The Pathalyzer: a Tool for Analysis of Signal Transduction Pathways
David L. Dill,
Merrill A. Knapp,
Keith Laderoute and
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.