The Pathalyzer: a Tool for Analysis of Signal Transduction Pathways

David L. Dill, Merrill A. Knapp, Pamela Gage, Carolyn Talcott, Keith Laderoute and Patrick Lincoln

The First Annual Recomb Satellite Workshop on Systems Biology, 2005.

The Pathalyzer is a program for 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 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.