Use a hyperlinked document as a bioinformatics lab book
I wrote previously about using the file system to organise your scripts and data. I use this method and it does help my organisation, but it doesn't replace a lab book. I want a system that explains the relationships between the different set of results, and shows the outline of my work.
I've tried several different ways of doing this. Keeping a written lab book is problematic, since my results are on my computer, furthermore it's tedious to describe code on paper. Another approach is writing a plain text log, however I didn't like this because I can't include pictures - which I like to have next to the relevant sections of text. I didn't consider a word document, because all of the formatting would get in the way of what is a simple task: to link scripts, pictures, results and text into a outline of what my work is about.
The most successful approach I have had is using a wiki; for one reason, hyperlinks. If I want to include a figure I include the hyperlink to file. I can do the same for the script that produced the figure. So what's so great about this I hear you ask? Well, here's why.
Dynamic content Because I'm using a link, if I update a figure, for example changing an axis label, this is automatically updated in the wiki. I don't have to insert a new image, remove the old one and set the new one it's place. Very useful with the number of incremental changes between the start of the a project and the final draft.
Easy to find scripts and data The second reason why a hyperlinked wiki is useful, is that you can jump to the data or script you need by following the links. Useful for quickly finding the relevant script that produced the figure - even with the most organised file system in the world.
It's true you don't really need a wiki to do this. But wiki's allow a really fast way to create a hyperlinked document. As to which wiki platform to use, I've tried MediaWiki (a bit overkill) and MoinMoin (I couldn't get it to display the pictures the way I want), until I finally settled on Instiki, which I've found the easiest to use. MoinMoin and Instiki are both platform independent. Neither take much time to setup, and I definitely say it's worth taking the time to try this approach out. What have you got to lose? A few hours, but if you can get the system to work for you the rewards in productivity are great.