “moleskine notebook”:http://www.moleskine.com (and nothing is ever going to make me stop using it) but this isn’t particularly searchable etc. So, I’ve been looking for a reasonably easy Wiki I could use on my laptop, work PC and this website. I chose MoinMoin but others may also be suitable.

MoinMoin is written in Python, which I am discovering makes it ideal for a little hacking. Until last week, I’d never written any Python scripts but then I started playing around with Python and the Amazon API. This gave me enough confidence to write two macros for MoinMoin.

h2. Installation

Download the two macros “BibKeys.txt”:/research/BibKeys.txt and “BibEntry.txt”:/research/BibEntry.txt and their dependant libraries (described at the end of this page). Install the libraries using their instructions. Copy the macros to your MoinMoin macros directory and change the extension from .txt to .py. Both of the macros need to know the location of your BibTeX file so open them up and edit the following line to reflect your configuration:

file = 'c:/Documents and Settings/jel03r/Desktop/PhD/reports/9mth Report/bibtex/references.bib'

h3. BibKeys.py

The first macro, BibKeys, creates a list of WikiNames from the keys in a BibTeX file. Insert this macro into your page like this

[[BibKeys]]


and you’ll get a list of the bibtex keys in your file. You can now go and write comments/quotes etc about each paper

[[BibKeys]]

h3. BibEntry.py

This macro, BibEntry inserts the BibTeX entry into the page like such:

[[BibEntry(Lawrence2004a)]]
[[BibEntry]]


The first line will insert the bibtex entry for the key “Lawrence2004a”:
@ARTICLE{Lawrence2004a,
author = {Jamie Lawrence and Terry Payne},
title = {Making use of Insignificant Interactions},
journal = {Equator All-hands Meeting},
year = {2004},
month = {February},
owner = {jamie},
pdf = {Lawrence2004a.pdf},
}

The second line is useful if you create pages from a BibKeys macro: It inserts the bibtex entry using the current pagename as the key. So, if the current page is called “Lawrence2004a” then is will have the same output as [[BibEntry(Lawrence2004a)]]

h2. Dependancies

These macros depend on “bibstuff”:http://www.pricklysoft.org/software/bibstuff.html, “seqdict”:http://home.germany.net/100-366919/Python/Modules/Modules.html, “Simple Parser”:http://simpleparse.sourceforge.net/ and “mxTextTools”:http://www.egenix.com/files/python/mxTextTools.html. These must be installed first. I’ve tested this on Apache/Apache2, Python 2.2/2.3 and MoinMoin 1.2.2/1.3.3, on both Linux and Windows.

Contact me via this website if you want more details, or leave a comment below