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In Silico Biology 5, 0014 (2004); ©2004, Bioinformation Systems e.V.  

STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks

Ina Koch1,*, Markus Schüler1 and Monika Heiner2

1Seestr. 64, 13347 Berlin, Germany
  Phone: ++49 (0)30 4504 3972, Fax: ++49 (0)30 4504 3959, Email:

2Brandenburg University of Technology at Cottbus, Dept. Computer Science, 03013 Cottbus, Germany
  Phone: ++49 (0)355 69 3884, Fax: ++49 (0)355 69 3830, Email:

* Corresponding author

Edited by E. Wingender; received October 04, 2004; revised and accepted December 03, 2004; published January 22, 2005


To understand biochemical processes caused by, e. g., mutations or deletions in the genome, the knowledge of possible alternative paths between two arbitrary chemical compounds is of increasing interest for biotechnology, pharmacology, medicine, and drug design. With the steadily increasing amount of data from high-throughput experiments new biochemical networks can be constructed and existing ones can be extended, which results in many large metabolic, signal transduction, and gene regulatory networks. The search for alternative paths within these complex and large networks can provide a huge amount of solutions, which can not be handled manually. Moreover, not all of the alternative paths are generally of interest. Therefore, we have developed and implemented a method, which allows us to define constraints to reduce the set of all structurally possible paths to the truly interesting path set. The paper describes the search algorithm and the constraints definition language. We give examples for path searches using this dedicated special language for a Petri net model of the sucrose-to-starch breakdown in the potato tuber.


Keywords: Petri nets, systems biology, biochemical networks, metabolic networks, signal transduction networks, path search with constraints, graph theory, sucrose-to-starch breakdown, potato tuber