The pathalyzer: a tool for analysis of signal transduction pathways

Authors:
David L. Dill;Merrill A. Knapp;Pamela Gage;Carolyn Talcott;Keith Laderoute;Patrick Lincoln
Affiliations:
Stanford University;SRI International;Highwire Press;SRI International;SRI International;SRI International
Venue:
RECOMB'05 Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics
Year:
2005

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Abstract

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 - 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.