Biology Reference
In-Depth Information
STEPP - Search Tool for Exploration of Petri
net Paths: A New Tool for Petri Net-Based
Path Analysis in Biochemical Networks
Ina Koch
a
,∗
, Markus Schuler
a
and Monika Heiner
b
a
Technical University of Applied Sciences Berlin, FBV, WG Bioinformatics, Seestr. 64, 13347 Berlin, Germany
Tel.: +49
(
0
)
30 4504 3972; Fax: +49
(
0
)
30 4504 3959;
E-mail:
@tfh-berlin.de
b
Brandenburg University of Technology at Cottbus, Department of Computer Science, 03013 Cottbus, Germany
Tel.: +49
(
0
)
355 69 3884; Fax: +49
(
0
)
355 69 3830; E-mail:
monika.heiner@informatik.tu-cottbus.de
{
ina.koch, markus.schueler
}
ABSTRACT:
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.
Availability:
http://sanaga.tfh-berlin.de/˜stepp/
KEYWORDS:
Petri nets, systems biology, biochemical networks, metabolic networks, signal transduction networks, path
search with constraints, graph theory, sucrose-to-starch breakdown, potato tuber
INTRODUCTION
Petri net theory provides a definite description formalism and various analysis techniques for systems
with concurrent processes. Since more than ten years Petri nets are also applied to model and analyse
biochemical systems qualitatively [Reddy
et al.,
1993; Reddy
et al.,
1996; Voss
et al.,
2003; Heiner
et
al.,
2004] as well as quantitatively [Hofest adt, 1994; Hofestadt and Thelen, 1998; Matsuno
et al.,
2003].
The results show that Petri net theory forms a useful theoretical basis for qualitative model validation
and analysis [Heiner and Koch, 2004].
The search for alternative paths and their analysis are a crucial point in the understanding of biochemical
networks. Changes in the system behaviour, caused by mutations in the genomic sequence or by absence
∗
Corresponding author.
