The Protocol Informatics Project

Introduction

The Protocol Informatics project is a software framework that allows for advanced sequence and protocol stream analysis by utilizing bioinformatics algorithms. The sole purpose of this software is to identify protocol fields in unknown or poorly documented network protocol formats. The algorithms that are used perform comparative analysis on a series of samples to better understand the underlying structure of the otherwise random-looking data. The PI framework was designed for experimentation through the use of a widget-based component set.

News

Date	Information
Oct-5-2004	Faster than expected. PI Prototype released. See example for usage.
Oct-4-2004	Danny O'Brien wrote an article in Wired about PI. Code debuting in one week.
Sept-25-2004	As promised, Toorcon presentation posted here.
Sept-16-2004	Join the PI mailing list here
Sept-15-2004	Finished slides for Toorcon presentation. Link available after conference.
Sept-14-2004	Project site established.

Download

Filename	Description	Size
PI-v0.01beta.tgz	Protocol Informatics prototype version 0.01 beta in python.	48k

Core Algorithms

Filename	Description	Size
needleman-wunsch.tgz	Needleman-Wunsch algorithm in C. For reference only	4k
smith-waterman.tgz	Smith-Waterman algorithm in C. For reference only	4k

Documentation

Title	Description
PI-Toorcon.pdf	Presentation slides from Toorcon 2004
FRAMEWORK	Description of PI framework modules
README	General project information
PI.pdf	Paper: Network Protocol Analysis using Bioinformatics Algorithms

Thanks

Many thanks to the following:

Christopher Abad
Terry Gaasterland
David Hulton
Danny O'Brien
Barclay Osborn
Tom Schneider

Contact

Author: Marshall Beddoe