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Cluster Based Analysis of Petri Net Properties

Authors:
Marcin Radom
Agnieszka Rybarczyk
Piotr Formanowicz

Keywords: Systems biology; Petri nets; model analysis

Abstract:
Systems biology is an interdisciplinary field of study based mainly on biology, mathematics and computer science. In systems biology, the analysis of complex biological systems of interacting objects is being made. Before the analysis starts, a model is being created, representing the analysed system. The theory of Petri nets offers a necessary tool for such a task. Places in such a net correspond to the static elements of the system like chemical compounds. Transitions correspond to the reactions. The rules of transitions activation and firing allow the modelling of the biological system dynamics. Having a Petri net one can start the analysis which is based on the invariants, maximum common transition sets and t-clusters. Such analysis requires various tools using different file formats which adds to the complexity of such a task. We have developed a Java-based environment to help in the process of net creation, simulation and the analysis in the classical and time Petri nets, while the different formats in which Petri net data is being stored can be used there. Exporting data to other Petri net tools has also been implemented.

Pages: 8 to 10

Copyright: Copyright (c) IARIA, 2015

Publication date: May 24, 2015

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-409-1

Location: Rome, Italy

Dates: from May 24, 2015 to May 29, 2015