[Home] [CV] [Publications]

Publications

Minus 1a5aa4f1c08b567c9107cba729de26bc87c17ab2b2f690eb45059193a1d6f587 The Pathalyzer: a tool for visualization and analysis of signal transduction pathways
Dill, David L. and Knapp, Merrill A. and Gage, Pamela and Talcott, Carolyn and Lincoln, Patrick and Laderoute, Keith - 2005

The Pathalyzer is a program for visualizing and analyzing large-scale signal transduction networks. Reactions and their substrates and products are represented as transitions and places in a safe Petri net. The user can interactively specify goal states, such as activation of a particular protein in a particular cell site, and the system will automatically find and display a pathway that results in the goal state – if possible. The user can also require that the pathway be generated without using certian proteins. The system can also find all individual places and all pairs of places which, if knocked out, would prevent the goals from being achieved. The tool is intended to be used by biologists with no significant understanding of Petri nets or any of the other concepts used in the implementation.

Keywords: signal transduction, Petri net, visualization