The Protocol Informatics Project


Couple of weeks ago I got distracted. (Oct 2004) A presentation on protocol analysis using bioinformatics tools. I downloaded the code, spent more time downloading python packages needed and had a lovely phylogenetic tree of various data I captured on our network.

Yesterday I got distracted again for a bit (Oct 14). I was playing with a thing called freemind (partially as my wife wants a package that can do work-breakdown-structures). FreeMind It occured to me that the FreeMind display lookes very like a phylogenetic tree. And the freemind file format is xml - and very simple xml too - simple enough that I can understand & generate it easily.

I hacked a dot file I had generated into freemind's xml form and it loaded nicely. It could be quite useful I think. You can browse the tree quickly, ... also hide or open branches, add notes/colours/whatever to nodes, export the tree to html.

Hacking dot files is hard work if you have to do it every time so I took a look into PI's code and I got sucked in and suddently I was attempting to program in python! eek. I succeded in generating freemind xml.

What's this all about huh? Here. A screenshot: (thanks to ImageMagick)

FreeMind comes precompiled for Windows/MacOSX/linux though I used the source package to install. It had no other dependancies. My machine here is getting a bit old and slow but freemind runs nice & zippily.

See here my train of thought starting to hack python

python ../PI/ -g -p ./icmp.dump >icmp.aligned.sequences-jamesey